Biology subjects

Lex, R. K.

Publications and source records attributed to Lex, R. K..

4 recordsLinked to original sources

bioRxiv2026

Dysregulation of epithelial differentiation architecture underlies field cancerization in head and neck cancer

Head and neck squamous cell carcinoma (HNSCC) has exceptionally high recurrence rates, exceeding 50%, contributing to mortality and morbidity. This recurrence rate is proposed to be due to field cancerization, a phenomenon where tumor-adjacent "field" tissue that appears histologically normal harbors molecular changes that prime it for subsequent tumor growth. Current models attribute field cancerization to shared driver mutations between tumors and adjacent at-risk tissue, but this assumption has never been directly tested. To comprehensively characterize this phenomenon, we profiled patient-matched tumor, normal-adjacent field (NAF), contralateral normal, and blood samples from HPV-negative HNSCC patients using whole genome sequencing, targeted driver gene sequencing, single-nucleus multiome profiling, spatial transcriptomics and functional proliferation assays. While histologically normal NAF tissues did harbor expanded mutant clones, these mutations rarely overlapped with paired tumors and were not shared across patients, suggesting molecular features beyond mutations are altered in NAF. Single-cell multiomics revealed that NAF epithelium loses its normal organizational hierarchy: basal stem cell markers persist in differentiated cells, while terminal differentiation programs fail to activate, with reconfiguration of both gene regulatory networks and cell-cell interactions. Proliferating cells appeared in tissue layers normally restricted to post-mitotic cells, a pattern typically seen only in overt dysplasia. Within this disrupted hierarchy, a distinct epithelial state arose in NAF that expressed both normal epithelial and tumor-associated markers, which we localized to the parabasal layers using immunofluorescence and spatial transcriptomics. Together, our findings demonstrate that field cancerization operates through epithelial hierarchy disorganization that disrupts differentiation, generates cells with tumor-like features, and may create a permissive environment for the expansion of cancer-associated mutations, all within tissue that appears histologically normal.

cancer biology↗

bioRxiv2023

BAF chromatin complexes do not mediate GLI transcriptional repression of Hedgehog target genes

Transcriptional responses to the Hedgehog (HH) signaling pathway are primarily modulated by GLI repression in the mouse limb. Previous studies suggested a role for the BAF chromatin remodeling complex in mediating GLI repression. Consistent with this possibility, the core BAF complex protein SMARCC1 is present at most active limb enhancers including the majority of GLI enhancers. However, in contrast to GLI repression which reduces chromatin accessibility, SMARCC1 maintains chromatin accessibility at most enhancers, including those bound by GLI. Moreover, SMARCC1 binding at GLI-regulated enhancers occurs independently of GLI3. Consistent with previous studies, some individual GLI target genes are mis-regulated in Smarcc1 conditional knockouts, though most GLI target genes are unaffected. Moreover, SMARCC1 is not necessary for mediating constitutive GLI repression in HH mutant limb buds. We conclude that SMARCC1 does not mediate GLI3 repression, which we propose utilizes alternative chromatin remodeling complexes.

developmental biology↗

bioRxiv2021

GLI transcriptional repression is inert prior to Hedgehog pathway activation

In the absence of Hedgehog (HH) signaling, GLI proteins are post-translationally modified within cilia into transcriptional repressors that subsequently prevent sub-threshold activation of HH target genes. GLI repression is presumably important for preventing precocious expression of target genes before the onset of HH pathway activation, a presumption that underlies the pre-patterning model of anterior-posterior limb polarity. Here, we report that GLI3 repressor is abundant and binds to target genes in early limb development. However, contrary to expectations, GLI3 repression neither regulates the activity of GLI enhancers nor expression of HH target genes as it does after HH signaling has been established. Within the cilia, the transition to active GLI repression is accompanied by increases in axonemal GLI3 localization, possibly signifying altered GLI3 processing. Together, our results demonstrate that GLI3 repression does not prevent precocious activation of HH target genes, or have a pre-patterning role in regulating anterior-posterior limb polarity.

developmental biology↗

bioRxiv2019

GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling

Transcriptional repression needs to be rapidly reversible during embryonic development. This extends to the Hedgehog pathway, which primarily serves to counter GLI repression by processing GLI proteins into transcriptional activators. In investigating the mechanisms underlying GLI repression, we find that a subset of these regions, termed HH-responsive enhancers, specifically loses acetylation in the absence of HH signaling. These regions are highly enriched around HH target genes and primarily drive HH-specific limb activity. They also retain H3K27ac enrichment in limb buds devoid of GLI activator and repressor, indicating that their activity is primarily regulated by GLI repression. The Polycomb repression complex is not active at most of these regions, suggesting it is not a major mechanism of GLI repression. We propose a model for tissue-specific enhancer activity in which an HDAC-associated GLI repression complex regulates target gene expression by altering the acetylation status at enhancers.

developmental biology↗