Biology subjects

Tsui, S. K.-W.

Publications and source records attributed to Tsui, S. K.-W..

10 recordsLinked to original sources

bioRxiv2026

Precursor of chemically expanded hepatocytes (pre-cHep) with 1-million-fold expansion potential and liver repopulation capacity

Primary human hepatocytes (PHHs) are the gold standard for toxicology and drug metabolism studies in industry. However, their limited availability, substantial batch-to-batch variability, and high cost restrict their use. Here, we report a novel culture condition that reprograms PHHs into a proliferative state. These proliferating cells, termed precursors of chemically expanded hepatocytes (pre-cHep), expand over 106-fold within 30 days while retaining liver repopulation capacity comparable to PHHs. pre-cHep can further differentiate into chemically expanded hepatocytes (cHep) as three-dimensional (3D) spheroids within 7 days in vitro, exhibiting global gene expression profiles, albumin production, and cytochrome P450 (CYP) activities similar to 3D-cultured PHH spheroids (3D PHH). Efficient genetic manipulation of pre-cHep using CRISPR/Cas9 is also achievable. Together, pre-cHep and cHep represent a promising alternative to high-quality PHHs, providing a more affordable, reproducible, and scalable source of human hepatocytes for toxicology, drug metabolism studies, disease modelling, towards precision drug development.

bioengineering↗

bioRxiv2026

nELAVL phosphorylation by CDKL5 regulates inter-condensates composition and communication to promote experience-dependent maturation of the visual cortex

Mutations in Cyclin-Dependent Kinase-Like 5 (CDKL5) cause CDKL5 deficiency disorder (CDD), an X-linked neurodevelopmental condition. Through a phosphoproteomic screen, we identified the neuron-specific nELAVL family of RNA-binding proteins as direct activity-dependent substrates of CDKL5. In support of this regulatory axis, single-nuclei transcriptomics of Cdkl5 knockout (KO) cortices revealed an enriched reduction in activity-dependent mRNAs. Mechanistically, we show that nELAVL proteins undergo phase separation to form biomolecular condensates, the size of which is gated by CDKL5 phosphorylation. Loss of CDKL5 leads to enlarged nELAVL condensates, which exhibit reduced binding affinity for the target mRNA Fos, resulting in its accelerated degradation. This disruption extends to inter-condensate communication: phosphodeficient nELAVL show diminished interaction with P-bodies, which themselves become enlarged in CDD mutant iNeurons. Functionally, the absence of nELAVL phosphorylation recapitulates the deficits in experience-dependent visual function observed in Cdkl5 KO mice. Our findings establish a critical molecular mechanism by which CDKL5-mediated phosphorylation governs mRNA metabolism by tuning the properties of nELAVL condensates and their communication with other biomolecular condensates, ultimately promoting experience-dependent maturation of the visual cortex.

neuroscience↗

bioRxiv2025

Few-shot in-context learning with large language models for antibody characterization

Large language models (LLMs) can learn new tasks by in-context learning (ICL), but it is unknown whether this ability reliably transfers to biological sequence classification. Here, we systematically evaluate how demonstration selection, shot count, and prompting strategies affect performance across 20 general-purpose LLMs. Using antibody characterization as a representative test case, we compare zero-shot, few-shot, and chain-of-thought (CoT) ICL on three classification tasks: humanness, antigen specificity, and isotype. Our results reveal a clear performance hierarchy: while zero-shot prompting performs near chance, few-shot prompting with randomly selected demonstrations improves performance, showing that LLMs can perform ICL using biological sequences from minimal supervision. However, matching protein-language model (pLM)-based classifier accuracy is only achieved when using label-diverse demonstrations drawn from antibodies similar to the query sequence. To leverage this insight, we introduce Sim-ICL, a framework that automatically retrieves such demonstrations. Using only 32-shot prompting, Sim-ICL achieves performance competitive with pLM-based classifiers, matching or outperforming them in two of the three tasks. Furthermore, reasoning-oriented prompts yield marginal gains and often produce fluent but biologically incorrect rationales, suggesting that current CoT explanations function as after-the-fact rationalizations rather than capturing mechanistic determinants of antibody properties. From these experiments, we derive practical design principles for ICL on biological sequences: use similarity-based, label-diverse demonstrations and modest shot counts, and treat reasoning prompts primarily as post hoc narratives rather than drivers of performance. Sim-ICL implements these principles in a streamlined, prompt-based framework for antibody sequence classification and, in principle, could be adapted to other biological sequence tasks.

