Biology subjects

Wong, K. H.

Publications and source records attributed to Wong, K. H..

10 recordsLinked to original sources

bioRxiv2026

The common evolution of fungicide persistence in cryptococcosis patients

Fungicide persistence, the ability of dormant fungal cells to survive lethal drug exposure, undermines treatment efficacy, yet its clinical evolution remains largely unexplored. We assembled a nationwide collection of clinical Cryptococcus neoformans isolates from China and revealed extensive inter strain variation in amphotericin B (AmB) persistence. This variation can arise from common evolutionary events in patients, generating previously undescribed high persistence cryptococcal variants refractory to AmB clearance. Genome wide fitness landscape analysis shows that persistence associated mutations generally impose minimal fitness costs, facilitating persistence evolution even in fungistatic resistant and hypervirulent genetic backgrounds. Machine learning identified deficient ACO2 expression as a key predictor of high persistence clinical isolates. ACO2 deficiency reproduces the high persistence phenotype by promoting POPC accumulation, which competes with AmB for its target. Moreover, the clinical stage antifungal T-2307 effectively eliminates high persistence strains across diverse genetic backgrounds. Collectively, our findings unveil common evolution of fungicide persistence in cryptococcosis patients, representing a previously overlooked clinical concern.

microbiology↗

bioRxiv2026

Active strains in the basal organ of Corti in gerbil

Optical coherence tomography (OCT) has allowed in vivo recording of sound-induced vibrations of different regions within the organ of Corti complex (OCC), including the basilar membrane (BM), outer hair cell/Deiters cell (OHC/DC) region, and reticular lamina (RL). In the hook region of the gerbil cochlea, where measurements can be made with a substantially transverse optical axis, the three regions have different and characteristic motion responses: The OHC/DC region has greater motions than the other two regions at frequencies below the best frequency (sub-BF); the RL region typically has the greatest BF peak and smallest sub-BF motion. The phase of the OHC/DC-region motion increasingly lags BM motion phase as frequency increases; the RL-region motion phase leads BM, but with a relatively small value. All three regions are compressively nonlinear in the BF peak, but only the OHC/DC region shows sub-BF compressive nonlinearity. In this paper, we describe the strain that exists within the RL and OHC-body regions. These strains are large where the motion varies over short distances, and a region of large strain can be as short as a single 2.7 {micro}m measurement pixel, or extend over several pixels, with the extensive strains appearing more often at 70 than at 50 dB SPL. Beyond the region of large strain, over a distance that can exceed 20 m, the OHC/DC region displays nearly unvarying motion spatially -- this region appears to vibrate as a body. Statement of SignificanceThe sensory tissue of the cochlea responds actively to a sound stimulus: cell-based forces amplify and enhance the vibration of the sensory tissue. Measurements employing optical coherence tomography have identified major vibration patterns along a sensory-tissue-spanning line that includes the active outer hair cells. In this article, we describe the transitional motion between these major vibration regions and the motion strains that exist as vibration morphs from one region to the next. The findings are presented in frequency response curves to convey the frequency tuning and its stimulus-level dependence, and in one-dimensional heat maps to convey the extent of regional motions and strains. These findings fuel and constrain conceptual and physics-based models of cochlear amplification.

biophysics↗

bioRxiv2025

Seasonal plasticity of symbiotic strategies clarifies coral holobiont resistance and resilience

As coral reefs face unprecedented declines driven by thermal stress and the breakdown of coral symbiosis (i.e., coral bleaching), restoration efforts increasingly rely on coral health and resilience rankings. However, seasonal plasticity in symbiosis and holobiont metabolism, along with the presence of cryptic species, can complicate data interpretation. Therefore, quantifying seasonal plasticity in coral physiology and incorporating genetic identification are essential for accurately interpreting and drawing conclusions from trait-based and fitness-based analyses. To test the effect of seasonal and site variation on physiological plasticity we sampled three ecologically dominant genera, Acropora, Pocillopora, and Porites across three lagoon sites (n=15 tagged colonies genus-1 site-1) on the north shore of Moorea French Polynesia in January, March, September, and December of 2020. We identified coral host and intracellular symbiotic Symbiodiniaceae to the highest taxonomic resolution possible and quantified 13 physiological variables within the holobiont. Genetic analyses identified A. pulchra along with cryptic lineages in Pocillopora (P. meandrina, P. tuahiniensis) and Porites (P. evermanni, P. lobata/lutea). A. pulchra was dominated by Durusdinium trenchii and also contained Symbiodinium microadriaticum. Symbiont communities differed between cryptic congeners, with P. meandrina hosting Cladocopium latusorum and P. tuahiniensis hosting Cladocopium pacificum, whereas P. evermanni and P. lobata/lutea both hosted Cladocopium (C15), but each with unique C15 profiles. Weedy taxa such as Acropora and Pocillopora displayed a cycle of symbiont boom and bust in response to seasonally variable light and temperature, likely contributing to the high stress sensitivity of these taxa. In contrast, despite seasonal environmental variability, Porites displayed greater symbiont stability, with temperature--rather than light--serving as the stronger explanatory variable of seasonal variation in host physiology. Increased host biomass under cooler conditions, which provides energy reserves, may serve as an important stabilizing factor in massive Porites well-documented stress resilience. Collectively, our data provide essential evidence of the need for integrative analyses considering baseline physiological states across seasons along with host and symbiont genetics, particularly in light of the plethora of climate change related stress test assays taking place throughout the year across coral taxa with cryptic lineages.

