Biology subjects

Wong, G. K.-S.

Publications and source records attributed to Wong, G. K.-S..

14 recordsLinked to original sources

bioRxiv2026

TransXplorer: An automated translational discovery platform for RNA-seq data

RNA-seq experiments routinely identify thousands of differentially expressed genes, but translating these into biological insights and therapeutic hypotheses often requires integrating multiple tools. Existing web platforms such as iDEP, NetworkAnalyst, and GEPIA2 address individual steps, differential expression, network visualization, or TCGA queries, but lack a unified environment spanning raw data processing to clinical and pharmacological interpretation. TransXplorer (https://transxplorer.org) is a freely available web platform that addresses this limitation by integrating the complete RNA-seq analytical workflow. It supports processing from raw FASTQ files using HISAT2 or Salmon, as well as direct GEO dataset import with automated metadata handling. Differential expression analysis is implemented via DESeq2, edgeR, and limma-voom, followed by functional enrichment across more than 1,800 species using Bioconductor resources. Batch effects are automatically detected and corrected using a composite of PVCA, kBET, and Silhouette metrics without requiring predefined batch annotations. Downstream analyses include co-expression network construction (WGCNA), protein-protein interaction mapping (STRING), cell-type deconvolution, and transcription factor inference using integrated DoRothEA and TFLink resources. The platform further links gene signatures to drug candidates through DGIdb and OpenTargets and enables survival and tumour-normal comparisons across TCGA cohorts. Application to cardiac endothelial differentiation (GSE151427) and kidney renal papillary cell carcinoma (TCGA-KIRP) datasets demonstrates accurate batch correction, biologically consistent pathway enrichment, recovery of expected cell-type proportions, and identification of clinically relevant genes and drug candidates. TransXplorer is freely available without a login.

bioinformatics↗

bioRxiv2026

Chromosome-level genome assembly of Helichrysum odoratissimum, a medicinal plant from Southern Africa

Helichrysum odoratissimum, a plant species native to Southern Africa, holds deep cultural significance and is widely used in traditional medicine. It is valued for its antimicrobial and anti-inflammatory properties and is cultivated and traded in South Africa due to its growing commercial relevance to the pharmaceutical and cosmetic industries. Despite its ecological and economic importance, genomic resources for this species remain limited. Here, we report a high-quality chromosome-level genome assembly for H. odoratissimum to facilitate investigations into its genetic basis of bioactivity, environmental adaptation, and taxonomic relationships. High-molecular-weight DNA extracted from leaf tissue was sequenced using Oxford Nanopore Technologies (ONT) long-read sequencing, and Hi-C proximity ligation data were generated to enable chromosome-scale scaffolding. The final assembly spans 2.4 Gb, with a scaffold N50 of 354 Mb, and was anchored and oriented into seven chromosomes, with 2,935 smaller scaffolds remaining unplaced. Assembly quality and completeness were evaluated using QUAST and BUSCO, and chromosomal structure was validated using Hi-C contact maps. This genome provides a foundational resource for functional genomics, conservation planning, molecular breeding, and the discovery of bioactive compounds underpinning the medicinal and commercial value of H. odoratissimum.

genomics↗

bioRxiv2025

Cell State Chaos Underpins the Evolution of SMARCA4-Deficient Dedifferentiated Endometrial Cancer

Dedifferentiated endometrial carcinoma (DDEC) is a histologically unique cancer type, wherein well-differentiated regions lie adjacent to morphologically distinct, high-grade lesions that are histologically undifferentiated. Previous studies have determined that in nearly half of the cases dedifferentiation is associated with the genomic inactivation of SMARCA4, a catalytic subunit belonging to the SWI/SNF chromatin remodelling complex (SWI/SNF CRC), suggesting that SMARCA4 loss causes dedifferentiation. Herein, using gene editing, we reveal that when serially passaged in mice, SMARCA4-deficient endometrial cancer cells repeatably and predictably generate heterogeneous admixtures of differentiated and undifferentiated cells, resembling human DDEC. Surprisingly, despite this metamorphosis, SMARCA4 loss does not induce lineage plasticity nor reprogramming to a less differentiated fate. Rather, single-cell sequencing combined with barcoding demonstrated that SMARCA4 loss induces a dysregulated epigenome that allows cells to randomly move through cellular states that are otherwise shared with SMARCA4-expressing well-differentiated cancer cells. This finding was validated using a cohort of patient samples, such that epithelial fate markers (E-CADHERIN) can be detected in morphologically undifferentiated cells. Collectively, this work constitutes the first repeatable model of human dedifferentiated cancer and suggests that histological dedifferentiation is not due to the acquisition of a stem cell-like fate. Rather, undifferentiated tissue emerges due to epigenomic dysfunction concomitant with the arbitrary movement of cancer cells between cellular states.