bioinformatics↗

bioRxiv2024

Commonly used software tools produce conflicting and overly-optimistic AUPRC values

The precision-recall curve (PRC) and the area under it (AUPRC) are useful for quantifying classification performance. They are commonly used in situations with imbalanced classes, such as cancer diagnosis and cell type annotation. We evaluated 10 popular tools for plotting PRC and computing AUPRC, which were collectively used in >3,000 published studies. We found the AUPRC values computed by the tools rank classifiers differently and some tools produce overly-optimistic results.

bioinformatics↗

bioRxiv2023

Comprehensive Allergen Profile of Blomia tropicalis Provides Insights into the Component-Resolved Diagnosis of Mite Allergy

BackgroundBlomia (B.) tropicalis, as an important species of house dust mites (HDMs), plays a critical role in allergic diseases in tropical populations, but its allergen components are less investigated than those of other HDMs. Multiple omics methods have largely improved the identification of mite allergens. Here, we sought to identify a comprehensive allergen profile of B. tropicalis and advance the allergen component-resolved diagnosis (CRD) of mite allergy. MethodsReference mite allergen sequences were searched in a high-quality genome of B. tropicalis. Comparative analysis was performed for important allergen groups. ELISA was used to assess the allergenicities of recombinant proteins of specific allergens. ResultsA complete allergen profile of B. tropicalis was revealed, including thirty-seven allergen groups (up to Blo t 42). In-depth comparative analysis not only determined the homology of major allergen groups 5 and 21 but also shed light on the emergence and divergence of chitin-binding allergens. The specific Blo t 12 was identified to be a chitin-binding protein originating from the chitinase of allergen group 15. Immunoassays of recombinant proteins verified three novel allergens and the ELISA results suggested geographical differences in the B. tropicalis sensitization rate. ConclusionsThe comprehensive allergen profile revealed in B. tropicalis, the comparative analysis of allergen groups and the immunoassay assessment of recombinant proteins largely expanded our knowledge to B. tropicalis allergens and could ultimately benefit the CRD of HDM allergy.

immunology↗

bioRxiv2022

Multi-Omic Analysis of Tyrophagus putrescentiae Reveals Insights into the Allergen Complexity of Storage Mites

BackgroundThe storage mite Tyrophagus putrescentiae is one of the major mites causing allergies in Chinese and Korean populations, but its allergen profile in incomplete when compared with that of house dust mites. Multiple genome-based methods have been introduced into the allergen study of mites and have enabled a better understanding of these medically important organisms. ObjectiveWe sought to reveal a comprehensive allergen profile of Tyrophagus putrescentiae and advance the allergen study of storage mites. MethodsBased on a high-quality assembled and annotated genome, an in silico analysis was performed by searching reference sequences to identify allergens. Immunoassay ELISA assessed the allergenicities of recombinant proteins. MALDI-TOF mass spectrometry identified the IgE-binding proteins. Comparative genomics analysis was employed for the important allergen gene families. ResultsA complete allergen profile of Tyrophagus putrescentiae was revealed, including thirty-seven allergen groups (up to Tyr p 42). Among them, five novel allergens were verified using the sera of allergy patients. Massive allergen homologs were identified as the result of gene duplications in genome evolution. Proteomic identification again revealed a wide range of allergen homologs. In the NPC2 family and GSTs, comparative analysis shed light on the expansion and diversification of the allergen groups. ConclusionUsing multi-omic approaches, the comprehensive allergen profile including massive homologs was disclosed in Tyrophagus putrescentiae, which revealed the allergen complexity of the storage mite and could ultimately facilitate the component-resolved diagnosis.

immunology↗

bioRxiv2022

Endogenous Plasmids and Reductive Genome Evolution in Host-Associated Bacteria

Reductive genome evolution is commonly observed among host-associated bacteria including many important pathogens, such as Mycobacterium leprae but its molecular mechanism is not well understood 1-5. One of the most widely accepted hypotheses to explain bacterial genome reduction is Mullers ratchet, in which the associated bacteria tend to accumulate deleterious mutations for reduction in the absence of chromosomal recombination inside the eukaryotic host organism 1,2. Cardinium species belong to the family Amoebophilaceae of the CFB group bacteria, which are a group of endosymbiont bacteria widely distributed among arthropods, that along with Wolbachia can cause cytoplasmic incompatibility 6,7. In this study, we explored bacterial reductive evolution within the de novo assembled genomes of Cardinium endosymbionts in two astigmatic mites 8,9. Our results shed light on the reduction mechanism driven by endogenous plasmids and their encoded enzymes.