physiology↗

bioRxiv2023

Multi-omic analysis of coral development elucidates the metabolic transitions from parental provisioning to endosymbiotic nutritional exchange

Climate change accelerates coral reef decline and jeopardizes recruitment essential for ecosystem recovery. Adult corals rely on a vital nutritional exchange with their symbiotic algae (Symbiodiniaceae), but the dynamics and sensitivity of this reliance from fertilization to recruitment are understudied. We investigated the physiological, metabolomic, and transcriptomic changes across 13 developmental stages of Montipora capitata, a coral in Hawai i that inherits symbionts from parent to egg. We found that embryonic development depends on maternally provisioned mRNAs and lipids, with a rapid shift to symbiont-derived nutrition in swimming larvae. Symbiont density and photosynthesis peak once swimming to fuel pelagic larval dispersal. In contrast, respiratory demand increases significantly during metamorphosis, settlement, and calcification, reflecting this energy-intensive morphological reorganization. Symbiont ontogenetic proliferation is driven by symbiont ammonium assimilation with little evidence of nitrogen metabolism in the coral host. As development progresses, the host enhances nitrogen sequestration, regulating symbiont populations, and ensuring the transfer of fixed carbon to support metamorphosis, with both metabolomic and transcriptomic indicators of increased carbohydrate availability. Although algal symbiont communities remained stable, bacterial communities shifted with ontogeny, associated with holobiont metabolic reorganization. Our study reveals extensive metabolic changes during development, increasingly reliant on symbiont nutrition. Metamorphosis and settlement emerge as the most critical periods of energetic vulnerability to projected climate scenarios that destabilize symbiosis. This highly detailed elucidation of symbiotic nutritional exchange relative to sensitive early life stages provides essential knowledge for understanding and forecasting nutritional symbiosis integration, and specifically, coral survival and recruitment in a future of climate change.

physiology↗

bioRxiv2022

The Genome of the Mustard Hill Coral, Porites astreoides

Coral reefs are threatened both locally and globally by anthropogenic impacts, which to date have contributed to substantial declines in coral cover worldwide. However, some corals are more resilient to these environmental changes and therefore have increased relative abundance on local scales and may represent prominent members shaping future reef communities. Here, we provide the first draft reference genome for one such reef-building coral, the mustard hill coral, Porites astreoides. This reference genome was generated from a sample collected in Bermuda, with DNA sequenced via Pacific Biosciences HiFi long-read technology to provide an initial draft reference genome assembly. Assembly of the PacBio reads with FALCON UnZip resulted in a 678 Mbp assembly with 3,051 contigs with an N50 of 412,256. The genome BUSCO completeness analysis resulted in 90.9% of the metazoan gene set. An ab initio transcriptome was also produced with 64,636 gene models with a transcriptome BUSCO completeness analysis of 77.5% when compared to the metazoan gene set. The function annotation was obtained through a hierarchical approach of SwissProt, TrEMBL, and NCBI nr database of which 86.6% of proteins were annotated. Through our ab initio gene prediction for structural annotation and generation of a functional annotation for the P. astreoides draft genome assembly, we provide valuable resources for improving biological knowledge, which can facilitate comparative genomic analyses for corals, and enhance our capacity to test for the molecular underpinnings of adaptation and acclimatization to support evidence-based restoration and human assisted evolution of corals. ClassificationsGenetics and Genomics; Animal Genetics; Marine Biology

genomics↗

bioRxiv2021

Temporal transcriptional response of Candida glabrata during macrophage infection reveals a multifaceted transcriptional regulator CgXbp1 important for macrophage response and drug resistance