cancer biology↗

bioRxiv2021

Cation and anion channelrhodopsins: Sequence motifs and taxonomic distribution

Cation and anion channelrhodopsins (CCRs and ACRs, respectively) primarily from two algal species, Chlamydomonas reinhardtii and Guillardia theta, have become widely used as optogenetic tools to control cell membrane potential with light. We mined algal and other protist polynucleotide sequencing projects and metagenomic samples to identify 75 channelrhodopsin homologs from three channelrhodopsin families, including one revealed in dinoflagellates in this study. We carried out electrophysiological analysis of 33 natural channelrhodopsin variants from different phylogenetic lineages and 10 metagenomic homologs in search of sequence determinants of ion selectivity, photocurrent desensitization, and spectral tuning in channelrhodopsins. Our results show that association of a reduced number of glutamates near the conductance path with anion selectivity depends on a wider protein context, because prasinophyte homologs with the identical glutamate pattern as in cryptophyte ACRs are cation-selective. Desensitization is also broadly context-dependent, as in one branch of stramenopile ACRs and their metagenomic homologs its extent roughly correlates with phylogenetic relationship of their sequences. Regarding spectral tuning, two prasinophyte CCRs exhibit red-shifted spectra to 585 nm, although their retinal-binding pockets do not match those of previously known similarly red-shifted channelrhodopsins. In cryptophyte ACRs we identified three specific residue positions in the retinal-binding pocket that define the wavelength of their spectral maxima. Lastly, we found that dinoflagellate rhodopsins with a TCP motif in the third transmembrane helix and a metagenomic homolog exhibit channel activity. IMPORTANCEChannelrhodopsins are widely used in neuroscience and cardiology as research tools and are considered as prospective therapeutics, but their natural diversity and mechanisms remain poorly characterized. Genomic and metagenomic sequencing projects are producing an ever-increasing wealth of data, whereas biophysical characterization of the encoded proteins lags behind. In this study we used manual and automated patch clamp recording of representative members of four channelrhodopsin families including a family that we report in this study in dinoflagellates. Our results contribute to a better understanding of molecular determinants of ionic selectivity, photocurrent desensitization, and spectral tuning in channelrhodopsins.

biochemistry↗

bioRxiv2020

Fecal microbiota transplantation efficacy for Clostridium difficile infection: A trans-kingdom battle between donor and recipient gut microbiomes

Fundamental restoration ecology and community ecology theories can help us better understand the underlying mechanisms of fecal microbiota transplantation (FMT) and to better design future microbial therapeutics for recurrent Clostridium difficile infections (rCDI) and other dysbiosis-related conditions. In a single cohort study, stool samples were collected from donors and rCDI patients one week prior to FMT (pre-FMT) as well as from patients one week following FMT (post-FMT). Using metagenomic sequencing and machine learning methods, our results suggested that the FMT outcome is not only dependent on the ecological structure of the recipients, but also the interactions between the donor and recipient microbiomes, both at the taxonomical and functional levels. Importantly, we observed that the presence of specific bacteria in donors (Clostridiodes spp., Desulfovibrio spp., Odoribacter spp. and Oscillibacter spp.) and the absence of specific fungi (Yarrowia spp.) and bacteria (Wigglesworthia spp.) in recipients prior to FMT could accurately predict FMT success. Our results also suggested a series of interlocked mechanisms for FMT success, including the repair of the disturbed gut microbial ecosystem by transient colonization of nexus species followed by secondary succession of bile acid metabolizers, sporulators, and short chain fatty acid producers. Therefore, a better understanding of such mechanisms can be fundamental key elements to develop adaptive, personalized microbial-based strategies for the restoration of the gut ecosystem. ImportanceThere have been a number of studies focusing on understanding the underlying mechanisms in FMT treatment, which can accordingly be used for the optimization of future treatments. However, the current scientific lens has mainly had a uni-kingdom major focus on bacteria, leading to the proposition of the existence of FMT "super-donors". On the contrary, our preliminary study here suggests that FMT is not necessarily a one stool fits all approach and that donor-recipient cross-kingdom microbiota interactions, along with their short-term fluctuations in the gut, bring profound implications in FMT success. The results also conceptualize a series of interlocked mechanisms for FMT success, including first repairing the disturbed gut microbial ecosystem by transient species, followed by secondary succession of indigenous or exogenous bile acid metabolizers, sporulators, and short chain fatty acid producers.

