A groundbreaking study reveals the pivotal role of the transcription factor GLIS3 in orchestrating a fibrotic cell circuit linked to inflammatory and fibrotic tissue remodeling. Employing state-of-the-art bidirectional CRISPR screens combined with RNA sequencing and chromatin immunoprecipitation assays, researchers have delineated a GLIS3-dependent program governing the behavior of inflammatory activated fibroblasts (IAFs), cells crucial to the pathology of diseases such as ulcerative colitis (UC).
This intricate investigation started by manipulating GLIS3 expression in primary fibroblasts through CRISPR knockout (CRISPRko) and activation (CRISPRa) approaches, subsequently stimulating these cells with pro-fibrotic cytokines TGFβ and IL-1β. Transcriptomic analyses revealed over 150 genes exhibiting decreased expression upon GLIS3 disruption but were conversely induced with GLIS3 activation. Significantly, these GLIS3 effector genes include IL11, a cytokine implicated in fibroblast-driven tissue damage, along with LIF and FAP, markers tied to fibroblast activation and intestinal stricture development respectively.
Further transcriptional targets identified comprise MMP2, an enzyme facilitating monocyte infiltration into damaged tissues, directly linking GLIS3 activity to macrophage-fibroblast cross-talk mechanisms. Other GLIS3-regulated genes such as PTGFR and SERPINE1 contribute to epithelial regeneration and mucosal injury processes in colitis, indicating a broad regulatory network modulated by GLIS3 that transcends mere fibrotic signaling.
To verify direct DNA binding targets of GLIS3, researchers conducted chromatin immunoprecipitation sequencing (ChIP-seq) using fibroblasts engineered to express GLIS3 tagged with a 3xFlag epitope. This approach identified 1,291 GLIS3-bound genomic loci, with a notable fraction enriched near transcription start sites and intragenic regulatory regions. Importantly, GLIS3 occupancy was enhanced upon stimulation, suggesting dynamic control of key genes involved in extracellular matrix organization and inflammatory responses.
Among direct GLIS3 targets is IL11, with binding peaks mapped upstream of its transcription start site. Motif enrichment analysis of GLIS3-bound regions uncovered co-enrichment of binding sites for transcription factors FOSL1 — a member of the AP-1 complex known to regulate IL-11 in other disease contexts — and TEAD family members, which act downstream of the YAP/TAZ mechanotransduction pathway implicated in fibrosis. These findings imply a cooperative transcriptional network wherein GLIS3 facilitates recruitment or stabilization of additional regulators critical for fibrotic gene expression.
Functional follow-up experiments using chromatin immunoprecipitation followed by quantitative PCR (ChIP-qPCR) demonstrated that GLIS3 absence impairs the binding of both FOSL1 and TEAD1 to their respective target genes, corroborating its role as a master regulator of this fibrotic gene network. Interestingly, IL11 expression was uniquely dependent on GLIS3 and TEAD1/TEAD3, highlighting distinct regulatory mechanisms at this key cytokine locus.
Given these insights from in vitro experiments, the team formulated a GLIS3 gene signature comprising effector genes bound and regulated by GLIS3, tightly associated with the IAF phenotype. This signature was then projected onto transcriptomic data from the well-characterized PROTECT cohort, comprising treatment-naive pediatric UC patients. Remarkably, GLIS3 signature enrichment correlated positively with disease severity scores (Mayo score), and further analyses refined a 50-gene subset predictive of clinical status.
Integrative cellular deconvolution of bulk RNA sequencing data from patient biopsies revealed that increasing disease severity was accompanied by elevated proportions of IAFs and activated macrophages within the colon. Both cell types showed strong correlations with the GLIS3 gene signature, underscoring the centrality of a GLIS3-driven fibrotic and inflammatory circuit in the pathogenesis of UC.
Altogether, this comprehensive body of work illuminates GLIS3 as a master transcriptional regulator shaping the identity and pathological function of inflammatory activated fibroblasts in fibrotic disease contexts. By controlling a core gene network involved in extracellular matrix remodeling, immune cell recruitment, and epithelial integrity, GLIS3 emerges as a promising therapeutic target for fibrotic disorders, including inflammatory bowel disease.
These findings have broad implications beyond the gut, given the conserved transcriptional pathways and cellular interactions mediated by GLIS3. The dependence on cooperative factors such as AP-1 and YAP/TAZ signaling components posits combination-targeting strategies to intercept fibroblast-driven tissue fibrosis and inflammation. Future investigations leveraging single-cell multiomics and in vivo models will be essential to fully unravel the cellular circuitries governed by GLIS3 in diverse fibrotic diseases.
By decoding the GLIS3-dependent transcriptional landscape, this research paves the way toward precision therapies aimed at curbing fibrosis by manipulating fibroblast states. As the global burden of fibrotic diseases escalates, these mechanistic insights into cell-type specific transcriptional control offer new avenues for intervention and biomarker development.
The study is a testament to the power of integrative genomics, functional perturbation screens, and patient-based translational analyses to uncover key drivers of pathological cell states. By bridging in vitro models and human disease cohorts, the authors exemplify the future of molecular medicine directed at complex tissue remodeling processes.
In conclusion, GLIS3 operates as a critical switch in inflammatory activated fibroblasts to promote a fibrotic program through cooperation with other transcriptional regulators. This discovery enriches our understanding of fibroblast biology in chronic inflammation and fibrosis and sets the stage for targeting GLIS3-mediated pathways in clinical fibrotic diseases.
Subject of Research:
GLIS3-dependent transcriptional regulation of inflammatory activated fibroblasts shaping fibrotic tissue remodeling in inflammatory bowel disease.
Article Title:
Bidirectional CRISPR screens decode a GLIS3-dependent fibrotic cell circuit.
Article References:
Pokatayev, V., Jaiswal, A., Shih, A.R. et al. Bidirectional CRISPR screens decode a GLIS3-dependent fibrotic cell circuit. Nature (2026). https://doi.org/10.1038/s41586-025-09907-x
Image Credits: AI Generated
DOI:
https://doi.org/10.1038/s41586-025-09907-x
Keywords:
GLIS3, inflammatory activated fibroblasts, fibrosis, IL11, CRISPR screens, chromatin immunoprecipitation, transcriptional regulation, extracellular matrix remodeling, ulcerative colitis, inflammation, YAP/TAZ signaling, AP-1 complex
Tags: Bidirectional CRISPR technologyCRISPR knockout and activation methodscytokine signaling pathwaysfibrotic cell circuitfibrotic disease pathologygene expression regulation in fibrosisGLIS3 transcription factor roleinflammatory activated fibroblastsmacrophage-fibroblast interactionstissue remodeling mechanismstranscriptional targets of GLIS3ulcerative colitis research