Candida glabrata can thrive inside macrophages and tolerate high levels of azole antifungals. These innate abilities render infections by this human pathogen a clinical challenge. How C. glabrata reacts inside macrophages and what is the molecular basis of its drug tolerance are not well understood. Here, we mapped genome-wide RNA polymerase II (RNAPII) occupancy in C. glabrata to delineate its transcriptional responses during macrophage infection in high temporal resolution. RNAPII profiles revealed dynamic C. glabrata responses to macrophage with genes of specialized pathways activated chronologically at different times of infection. We identified an uncharacterized transcription factor (CgXbp1) important for the chronological macrophage response, survival in macrophages, and virulence. Genome-wide mapping of CgXbp1 direct targets further revealed its multi-faceted functions, regulating not only virulence-related genes but also genes associated with drug resistance. Finally, we showed that CgXbp1 indeed also affects azole resistance. Overall, this work presents a powerful approach for examining host-pathogen interaction and uncovers a novel transcription factor important for C. glabratas survival in macrophages and drug tolerance.

microbiology↗

bioRxiv2021

Heterogeneity in the transcriptional response of the human pathogen Aspergillus fumigatus to the antifungal agent caspofungin

Aspergillus fumigatus is the main causative agent of invasive pulmonary aspergillosis (IPA), a severe disease that affects immunosuppressed patients worldwide. The fungistatic drug caspofungin is the second line therapy against IPA but has increasingly been used against clinical strains that are resistant to azoles, the first line antifungal therapy. In high concentrations, caspofungin induces a tolerance phenotype with partial reestablishment of fungal growth called caspofungin paradoxical effect (CPE), resulting from a change in the composition of the cell wall. An increasing number of studies has shown that different isolates of A. fumigatus exhibit phenotypic heterogeneity, including heterogeneity in their CPE response. To gain insights into the underlying molecular mechanisms of CPE response heterogeneity, we analyzed the transcriptomes of two A. fumigatus reference strains, Af293 and CEA17, exposed to low and high caspofungin concentrations. We found that there is a core transcriptional response that involves genes related to cell wall remodeling processes, mitochondrial function, transmembrane transport, and amino acid and ergosterol metabolism, and a variable response related to secondary metabolite (SM) biosynthesis and iron homeostasis. Specifically, we show here that the overexpression of a SM pathway that works as an iron chelator extinguishes the CPE in both backgrounds, whereas iron depletion is detrimental for the CPE in Af293 but not in CEA17. We next investigated the function of the transcription factor CrzA, whose deletion was previously shown to result in heterogeneity in the CPE response of the Af293 and CEA17 strains. We found that CrzA constitutively binds to and modulates the expression of several genes related to processes involved in caspofungin tolerance, and that crzA deletion differentially impacts the SM production and growth of Af293 and CEA17. As opposed to the {Delta}crzACEA17 mutant, the {Delta}crzAAf293 mutant fails to activate cell wall remodeling genes upon caspofungin exposure, which most likely severely affects its macrostructure and extinguishes its CPE. This work describes how heterogeneity in the response to an antifungal agent between A. fumigatus strains stems from heterogeneity in the function of a transcription factor and its downstream target genes.

microbiology↗

bioRxiv2021

Screening of chemical libraries for new antifungal drugs against Aspergillus fumigatus reveals the potential mechanism of action of miltefosine