microbiology↗

bioRxiv2020

Conductance mechanisms of rapidly desensitizing cation channelrhodopsins from cryptophyte algae

Channelrhodopsins guide algal phototaxis and are widely used as optogenetic probes for control of membrane potential with light. "Bacteriorhodopsin-like" cation channelrhodopsins (BCCRs) from cryptophytes differ in primary structure from other CCRs, lacking usual residues important for their cation conductance. Instead, BCCR sequences match more closely those of rhodopsin proton pumps, containing residues responsible for critical proton transfer reactions. We report 19 new BCCRs, which, together with the earlier 6 known members of this family, form three branches (subfamilies) of a phylogenetic tree. Here we show that the conductance mechanisms in two subfamilies differ with respect to involvement of the homolog of the proton donor in rhodopsin pumps. Two BCCRs from the genus Rhodomonas generate photocurrents that rapidly desensitize under continuous illumination. Using a combination of patch clamp electrophysiology, absorption and Raman spectroscopy, and flash photolysis, we found that the desensitization is due to rapid accumulation of a long-lived nonconducting intermediate of the photocycle with unusually blue-shifted absorption with a maximum at 330 nm. These observations reveal diversity within the BCCR family and contribute to deeper understanding of their independently evolved cation channel function. IMPORTANCECation channelrhodopsins, light-gated channels from flagellate green algae, are extensively used as optogenetic photoactivators of neurons in research and recently have progressed to clinical trials for vision restoration. However, the molecular mechanisms of their photoactivation remain poorly understood. We recently identified cryptophyte cation channelrhodopsins, structurally different from those of green algae, which have separately evolved to converge on light-gated cation conductance. This study reveals diversity within this new protein family and describes a subclade with unusually rapid desensitization that results in short transient photocurrents in continuous light. Such transient currents have not been observed in the green algae channelrhodopsins and are potentially useful in optogenetic protocols. Kinetic UV-vis spectroscopy and photoelectrophysiology reveal the desensitization is caused by rapid accumulation of a non-conductive photointermediate in the photochemical reaction cycle. The absorption maximum of the intermediate is 330 nm, the shortest wavelength reported in any rhodopsin, indicating a novel chromophore structure.

biochemistry↗

bioRxiv2019

Independent evolution of cutaneous lymphoma subclones in different microenvironments of the skin

Mycosis fungoides (MF) is the most common, yet incurable, cutaneous T-cell lymphoma. We have recently shown that the disease is initiated by hematogenous seeding the skin with clonotypically diverse neoplastic T-cells which proliferate accumulating numerous mutations and produce lesions of high intratumoral heterogeneity (ITH). A characteristic but a poorly studied feature of MF is epidermotropism, the tendency to infiltrate skin epithelial layer (epidermis) in addition to the vascularized dermis. By sequencing the exomes of the microdissected clusters of lymphoma cells from the epidermis and the dermis, we found that those microenvironments harbored different malignant clonotypes and exhibited different patterns of driver gene mutation. Phylogenetic relationships between cancer subclones witnessed to the independent mutational evolution in the epidermis and dermis. Thus, the invasion of MF to different skin layers does not occur by gradual infiltration of the expanding tumor mass, but is caused by separate seeding processes with different malignant clones that develop independently of one another via a neutral, branched evolution. In conclusion, tissue microenvironments shape the subclonal architecture in MF leading to \"ecological heterogeneity\" which contributes to the total ITH. Since ITH adversely affects cancer prognosis, targeting the microenvironment may present therapeutic opportunities in MF and other cancers.

cancer biology↗

bioRxiv2019

Molecular profiling of lymphovascular invasive cancer cells in TNBC using G&T-seq

