Biology subjects

Huang, P.-H.

Publications and source records attributed to Huang, P.-H..

6 recordsLinked to original sources

bioRxiv2025

NSUN2 drives intestinal stem cell expansion and colorectal tumour initiation via MAPK/ERK signalling

Colorectal cancer is initiated by loss of the APC gene, which drives expansion of LGR5+ intestinal stem cell (ISC) populations. Whilst LGR5+ ISC expansion is a critical step for tumour initiation and progression, its regulation is poorly understood. Emerging evidence suggests post-transcriptional RNA modifications play a key role in cancer biology, but their role in CRC initiation has not been explored. Here, we identify the m5C methyltransferase NSUN2 as a key regulator of ISC expansion and intestinal tumourigenesis. NSUN2 is upregulated in multiple CRC mouse models and human tumours and its depletion impairs ISC expansion and hyperproliferation, leading to reduced tumour initiation. Transcriptome-wide bisulphite sequencing revealed that NSUN2-mediates m5C methylation on mRNAs encoding key ISC regulators and components of the MAPK/ERK pathway. Mechanistically, loss of NSUN2 reduces ERK phosphorylation in Apc-deficient models and oncogenic KrasG12Dexpression is sufficient to restore ERK signalling and rescue ISC expansion. Together, this establishes NSUN2 as a key regulator of ISC-driven CRC initiation and describes a novel molecular mechanism linking m5C methylation to MAPK driven stem cell transformation.

cancer biology↗

bioRxiv2025

Leveraging Comparative Phylogenetics for Evolutionary Medicine: Applications to Comparative Oncology

Comparative phylogenetics provides a wealth of computational tools to understand evolutionary processes and their outcomes. Advances in these methodologies have occurred in parallel with a surge in cross-species genomic and phenotypic data. To date, however, the majority of published studies have focused on classical questions in evolutionary biology, such as speciation and the ecological drivers of trait evolution. Here, we argue that evolutionary medicine in general, and our understanding of the origin and diversification of disease traits in particular, would be greatly expanded by a wider integration of phylogenetic comparative methods (PCMs). We use comparative oncology - the study of cancer across the tree of life - as a case study to demonstrate the power of the approach and show that implementing PCMs can highlight the mode and tempo of the evolutionary changes in intrinsic, species-level disease vulnerabilities.

evolutionary biology↗

bioRxiv2024

Enolase-1 is essential for neutrophil recruitment during acute inflammation

Enolase-1 (ENO1) is a moonlighting protein with multiple functions. When expressed on the cell surface, ENO1 binds plasminogen (PLG) and promotes cell migration by facilitating plasmin (PLM)-mediated extracellular matrix degradation. Here, we observed that inflammatory stimulation significantly upregulated ENO1 expression on the neutrophil surface, both in vitro and in vivo. An anti-ENO1 monoclonal antibody (mAb), 7E5, which blocks the ENO1-PLG interaction, effectively suppressed neutrophil transmigration. In mouse models of acute inflammation, including lipopolysaccharide (LPS)-induced lung injury and necrotic cell challenge, 7E5 treatment markedly reduced neutrophil recruitment and neutrophil extracellular trap (NET) formation. Moreover, 7E5 neutralized the immunostimulatory activity of soluble ENO1, which was significantly elevated in circulation during acute inflammation. These findings highlight ENO1 as a key regulator of inflammation and neutrophil infiltration. Targeting ENO1 with antibodies could be a promising strategy to mitigate tissue damage caused by excessive neutrophilic inflammation.

immunology↗

bioRxiv2023

A mutant fitness compendium in Bifidobacteria reveals molecular determinants of colonization and host-microbe interactions

Bifidobacteria commonly represent a dominant constituent of human gut microbiomes during infancy, influencing nutrition, immune development, and resistance to infection. Despite interest as a probiotic therapy, predicting the nutritional requirements and health-promoting effects of Bifidobacteria is challenging due to major knowledge gaps. To overcome these deficiencies, we used large-scale genetics to create a compendium of mutant fitness in Bifidobacterium breve (Bb). We generated a high density, randomly barcoded transposon insertion pool in Bb, and used this pool to determine Bb fitness requirements during colonization of germ-free mice and chickens with multiple diets and in response to hundreds of in vitro perturbations. To enable mechanistic investigation, we constructed an ordered collection of insertion strains covering 1462 genes. We leveraged these tools to improve models of metabolic pathways, reveal unexpected host- and diet-specific requirements for colonization, and connect the production of immunomodulatory molecules to growth benefits. These resources will greatly reduce the barrier to future investigations of this important beneficial microbe.

microbiology↗

bioRxiv2022

A versatile method to archive and delipidate brain tissues for ensuing multiplexed immunolabeling and organ-level imaging

Tissue clearing and labeling techniques have revolutionized brain-wide imaging and analysis, yet their application to clinical formalin-fixed paraffin-embedded (FFPE) blocks remains challenging. We introduce HIF-Clear, a novel method for efficiently clearing and labeling centimeter-thick FFPE specimens using elevated temperature and concentrated detergents. HIF-Clear with multi-round immunolabeling reveals neuron circuitry regulating multiple neurotransmitter systems in a whole FFPE mouse brain, and is able to be used as the evaluation of disease treatment efficiency. HIF-Clear also supports expansion microscopy and can be performed on a non-sectioned 15-year-old FFPE specimen, as well as a 3-month formalin-fixed mouse brain. Thus, HIF-Clear represents a feasible approach for researching archived FFPE specimens for future neuroscientific and 3D neuropathological analyses.

bioengineering↗

bioRxiv2022

M-TUBE: a fabrication-free microfluidic device for large-volume bacterial electroporation requiring minimal assembly

Conventional cuvette-based and microfluidics-based bacterial electroporation approaches have distinct advantages, but they are typically limited to relatively small sample volumes, reducing their utility for applications requiring high throughput such as the generation of mutant libraries. Here, we present a disposable, user-friendly microfluidic electroporation device capable of processing large volume bacterial samples yet requiring minimal device fabrication and straightforward operation. We demonstrate that the proposed device can outperform conventional cuvettes in a range of situations, including across Escherichia coli strains with a range of electroporation efficiencies, and we use its large-volume bacterial electroporation capability to generate a library of transposon mutants in the anaerobic gut commensal Bifidobacterium longum.

bioengineering↗