Biology subjects

Coyle, M.

Publications and source records attributed to Coyle, M..

3 recordsLinked to original sources

bioRxiv2026

Chromatin Landscape of Cancer Cell Lines Identifies Enhancer Subtypes

Epigenetic aberrations are a hallmark of cancer; however, systematic chromatin state maps of cancer cells are unavailable. We generated and analyzed 803 histone mark profiles in 142 cancer cell lines and 114 human tumors belonging to 9 solid tumor types. Irrespective of their cell-of-origin, cancer cells segregate from normal tissues based on their enhancer patterns, suggesting enhancer deregulation is a fundamental epigenetic feature in cancer. Enhancer based clustering defined 5 distinct subgroups of cancer cells (EpiC1-5) with unique developmental trajectories, molecular features and dependencies. Importantly, we define a set of core TFs that are critical for EpiC-specific enhancer patterns and survival. Notably, EpiC4 represented a predominantly epigenetic, pan-cancer subtype that displays poor survival, activation and dependence on a FN1-CAV1-SRC-PI3K-AKT signaling network. Together, these data uncover enhancer heterogeneity in pan-cancer systems with identification of a novel enhancer-based subtype and identify potential new therapeutic targets associated with unique epigenetic features.

cancer biology↗

bioRxiv2024

Rostral Pedunculopontine Nucleus Infusion of M4 Positive Allosteric Modulator VU0467154 Augments L-DOPA Effects in Hemiparkinsonian Rats

Standard treatment for Parkinsons disease (PD) is dopamine replacement therapy with L-DOPA. However, chronic treatment often results in abnormal involuntary movements called L-DOPA-induced dyskinesia (LID). Prior evidence indicates that heightened striatal cholinergic tone may contribute to LID. Restoring cholinergic inhibition by targeting the inhibitory M4 muscarinic acetylcholine (ACh) receptor (M4) reduces LID in preclinical models. Although intrinsic striatal sources of ACh have been considered for their role in LID, extrinsic sources of ACh such as the pedunculopontine nucleus (PPN) have not been well investigated for their role in LID. Therefore, the current study employed hemiparkinsonian Long-Evans rats with a PPN-targeted cannula ipsilateral to 6-OHDA lesion. Following chronic treatment with L-DOPA, we examined the effect of local unilateral PPN infusion of M4 PAM VU0467154 on LID, motor performance, and c-fos expression within the PPN. It was expected that PPN infusion of VU0467154 would reduce LID, reduce L-DOPAs motor benefit, and globally reduce c-fos expression in the PPN. Contrary to our expectations, PPN infusion of M4 PAM did not significantly affect LID severity. Furthermore, the group receiving M4 PAM showed slightly elevated motor improvement compared to L-DOPA, and decreased c-fos expression specifically in PPN cholinergic neurons. These results suggest that local PPN ACh dynamics differ from those of the striatum. Specifically, our results suggest that PPN cholinergic neurons may be a promising therapeutic target for augmenting L-DOPA-mediated motor benefit without increasing LID.

neuroscience↗

bioRxiv2022

An RFX transcription factor regulated ciliogenesis in the progenitors of choanoflagellates and animals

Little is known about the origins of the transcriptional modules that coordinate cell-type specific functions in animals. The controlled expression of one cellular feature - the cilium - was likely critical during early animal evolution. Two key transcription factors, RFX and FoxJ1, coordinate ciliogenesis in animals but are absent from the genomes of most other ciliated eukaryotes, raising the question of how the transcriptional regulation of ciliogenesis has evolved. To reconstruct the evolution of the RFX/FoxJ1 transcriptional module and its role in the regulation of ciliogenesis, we investigated RFX and FoxJ1 function in one of the closest living relatives of animals, the choanoflagellate Salpingoeca rosetta. Targeted disruption of the S. rosetta RFX homolog cRFXa resulted in delayed cell proliferation and aberrant ciliogenesis, marked by the collapse and resorption of nascent cilia. Ciliogenesis genes and foxJ1 were significantly down-regulated in cRFXa mutants, consistent with a pre-animal ancestry for this transcriptional module. We also found that cRFXa protein preferentially binds to a sequence motif that is enriched in the promoters of S. rosetta ciliary genes and matches the sequence motif bound by animal RFX proteins. These findings suggest that RFX coordinated ciliogenesis before the divergence of animals and choanoflagellates, and that the deployment of this module may have provided a mechanism to differentiate ciliated and non-ciliated cell types in early animal evolution.

evolutionary biology↗