Biology subjects

Wang, W.-H.

Publications and source records attributed to Wang, W.-H..

9 recordsLinked to original sources

bioRxiv2026

Temperature-Dependent Rotamer Population Shifts Govern Tryptophan Fluorescence in Proteins

Intrinsic tryptophan fluorescence is widely used as a sensitive reporter of protein conformational dynamics, yet the molecular origin of its temperature-dependent modulation remains unclear. Here we investigate the conformational dynamics of Trp134 in bovine serum albumin (BSA) using molecular dynamics (MD) simulations, free-energy calculations based on umbrella sampling and WHAM, quantum mechanical (QM) calculations, and QM/MM approaches. MD simulations show that the global structure of BSA remains stable while temperature induces a gradual population shift from the Ia+ to the Ia- rotamer. The corresponding free-energy landscapes reveal that this shift arises from subtle changes in basin stability and transition barriers along the rotameric coordinate. In contrast, standalone QM calculations on isolated tryptophan predict different energetic trends, highlighting the sensitivity of rotamer stability to electronic-structure treatments and environmental effects. QM/MM calculations partially reconcile these differences by incorporating the protein environment. Together, these results suggest that temperature reshapes the rotamer free-energy landscape of Trp134, leading to population shifts that modulate intrinsic tryptophan fluorescence in proteins.

biochemistry↗

bioRxiv2025

Fusobacterium nucleatum produces previously unappreciated AHR-activating metabolites and promotes CRC cell proliferation via the AHR-TERT axis

Fusobacterium nucleatum (Fn) is prevalently enriched in colorectal cancer (CRC), promoting CRC progression. However, Fn-derived small molecules and their host target pathways in CRC remain largely underexplored. Here, we identify that Fn produces previously unrecognized three indole-containing metabolites, fusotrisindoline (FTIN), streptindole (STIN), and trisindoline (TIN). Using AHR reporter, CYP1A1 mRNA induction, CYP1A enzyme assay, photoaffinity AHR-ligand competition, and in silico docking, we establish that these metabolites are bona fide agonists of the aryl hydrocarbon receptor (AHR), with FTIN being the most potent AHR ligand (EC50 [~]41 nM in HepG2 cells). Genetic and pharmacological perturbations demonstrate that FTIN-activated AHR promotes proliferation, migration, and invasion in EGFR blockade-responsive CRC cell lines, such as SNU-C4, but not in EGFR blockade-resistant cell lines, such as HCT116. We show that FTIN-activated AHR signaling is critical for Fn-mediated promotion of CRC cell growth. A {Delta}tnaA mutant defective in indole production lacked FTIN/STIN/TIN production and was unable to activate AHR or enhance CRC cell growth in vitro and SNU-C4 xenograft growth in vivo. RNA-seq and follow-up functional validation identified TERT as a key downstream effector of FTIN-activated AHR signaling. FTIN upregulated TERT transcription and telomerase activity, and TERT knockdown abrogated FTIN-promoted CRC cell proliferation. FTIN production was conserved across Fn subspecies, as well as other Fusobacterium species, and detected in additional CRC- associated genera. In 30 patient pairs of CRC-matched normal colon tissues, FTIN was quantifiable in most CRC tissues and significantly enriched relative to matched normal colon tissues, whereas STIN/TIN were undetectable. Our findings reveal a metabolite-centered FTIN-AHR-TERT axis by which intratumoral bacteria, such as Fn, accelerate CRC growth and uncover FTIN as a potential biomarker in CRC.

microbiology↗

bioRxiv2025

Uncovering the Genetic Basis of Heterodichogamy in Pterocarya and Cyclocarya Using a Low-Input Pan-Genomic Approach

The heterodichogamous mating system, characterized by two distinct mating types (protogyny and protandry), is rare among flowering plants, but it is present in nearly all species in Juglandaceae (the walnut family). Recent studies have identified distinct structural variations underlying heterodichogamy in Juglans and Carya. To verify the independent origins of this trait in Juglandaceae and investigate whether structural variations also drive heterodichogamy in Juglans closely related genera, we explored its genetic basis in Pterocarya and Cyclocarya. Using a pan-genome graph approach, we identified a structural variation region associated with mating types across the Pterocarya genus. This region includes 30 kb tandem repeats in the dominant allele and an insertion in the recessive allele, with shared polymorphisms spanning 78 kb from the 3'UTR of S12e, covering a FAF-like gene, to a Gypsy transposable element. Downstream analyses suggest that the specific expression of FAF-like gene and small RNAs uniquely expressed from the tandem repeats of dominant allele regulate heterodichogamy. Further investigation in Cyclocarya identified nine candidate loci associated with heterodichogamy, which are non-homologous regions with those found in Pterocarya, Juglans, and Carya. These findings provide novel evidence for the multiple independent originations of convergent genetic basis in regulating heterodichogamy in Juglandaceae and highlight the utility of pan-genome approaches in deciphering structural variation-associated traits.

evolutionary biology↗

bioRxiv2025

Distinct cell types along thick ascending limb express pathways for monovalent and divalent cation transport

