Biology subjects

Chen, W.-Y.

Publications and source records attributed to Chen, W.-Y..

8 recordsLinked to original sources

bioRxiv2025

Temporal Dynamics of High-Frequency Oscillations in Alzheimer's Disease: A Longitudinal Study in hAPP-J20 Mice

Alzheimers disease (AD) is characterized by progressive cognitive decline and increased seizure susceptibility; yet both the mechanistic and temporal links between AD and epileptogenesis remain poorly defined. In this study, we conducted a longitudinal analysis of epileptogenesis in relation to AD pathology using hAPP-J20 transgenic mice aged 9 to 27 weeks, encompassing the AD conversion phase. Wireless electroencephalography (EEG) was employed to monitor hippocampal high-frequency oscillations (HFOs), including ripples (80-200 Hz) and fast ripples (250-600 Hz), in conjunction with histological, behavioral, and neurophysiological assessments to characterize underlying neural circuit alterations. We identified three distinct epileptogenic stages in transgenic mice: (1) 9-15 weeks: emerging memory deficits, increased excitatory/inhibitory (E/I) neuron ratio, mossy fiber sprouting, and peak seizure-related mortality, alongside the initial emergence of pathological HFOs; (2) 15-21 weeks: a pronounced escalation of pathological HFO activity and persistent network hyperexcitability preceding detectable amyloid plaque deposition, indicating rapid epileptogenic progression; (3) 21-27 weeks: stabilization of HFO activity despite continued progression of amyloid accumulation, suggesting a plateau in epileptogenic remodeling amid advancing Alzheimers pathology. These findings indicate that neuronal hyperexcitability precedes amyloid plaque deposition and likely contributes to disease progression, highlighting a critical early window for therapeutic intervention in AD. Moreover, pathological HFOs hold promise as electrophysiological biomarkers of early circuit dysfunction and represent a promising target for modifying the course of AD. O_FIG O_LINKSMALLFIG WIDTH=146 HEIGHT=200 SRC="FIGDIR/small/693578v2_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@2e4a24org.highwire.dtl.DTLVardef@1059f53org.highwire.dtl.DTLVardef@1f1d57org.highwire.dtl.DTLVardef@bf3cde_HPS_FORMAT_FIGEXP M_FIG C_FIG Figure abstractThis study examines the temporal dynamics of epileptogenic activity and amyloid pathology in hAPP-J20 transgenic mice, a model of Alzheimers disease (AD). Top: Illustration of pre-plaque and post-plaque stages in hAPP-J20 mice, depicting neural network alterations, amyloid plaque deposition, and electrophysiological changes. The top panel shows the transition from a pre-plaque to a post-plaque state, where early hippocampal activity is stable and amyloid plaques are absent. As pathology advances, the network exhibits progressive hyperexcitability, characterized by increased pathological HFOs (ripple-IEDs, fast ripples), neuronal loss, NPY sprouting, and amyloid plaque formation. Bottom: The progression of key biomarkers and disease hallmarks, comparing hAPP-J20 transgenic (Tg) mice with non-transgenic (nTg) controls. The bottom panel quantifies biomarker progression over time, revealing that CaMK2+/PV (C/P) imbalance emerges first, followed by a peak in pathological HFOs incident rate (patho-ripple, fast ripple rate), and finally, amyloid beta plaque (A{beta} plaque). These findings establish a temporal relationship between early network hyperactivity and amyloid accumulation, underscoring the importance of targeting neural hyperexcitability as a therapeutic strategy to mitigate AD progression.

neuroscience↗

bioRxiv2023

Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum Nematomorpha)

In recent years, parasite conservation has become a globally significant issue. Because of this, there is a need for standardised methods for inferring population status and possible cryptic diversity. However, given the lack of molecular data for some groups, it is challenging to establish procedures for genetic diversity estimation. Therefore, universal tools, such as double digest restriction-site associated DNA sequencing (ddRADseq), could be useful when conducting conservation genetic studies on rarely studied parasites. Here, we generated a ddRADseq dataset that includes all three described Taiwanese horsehair worms (Phylum Nematomorpha), possibly one of the most understudied animal groups. Additionally, we produced data for a fragment of the cytochrome c oxidase subunit I (COXI) for said species. We used the COXI dataset in combination with previously published sequences of the same locus for inferring the effective population size (Ne) trends and possible population structure. We found that a larger and geographically broader sample size combined with more sequenced loci resulted in a better estimation of changes in Ne. We were able to detect demographic changes associated with Pleistocene events in all the species. Furthermore, the ddRADseq dataset for Chordodes formosanus did not reveal a genetic structure based on geography, implying a great dispersal ability, possibly due to its hosts. We showed that different molecular tools can be used to reveal genetic structure and demographic history at different historical times and geographical scales, which can help with conservation genetic studies in rarely studied parasites.