microbiology↗

bioRxiv2022

Massive Horizontal Gene Transfer in Amphioxus Illuminates the Early Evolution of Deuterostomes

Amphioxus is considered the best-known living proxy to the chordate ancestor and an irreplaceable model organism for evolutionary studies of chordates and deuterostomes. In this study, a high-quality genome of the Beihai amphioxus, Branchiostoma belcheri beihai, was de novo assembled and annotated. Within four amphioxus genomes, twenty-eight groups of gene novelties were identified, revealing new genes that lack homologs in non-deuterostome metazoa, but share unexpectedly high similarities with those from non-metazoan species. These gene innovation events have played roles in amphioxus adaptations, including innate immunity responses, glycolysis, and regulation of calcium balance. The gene novelties related to innate immunity, such as a group of lipoxygenases and a DEAD-box helicase, boosted amphioxus immune responses. The novel genes for alcohol dehydrogenase and ferredoxin could aid in the glycolysis of amphioxus. A proximally arrayed cluster of EF-hand calcium-binding protein genes were identified to resemble those of bacteria. The copy number of this gene cluster was negatively correlated to the sea salinity of the collection region, suggesting that it may enhance their survival at different calcium concentrations. This comprehensive study collectively reveals insights into adaptive evolution of cephalochordates and provides valuable resources for research on early evolution of deuterostomes.

evolutionary biology↗

bioRxiv2022

Unique gut microbiome signatures among adult patients with moderate to severe atopic dermatitis in southern Chinese

Imbalance of the immune system caused by alterations of gut microbiome is considered to be a critical factor in the pathogenesis of infant eczema but the exact role of the gut microbiome in adult atopic dermatitis (AD) patients remains to be clarified. To investigate the differences of the gut microbiome between adult AD patients and healthy individuals, stool samples of 234 adults, containing 104 AD patients and 130 healthy subjects were collected for amplicon sequencing. Altered structure and metabolic dysfunctions of the gut microbiome were identified in adult AD patients. Our results illustrated that the adult AD patients were more likely to have allergies, particularly non-food allergies. And the gut microbiome composition of the AD and normal groups were considerably different. Besides, Romboutsia and Clostridium_sensu_stricto_1 was enriched in the normal group, whereas Blautia, Butyricicoccus, Lachnoclostridium, Eubacterium_hallii_group, Erysipelatoclostridium, Megasphaera, Oscillibacter, Flavonifractor were dominated in the AD group. Moreover, purine nucleotide degradation pathways were significantly enriched in the AD group and the enrichment of proteinogenic amino acid biosynthesis pathways was found in the normal group. This study provides insights into new therapeutic strategies targeting the gut microbiome for AD and evidence for the involvement of gut-skin axis in AD patients.

microbiology↗

bioRxiv2017

SSEalign: accurate function prediction of bacterial unannotated protein, based on effective training dataset

The functions of numerous bacterial proteins remain unknown because of the variety of their sequences. The performances of existing prediction methods are highly weak toward these proteins, leading to the annotation of \"hypothetical protein\" deposited in NCBI database. Elucidating the functions of these unannotated proteins is an urgent task in computational biology. We report a method about secondary structure element alignment called SSEalign based on an effective training dataset extracting from 20 well-studied bacterial genomes. The experimentally validated same genes in different species were selected as training positives, while different genes in different species were selected as training negatives. Moreover, SSEalign used a set of well-defined basic alignment elements with the backtracking line search algorithm to derive the best parameters for accurate prediction. Experimental results showed that SSEalign achieved 91.2% test accuracy, better than existing prediction methods. SSEalign was subsequently applied to identify the functions of those unannotated proteins in the latest published minimal bacteria genome JCVI-syn3.0. Results indicated that At least 99 proteins out of 149 unannotated proteins in the JCVI-syn3.0 genome could be annotated by SSEalign. In conclusion, our method is effective for the identification of protein homology and the annotation of uncharacterized proteins in the genome.

bioinformatics↗