Kidney thick ascending limb cells reabsorb sodium, potassium, calcium, and magnesium and contribute to urinary concentration. These cells are typically viewed as of a single type that recycles potassium across the apical membrane and generates a lumen-positive transepithelial voltage driving calcium and magnesium reabsorption, although variability in potassium channel expression has been reported. Additionally, recent transcriptomic analyses suggest that different cell types exist along this segment, but classifications have varied and have not led to a new consensus model. We used immunolocalization, electrophysiology and enriched single nucleus RNA-Seq to identify thick ascending limb cell types in rat, mouse and human. We identified three major TAL cell types defined by expression of potassium channels and claudins. One has apical potassium channels, low basolateral potassium conductance, and is bordered by a sodium-permeable claudin. A second lacks apical potassium channels, has high basolateral potassium conductance and is bordered by calcium- and magnesium-permeable claudins. A third type also lacks apical potassium channels and has a high basolateral potassium conductance, but these cells are ringed by sodium-permeable claudins. The recognition of diverse cell types resolves longstanding questions about how solute transport can be modulated selectively and how disruption of these cells leads to human disease.

physiology↗

bioRxiv2024

Role of Kir4.1/Kir5.1 in mediating Angiotensin-II (Ang-II)-induced stimulation of thiazide-sensitive Na-Cl cotransporter.

BackgroundAngiotensin-II (Ang-II) perfusion stimulates Kir4.1/Kir5.1 in the distal-convoluted-tubule (DCT) and thiazide-sensitive Na-Cl-cotransporter (NCC). However, the role of Kir4.1/Kir5.1 in mediating the effect of Ang-II on NCC is not understood. MethodsWe used immunoblotting and patch-clamp-experiments to examine whether Ang-II-induced stimulation of NCC is achieved by activation of Kir4.1/Kir5.1 of the DCT using kidney-renal-tubule-specific AT1aR-knockout (Ks-AT1aR-KO), Ks-Kir4.1-knockout and the corresponding wild-type mice. ResultsAng-II perfusion for 1, 3 and 7 days progressively increased phosphor-NCC (pNCC) and total-NCC (tNCC) expression and the effect of Ang-II-perfusion on pNCC and tNCC was abolished in Ks-AT1aR-KO. Ang-II perfusion for 1-day robustly stimulates Kir4.1/Kir5.1 in the late DCT (DCT2) and to a lesser degree in the early DCT (DCT1), an effect was absent in Ks-AT1aR-KO mice. However, Ang-II perfusion for 7-days did not further stimulate Kir4.1/Kir5.1 in the DCT2 and only modestly increased Kir4.1/Kir5.1-mediated K+ currents in DCT1. Deletion of Kir4.1 not only significantly decreased the expression of pNCC and tNCC but also abolished the effect of 1-day Ang-II perfusion on the expression of phospho-with-no-lysine-kinase-4 (pWNK4), phosphor-ste-20-proline-alanine-rich-kinase (pSPAK), pNCC and tNCC. However, 7-days Ang-II perfusion was still able to significantly stimulate the expression of pSPAK, pWNK4, pNCC and tNCC, and increased thiazide-induced natriuresis in kidney-tubule-specific Kir4.1 knockout (Ks-Kir4.1 KO) mice without obvious changes in K+ channel activity in the DCT. ConclusionsShort-term Ang-II induced stimulation of pWNK4, pSPAK and pNCC depends on Kir4.1/Kir5.1 activity. However, long-term Ang-II is able to directly stimulate pWNK4, pSPAK and pNCC by a Kir4.1/Kir5.1 independent mechanism.

physiology↗

bioRxiv2023

ERG1a K+ Channel Increases Intracellular Calcium Concentration through Modulation of Calsequestrin 1 in C2C12 Myotubes

The ERG1A K+ channel modulates the protein degradation that contributes to skeletal muscle atrophy by increasing intracellular calcium concentration ([Ca2+]i) and enhancing calpain activity, but the mechanism by which the channel regulates the [Ca2+]i is not known. Here, we have investigated the effect of human ERG1A (HERG) on [Ca2+]i in C2C12 myotubes, using Fura-2 calcium assays, immunoblot, RT-qPCR, and electrophysiology. We hypothesized that HERG would modulate L-type calcium channel activity, specifically the Cav1.1 channel known to carry signal from the sarcoplasmic membrane of skeletal muscle to the sarcomeres of the myofibrils. However, we find that HERG has no effect on the amplitude of L-type channel current nor does it affect the mRNA levels nor protein abundance of the Cav1.1 channel. Instead we find that, although the rise in [Ca2+]i (induced by depolarization) is greater in myotubes over-expressing HERG relative to controls, the difference between the KCl-stimulated Ca2+ increase in control and HERG over-expressing cells cannot be accounted for by L-type channel mediated Ca2+ influx, which suggests that HERG could modulate excitation coupled calcium entry (ECCE). Indeed, the HERG-enhanced increase in [Ca2+]i induced by depolarization is blocked by 2-APB, an inhibitor of ECCE (and SOCE). Further, we show data suggesting that HERG also modulates the activity of ryanodine receptors, a component of ECCE, as well as store operated calcium entry (SOCE). Therefore, we investigated the effect of HERG on calsequestrin1, a calcium buffering/binding protein known to modulate ryanodine receptor 1 and store operated Ca2+ entry activities. Indeed, we find that calsequestrin1 mRNA levels are decreased 0.83-fold (p<0.05) and the total protein abundance is lowered 77% (p<0.05) in myotubes over-expressing HERG relative to controls. In summary, the data show that ERG1A overexpression modulates [Ca2+]i in skeletal muscle cells by lowering the abundance of the calcium buffering/binding protein calsequestrin1.