Lymphovascular invasion (LVI) is a critical step in the metastatic process but have received relatively little attention due to the technical challenges associated with their isolation. In this study, we used laser capture microdissection (LCM) to isolate 97 cancer cell clusters from pathological frozen sections within lymphatic vessels, primary tumor tissue, and axillary lymph nodes of a triple negative breast cancer (TNBC) patient. Simultaneous genome and transcriptome amplification and sequencing (G&T-seq) performed on these clusters permitted a comprehensive depiction of the genomic and transcriptional profiles of cancer cells associated with LVI. Combination phylogeny analysis pointed to three evolutionarily distinct pathways of tumor clone development and metastasis in this patient, each of which was associated with a unique mRNA signature, and correlated to disparate overall survival outcomes. Moreover, hub gene evaluation found extensive down regulation of ribosomal protein mRNA to be a potential marker of poor prognosis in breast cancer patients.

cancer biology↗

bioRxiv2019

An ancestral signalling pathway is conserved in plant lineages forming intracellular symbioses

Plants are the foundation of terrestrial ecosystems and their colonization of land was facilitated by mutualistic associations with arbuscular mycorrhizal fungi. Following that founding event, plant diversification has led to the emergence of a tremendous diversity of mutualistic symbioses with microorganisms, ranging from extracellular associations to the most intimate intracellular associations, where fungal or bacterial symbionts are hosted inside plant cells. Through analysis of 271 transcriptomes and 122 plant genomes, we demonstrate that the common symbiosis signalling pathway controlling the association with arbuscular mycorrhizal fungi and with nitrogen-fixing bacteria specifically co-evolved with intracellular endosymbioses, including ericoid and orchid mycorrhizae in angiosperms and ericoid-like associations of bryophytes. In contrast, species forming exclusively extracellular symbioses like ectomycorrhizae or associations with cyanobacteria have lost this signalling pathway. This work unifies intracellular symbioses, revealing conservation in their evolution across 450 million years of plant diversification.

plant biology↗

bioRxiv2019

Branched evolution and genomic intratumor heterogeneity in the pathogenesis of cutaneous T-cell lymphoma

Mycosis fungoides (MF) is a slowly progressive cutaneous T-cell lymphoma (CTCL) for which there is no cure. In the early plaque stage the disease is indolent, but development of tumors heralds an increased risk of metastasis and death. Previous research into the genomic landscape of CTCL revealed a complex pattern of >50 driver mutations implicated in more than a dozen of signaling pathways. However, the genomic mechanisms governing disease progression and treatment resistance remain unknown. Building on our previous discovery of the clonotypic heterogeneity of MF, we hypothesized that this lymphoma does not progress in a linear fashion as currently thought, but comprises heterogeneous mutational subclones. We sequenced exomes of 49 cases of MF and identified 28 previously unreported putative driver genes. MF exhibited extensive intratumoral heterogeneity (ITH) of a median of six subclones showing branched pattern of phylogenetic relationships. Stage progression was correlated with an increase in ITH and redistribution of mutations from the stem to the clades. The pattern of clonal driver mutations was highly variable with no consistent mutations between patients. A similar intratumoral heterogeneity was detected in leukemic CTCL (Sezary syndrome). Based on these findings we propose a model of the pathogenesis of MF comprising neutral, divergent evolution of cancer subclones and discuss how ITH impacts the efficacy of targeted drug therapies and immunotherapies of CTCL.

cancer biology↗

bioRxiv2018

A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-medoids Clustering

Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost associated with developing targeted sequencing approaches is preliminary data needed for identifying orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used multiple sequence alignments from over 600 angiosperms for 353 putatively single-copy protein-coding genes to design a set of targeted sequencing probes for phylogenetic studies of any angiosperm lineage. To maximize the phylogenetic potential of the probes while minimizing the cost of production, we introduce a k-medoids clustering approach to identify the minimum number of sequences necessary to represent each coding sequence in the final probe set. Using this method, five to 15 representative sequences were selected per orthologous locus, representing the sequence diversity of angiosperms more efficiently than if probes were designed using available sequenced genomes alone. To test our approximately 80,000 probes, we hybridized libraries from 42 species spanning all higher-order lineages of angiosperms, with a focus on taxa not present in the sequence alignments used to design the probes. Out of a possible 353 coding sequences, we recovered an average of 283 per species and at least 100 in all species. Differences among taxa in sequence recovery could not be explained by relatedness to the representative taxa selected for probe design, suggesting that there is no phylogenetic bias in the probe set. Our probe set, which targeted 260 kbp of coding sequence, achieved a median recovery of 137 kbp per taxon in coding regions, a maximum recovery of 250 kbp, and an additional median of 212 kbp per taxon in flanking non-coding regions across all species. These results suggest that the Angiosperms353 probe set described here is effective for any group of flowering plants and would be useful for phylogenetic studies from the species level to higher-order lineages, including all angiosperms.