Aspergillus fumigatus is an important fungal pathogen and the main etiological agent of aspergillosis, a disease characterized by a noninvasive process that can evolve to a more severe clinical manifestation called invasive pulmonary aspergillosis (IPA) in immunocompromised patients. The antifungal arsenal to threat aspergillosis is very restricted. Azoles are the main therapeutic approach to control IPA, but the emergence of azole-resistant A. fumigatus isolates has significantly increased over the last decades. Therefore, new strategies are necessary to combat aspergillosis and drug repurposing has emerged as an efficient and alternative approach for identifying new antifungal drugs. Here, we used a screening approach to analyze A. fumigatus in vitro susceptibility to 1,127 compounds. A. fumigatus was more susceptible to 10 compounds, including miltefosine, a drug that displayed fungicidal activity against A. fumigatus. By screening an A. fumigatus transcription factor null library, we identified a single mutant, which has the rmiA (resistant to miltefosine) gene deleted, conferring a phenotype of susceptibility to miltefosine. The transcriptional profiling (RNA-seq) of the wild-type and the {Delta}rmiA strains and the Chromatin Immunoprecipitation coupled to next generation sequencing (ChIP-Seq) of a RmiA-tagged strain exposed to miltefosine revealed genes of the sphingolipids pathway that are directly or indirectly regulated by RmiA. Sphingolipids analysis demonstrated that the mutant has overall decreased levels of sphingolipids when growing in the presence of miltefosine. The identification of RmiA represents the first genetic element described and characterized which plays a direct role in miltefosine response in fungi. Author summaryThe filamentous fungus Aspergillus fumigatus causes a group of diseases named aspergillosis and their development occurs after the inhalation of conidia dispersed in the environment. Very few classes of antifungal drugs are available for aspergillosis treatment, e.g., azoles, but the emergence of global resistance to azoles in A. fumigatus clinical isolates has increased over the last decades. Repositioning or repurposing drugs already available on the market is an interesting and faster opportunity for the identification of novel antifungals agents. By using a repurposing strategy, we identified 10 different compounds that impact A. fumigatus survival. One of these compounds, miltefosine, demonstrated fungicidal activity against A. fumigatus. The mechanism of action of miltefosine is unknown and aiming to get more insights about it, we identified a transcription factor RmiA (Resistant to miltefosine) important for miltefosine resistance. Our results suggest that miltefosine plays antifungal activity against A. fumigatus interfering in the sphingolipids biosynthesis.

microbiology↗

bioRxiv2021

Chromatin profiling reveals genome stability heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus

Invasive Pulmonary aspergillosis is a life-threatening infection in immunosuppressed patients caused by the filamentous fungus Aspergillus fumigatus. Chromatin structure regulation is important for genome stability maintenance and has the potential to lead to genome rearrangements driving differences in virulence and pathogenesis of different A. fumigatus isolates. Here, we compared the chromatin activities of the most investigated clinical isolates Af293 and CEA17 and uncovered striking differences in the number, locations and expression of transposable elements. We found evidence for higher genome instability in Af293 as compared to CEA17 and identified a spontaneous Af293 variant that exhibits gross chromosomal alterations including the loss of a 320 kb long segment in chromosome VIII and the amplification of a biosynthetic gene cluster. As a consequence of these re-arrangements, the variant shows increased secondary metabolites production, growth and virulence. Our work emphasizes genome stability heterogeneity as an evolutionary driver of A. fumigatus fitness and virulence.

molecular biology↗

bioRxiv2018

Artesunate pErk up HepG2 cells to die through apoptosis in vitro

The dilemma between in vitro and in vivo drug screening results persisted to hinder preclinical anti-cancer drug development. In this study, drug screening was initially performed on monolayer cultures of HepG2 cells, whereas in vivo drug testing was performed on the subcutaneous xenograft mouse model of HepG2 cells in athymic nude mice. Results showed that Artesunate inhibited HepG2 cell growth in vitro, but was ineffective in vivo. Hence, we investigated the difference between in vitro and in vivo settings using this cell-drug combination as a model. Immuno-staining of hepatocellular carcinoma (HCC) biomarkers showed that -fetoprotein (AFP) was unaffected by Artesunate treatment in vitro or in vivo, suggesting that AFP was neither a biomarker nor response indicator. Alternatively, high albumin was detected in both monolayer and organoid cultures; contrariwise, the xenograft tumors prevailed low albumin, in consistency to human HCC with poor prognosis. Artesunate treatment reduced intracellular albumin expression in vitro; Artesunate did not alter tissue and serum albumin in xenograft mice, in coincidence with its irresponsiveness in vivo. However, Artesunate binding to albumin was undetectable. Instead, we observed a transient stimulation of Erk1/2 phosphorylation followed by DAPK1 dephosphorylation and apoptosis. Combined treatment of Artesunate with U0126 revoked Erk1/2-DAPK1 phosphorylation and exerted modest proliferative advantage at early time points, but eventually did not rescue HepG2 cells from death. U0126 induced multiploid formation independent of Artesunate, resulting in cell cycle arrest within 24 h post-treatment.\n\nSignificanceSystematic investigation of HCC biomarkers AFP and albumin among the in vitro models of monolayer and organoid cultures, and the in vivo models of subcutaneous and liver implantation xenograft mice was conducted.

cell biology↗