Biology subjects

Ng, C. P.

Publications and source records attributed to Ng, C. P..

5 recordsLinked to original sources

bioRxiv2026

AI-derived Protein Structures Validation: AlphaFold2 Models in the Twilight Zone

In any field, unquestioningly accepting artificial intelligence (AI) results should be considered bad practise. Here, we devised a comparative modelling-based strategy for validating protein structures that exploits the well-known observation that protein folds are far more conserved than protein sequences. We identify proteins with a similar fold to the AlphaFold-generated query protein and determine their structural alignment to the query. The hypothesis is that if the sequence alignment coincides with the structural alignment, then the structure is validated. The strategy is implemented on a helix-by-helix and strand-by-strand basis using a multi-template pairwise local profile alignment method that works well into the twilight zone. The method is illustrated by application to the transmembrane transporter PEPT1, for which the structure is known, and the S-deacylases ABHD13 and ABHD16A, for which only AI-generated models exist. ABHD16A is particularly challenging because a sequence alignment search with BLASTp does not reveal any structural homologues and therefore requires work with extremely remote homologues; however, both models are validated through this strategy and are stable during classical molecular dynamics simulations. The ability of the strategy to identify errors is assessed with reference to misaligned ABHD13 models and misfolded decoy proteins.

bioinformatics↗

bioRxiv2026

Deacylation of SNAP25 protein family isoforms reveals distinct substrate selectivities of α/β hydrolase domain (ABHD) deacylases

Reversible S-acylation controls protein trafficking, localisation and activity within cells, yet the limited understanding of the regulatory mechanisms of S-acylation/deacylation cycles represents one of the biggest obstacles in exploiting this prevalent post-translational modification for therapeutic purposes. Here, we identified ABHD13 and ABHD16A as novel deacylases regulating the SNAP25 family of SNARE proteins responsible for vesicular membrane fusion. We determined the mechanism and structural determinants for ABHD13-mediated deacylation and substrate selectivity towards SNAP25b, and identified a novel mechanism of acyl chain extraction for integral membrane deacylases. This is the first report of deacylase selectivity mapped to a single amino acid position in full-length proteins.

molecular biology↗

bioRxiv2025

Modeling Hepatocellular Carcinoma and its microenvironment on a chip

Hepatocellular carcinoma (HCC) is the most common type of liver cancer. Its incidence is increasing and is closely related to advanced liver disease. Interactions in the HCC microenvironment between tumor cells and the associated stroma actively regulate tumor initiation, progression, metastasis, and therapy response. Effective drug development increasingly requires advanced models that can be utilized in the earliest stages of compound and target discovery. Here we report a phenotypic screen on an advanced HCC patient-derived chip (PDChip) model. The vascularized HCC PDChip models include relevant cellular players of the HCC microenvironment. We assessed the effect of 28 treatment conditions on a panel of 8 primary HCC tumors and 2 cell lines. Approximately 1200 HCC PDchips were grown under perfusion flow, exposed to treatments, and subsequently assessed for viability, tumor-associated vasculature responses and chemokine and cytokine changes. Although the SoC therapeutics sorafenib and lenvatinib reduced culture viability and produced profound changes in the organization of the vascular beds, they did not affect the tumor cell population in these cultures. Atorvastatin, a 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase inhibitor, reduced tumor viability but did not affect vascular bed organization. Sorafenib, lenvatinib and atorvastatin also affected chemokine and cytokine release. Tocilizumab, galunisertib, and vactosertib decreased the level of IL6, a relevant prognostic marker for HCC, while IL6 was increased by halofuginone. In conclusion, HCC PDChip models enabled a detailed evaluation of drug-induced responses in the tumor and associated microenvironment, highlighting their importance in preclinical research for understanding diseases and developing new drugs.

bioengineering↗

bioRxiv2022

Healthy and diseased placenta barrier on-a-chip models suitable for high-throughput studies

Preeclampsia is one of the leading causes of maternal and perinatal morbidity in the world. Its fundamental mechanisms are yet poorly understood due to a lack of good experimental models. Here we report an in vitro model of the placental barrier, based on co-culture of trophoblasts and endothelial cells against a collagen extracellular matrix in a microfluidic platform. The model yielded a functional syncytium with barrier properties, polarization, secretion of relevant extracellular membrane components, thinning of the materno-fetal space, hormone secretion, and transporter function. The model was exposed to low oxygen conditions and perfusion flow was modulated to induce preeclamptic characteristics, resulting in reduced barrier function, hormone secretion, and microvilli as well as increased nuclei count. The model was implemented in a titer plate microfluidic platform fully amenable to high-throughput screening. We thus believe this model could aid mechanistic understanding of preeclampsia as well as support future development of effective therapies through target and compound screening campaigns.

bioengineering↗

bioRxiv2021

Diversity and Function of Motile Ciliated Cell Types within Ependymal Lineages of the Zebrafish Brain

Motile cilia defects impair cerebrospinal fluid (CSF) flow, and can cause brain and spine disorders. To date, the development of ciliated cells, their impact on CSF flow and their function in brain and axial morphogenesis are not fully understood. Here, we have characterized motile ciliated cells within the zebrafish brain ventricles. We show that the ventricular surface undergoes significant restructuring through development, involving a transition from mono- to multiciliated cells (MCCs) driven by gmnc. MCCs are translationally polarized, co-exist with monociliated cells and generate directional flow patterns. Moreover, these ciliated cells have different developmental origins, and are genetically heterogenous with respect to expression of the Foxj1 family of ciliary master regulators. Finally, we show that cilia loss from specific brain regions or global perturbation of multiciliation does not affect overall brain or spine morphogenesis, but results in enlarged ventricles. Our findings establish that motile ciliated cells are generated by complementary and sequential transcriptional programs to support ventricular development.

neuroscience↗