evolutionary biology↗

bioRxiv2017

Origin and evolution of the nuclear auxin response system

The small signaling molecule auxin controls numerous developmental processes in land plants, acting mostly by regulating gene expression. Auxin response proteins are represented by large families of diverse functions, but neither their origin nor their evolution is understood. Here we use a deep phylogenomics approach to reconstruct both the origin and the evolutionary trajectory of all nuclear auxin response protein families. We found that, while all subdomains are ancient, a complete auxin response mechanism is limited to land plants. Functional phylogenomics predicts defined steps in the evolution of response system properties, and comparative transcriptomics across six ancient lineages revealed how these innovations shaped a sophisticated response mechanism. Genetic analysis in a basal land plant revealed unexpected contributions of ancient non-canonical proteins in auxin response as well as auxin-unrelated function of core transcription factors. Our study provides a functional evolutionary framework for understanding diverse functions of the auxin signal.

genomics↗

bioRxiv2017

Divergent gene expression levels between diploid and autotetraploid Tolmiea (Saxifragaceae) relative to the total transcriptome, the cell, and biomass

O_LIStudies of gene expression and polyploidy are typically restricted to characterizing differences in transcript concentration. Integrating multiple methods of transcript analysis, we document a difference in transcriptome size, and make multiple comparisons of transcript abundance in diploid and autotetraploid Tolmiea.\nC_LIO_LIWe use RNA spike-in standards to identify and correct for differences in transcriptome size, and compare levels of gene expression across multiple scales: per transcriptome, per cell, and per biomass.\nC_LIO_LIIn total, ~17% of all loci were identified as differentially expressed (DEGs) between the diploid and autopolyploid species. A shift in total transcriptome size resulted in only ~58% of the total DEGs being identified as differentially expressed following a per transcriptome normalization. When transcript abundance was normalized per cell, ~82% of the total DEGs were recovered. The discrepancy between per-transcriptome and per-cell recovery of DEGs occurs because per-transcriptome normalizations are concentration-based and therefore blind to differences in transcriptome size.\nC_LIO_LIWhile each normalization enables valid comparisons at biologically relevant scales, a holistic comparison of multiple normalizations provides additional explanatory power not available from any single approach. Notably, autotetraploid loci tend to conserve diploid-like transcript abundance per biomass through increased gene expression per cell, and these loci are enriched for photosynthesis-related functions.\nC_LI

genomics↗

bioRxiv2017

The complex origins of strigolactone signalling in land plants

Strigolactones (SLs) are a class of plant hormones that control many aspects of plant growth. The SL signalling mechanism is homologous to that of karrikins (KARs), smoke-derived compounds that stimulate seed germination. In angiosperms, the SL receptor is an /{beta} hydrolase known as DWARF14 (D14); its close homologue, KARRIKIN INSENSITIVE2 (KAI2), functions as a KAR receptor, and likely recognizes an uncharacterized, endogenous signal. Previous phylogenetic analyses have suggested that the KAI2 lineage is ancestral in land plants, and that canonical D14-type SL receptors only arose in seed plants; this is paradoxical, however, as non-vascular plants synthesize and respond to SLs. Here, we have used a combination of phylogenetic and structural approaches to re-assess the evolution of the D14/KAI2 family in land plants. We analyzed 339 members of the D14/KAI2 family from land plants and charophyte algae. Our phylogenetic analyses show that the divergence between the eu-KAI2 lineage and the DDK (D14/DLK2/KAI2) lineage that includes D14 occurred very early in land plant evolution. We identify characteristic structural features of D14 and KAI2 proteins, and use homology modelling to show that the earliest members of the DDK lineage structurally resemble KAI2, and not D14 proteins. Furthermore, we show that probable SL receptors in non-seed plants do not have D14-like structure. Our results suggest that SL perception has relatively relaxed structural requirements, and that the evolution from KAI2-like to D14-like protein structure in the DDK lineage may have been driven by interactions with protein partners, rather than being required for SL perception itself.

plant biology↗