physiology↗

bioRxiv2022

Prostaglandin E2 prevents radiotherapy-induced alopecia by attenuating transit amplifying cell apoptosis through promoting G1 arrest

Growing hair follicles (HFs) harbor actively dividing transit amplifying cells (TACs), rendering them highly sensitive to radiotherapy (RT). Clinically, there is still a lack of effective treatment for radiotherapy-induced alopecia (RIA). We aimed to dissect the effect and mechanism of local prostaglandin E2 (PGE2) pretreatment in RIA prevention. We found that PGE2 pretreatment reduced RIA by preventing premature termination of anagen through enhancing HF self-repair. Mechanistically, PGE2 did not activate HF stem cells, but preserved more TACs for regenerative attempts. Pretreatment of PGE2 lessened radiosensitivity of TACs by transiently arresting them in the G1 phase, thereby reducing TAC apoptosis and mitigating HF dystrophy. The preservation of more TACs accelerated HF self-repair and bypassed RT-induced premature catagen entry. Promoting G1 arrest by systemic administration of palbociclib isethionate (PD0332991), a CDK4/6 inhibitor, offered a similar protective effect against RT. Therefore, PGE2 protects HF TACs from RT by transiently inducing G1 arrest, and the regeneration of HF structures lost from RT is accelerated to resume anagen growth, thus bypassing the long downtime of hair loss. PGE2 has the potential to be repurposed as a preventive treatment for RIA.

cell biology↗

bioRxiv2020

RNA helicase DDX5 enables STAT1 mRNA translation and interferon signaling in hepatitis B virus replicating hepatocytes

ObjectiveRNA helicase DDX5 is downregulated during hepatitis B virus (HBV) replication, and poor prognosis HBV-related hepatocellular carcinoma (HCC). The objective of this study is to understand the significance of DDX5 downregulation during HBV infection and poor prognosis HCC, as it pertains to therapy of chronically HBV-infected patients with HCC. IFN- therapy is effective only for a subgroup of HBV-infected patients, for reasons not understood. Herein, we investigated a novel mechanism of STAT1 translational control, involving DDX5-mediated resolution of a G-quadruplex structure, located at the 5UTR of STAT1 mRNA, enabling STAT1 translation. Design and ResultsMolecular, pharmacologic, and biophysical assays were used together with cellular model of HBV replication, HCC cell lines, and HBV-related liver tumors. We observed, the protein level of DDX5 correlated with that of transcription factor STAT1. We show, DDX5 regulates STAT1 mRNA translation by resolving a G-quadruplex (rG4) RNA structure, proximal to the 5 end of STAT1 5UTR. We employed luciferase reporter assays comparing wild type (WT) vs. mutant (MT) rG4 sequence, rG4-stabilizing compounds, CRISPR/Cas9 editing of the rG4 sequence, and circular dichroism determination of rG4 structure. Ribonucleoprotein assays identified direct DDX5 binding to WT but not MT rG4. Importantly, liver cancer cell lines expressing low DDX5 exhibited reduced interferon response, while immunohistochemistry of HBV-related HCCs exhibiting absence of DDX5, also lacked STAT1. ConclusionDDX5 resolves a G-quadruplex structure in 5UTR of STAT1 mRNA, enabling STAT1 translation. DDX5 is a key regulator of the dynamic range of interferon response during innate immunity and adjuvant IFN- therapy.

cancer biology↗

bioRxiv2019

The Telomerase Reverse Transcriptase (TERT) and p53 Regulate Mammalian PNS and CNS Axon Regeneration downstream of c-Myc

Although several genes have been identified to promote axon regeneration in the central nervous system, our understanding of the molecular mechanisms by which mammalian axon regeneration is regulated is still limited and fragmented. Here by using sensory axon and optic nerve regeneration as model systems, we revealed an unexpected role of telomerase reverse transcriptase (TERT) in regulation of axon regeneration. We also provided strong evidence that TERT and p53 acted downstream of c-Myc to control sensory axon regeneration. More importantly, overexpression of p53 in sensory neurons and retinal ganglion cells (RGCs) was sufficient to promote sensory axon and optic never regeneration, respectively. The study revealed a novel c-Myc-TERT-p53 signaling pathway, expanding horizons for novel approaches promoting CNS axon regeneration.

neuroscience↗