Biology subjects

Liu, K.-C.

Publications and source records attributed to Liu, K.-C..

3 recordsLinked to original sources

bioRxiv2026

A high-throughput screening dataset of small-molecule inhibitors across human DNA glycosylases

The base excision repair pathway removes small base lesions from DNA and is initiated in humans by one of eleven DNA glycosylases with overlapping substrate specificities. Despite their central role in genome maintenance and transcription, systematic datasets describing small-molecule binders or inhibitors of DNA glycosylases are lacking. Here, through a collaborative effort across Scandinavia, we establish a high-throughput biochemical assay platform for human DNA glycosylases and use it to generate a systematic small-molecule screening dataset. A chemogenomic library was screened against nine glycosylases with assays of sufficient quality for hit identification, yielding primary screening and concentration-response data and identifying multiple previously unreported inhibitors. All primary and processed data, along with detailed assay protocols and metadata, are publicly available to support reuse in chemical biology, further compound optimization, assay development and comparative studies of DNA repair enzymes.

biochemistry↗

bioRxiv2025

Deciphering the zebrafish hepatic duct heterogeneity and cell plasticity using lineage tracing and single-cell transcriptomics

Despite the livers recognized regenerative potential, the role of the hepatic ductal cells (a.k.a. biliary epithelial cells), its heterogeneity, and functionality remain incompletely understood in this process. This study provides a comprehensive examination of the molecular and cellular mechanisms underpinning liver ductal development and liver regeneration in zebrafish, with a spotlight on the functional roles of her family genes in these processes. Using state-of-the-art knock-in zebrafish models and single-cell transcriptomics we reveal the differential expression patterns of the different her genes, of which her2, her6, and her9, were identified as specific molecular signatures for distinguishing different ductal cell types with unique morphology and spatial distribution. Particularly, her9 serves as a pan-ductal marker and shows responsiveness to the synergistic effect of Notch and BMP signaling. By analyzing multiple single-cell RNA-seq datasets, we identify numerous ductal markers which are functional proteins for ductal integrity, and most notably CRISPR mutagenesis demonstrates that her9 is essential for hepatocyte recovery. Using multiple transgenic and knock-in zebrafish lines and genetic fate mapping, we provide a detailed characterization of the ductal remodeling process under development and extreme loss of intra-hepatic duct, highlighting the remarkable ductal cell plasticity. Single-cell transcriptomics of lineage-traced her9-expressing liver ducts in static and regenerative states uncover distinct cell clusters with unique molecular signatures and morphology, reflecting the livers regenerative dynamics and highlight relevant key biological processes that could be leveraged to expedite liver regeneration.

developmental biology↗

bioRxiv2021

Regenerating insulin-producing β-cells ectopically from a mesodermal origin in the absence of endothelial specification

To investigate the role of the vasculature in pancreatic {beta}-cell regeneration, we crossed a zebrafish {beta}-cell ablation model into the avascular npas4l mutant (i.e. cloche). Surprisingly, {beta}-cell regeneration increased markedly in npas4l mutants owing to the ectopic differentiation of {beta}-cells in the mesenchyme, a phenotype not previously reported in any models. The ectopic {beta}-cells expressed endocrine markers of pancreatic {beta}-cells, and also reduced glucose levels in the {beta}-cell ablation model. Through lineage tracing, we determined that the vast majority of these ectopic {beta}-cells derived from the mesodermal lineage. Notably, ectopic {beta}-cells were found in npas4l mutants as well as following knockdown of the endothelial determinant Etv2. Together, these data indicate that in the absence of endothelial specification, mesodermal cells possess a remarkable plasticity enabling them to form {beta}-cells, which are normally endodermal in origin. Understanding the restriction of this differentiation plasticity will help exploit an alternative source for {beta}-cell regeneration.

developmental biology↗