zoology↗

bioRxiv2022

Sensitive and specific miRNA in situ hybridization using partially methylated phosphotriester antisense DNA probes

Neutralized DNA (nDNA) is an emerging class of DNA oligonucleotides chemically synthesized with site-specific internucleoside methyl phosphotriester linkages, changing the negatively charged DNA phosphodiester backbone to a neutral methyl phosphotriester backbone. The reduction of inter-strand charge repulsion of nucleotide duplexes results in stronger binding between nDNA and other nucleic acids, and as such, nDNA has been used as a sensitive antisense probe for sequencing nucleotides. From a thermodynamic perspective due to steric effects, a hybrid duplex between DNA and partially methylated nDNA should possess higher specificity than a duplex between DNA with fully methylated nDNA, while retaining binding affinity. However, the application of nDNA for ex vivo RNA hybridization at low transcript abundance remains completely unexplored. Here, we determined that partially methylated nDNA (N4 nDNA; with 4 methylated nucleotides) probes inhibited reverse transcription of oncogenic miRNA miR-21 more efficiently than canonical DNA probes or highly methylated nDNA probes (all probes share the same sequence) and with an efficiency rivaling LNA probes. Subsequently, we performed in situ hybridization analysis using a miR-21-expressing colorectal cancer cell line (HCT116). HCT116 stained with N4 nDNA probes revealed a greater detection intensity and specificity than HCT116 stained with canonical DNA probes. Consistently, enzyme-linked immunosorbent assays revealed that miRNA hybridization efficiency of N4 nDNA probes was greater than that of canonical DNA probes at cellular transcript levels. Given that N4 nDNA probe is immune-negative and DNase I-resistant, partially methylated nDNA could be further developed to have significant applications in biotechnology and medicine.

bioengineering↗

bioRxiv2022

Broadly neutralizing antibodies against Omicron variants of SARS-CoV-2 derived from mRNA-lipid nanoparticle-immunized mice

The COVID-19 pandemic continues to threaten human health worldwide, as new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged. Currently, the predominant circulating strains around the world are Omicron variants, which can evade many therapeutic antibodies. Thus, the development of new broadly neutralizing antibodies remains an urgent need. In this work, we address this need by using the mRNA-lipid nanoparticle immunization method to generate a set of Omicron-targeting monoclonal antibodies. Five of our novel K-RBD-mAbs show strong binding and neutralizing activities toward all SARS-CoV-2 variants of concern (Alpha, Beta, Gamma, Delta and Omicron). Notably, the epitopes of these five K-RBD-mAbs are overlapping and localized around K417 and F486 of the spike protein receptor binding domain (RBD). Chimeric derivatives of the five antibodies (K-RBD-chAbs) neutralize Omicron sublineages BA.1 and BA.2 with low IC50 values that range from 5.7 to 12.9 ng/mL. Additionally, we performed antibody humanization on a broadly neutralizing chimeric antibody to create K-RBD-hAb-62, which still retains excellent neutralizing activity against Omicron. Our results collectively suggest that these five therapeutic antibodies may effectively combat current and emerging SARS-CoV-2 variants, including Omicron BA.1 and BA.2. Therefore, the antibodies can potentially be used as universal neutralizing antibodies against SARS-CoV-2.

immunology↗

bioRxiv2022

Mettl3-mediated m6A modification of Fgf16 restricts cardiomyocyte proliferation during heart regeneration

Cardiovascular disease is the leading cause of death worldwide due to the inability of adult heart to regenerate after injury. N6-methyladenosine (m6A) methylation catalyzed by the enzyme methyltransferase-like 3 (Mettl3) plays important roles in various physiological and pathological bioprocesses. However, the role of m6A in heart regeneration remains largely unclear. To study m6A function in heart regeneration, we modulated Mettl3 expression in vitro and in vivo. Knockdown of Mettl3 significantly increased the proliferation of cardiomyocytes and accelerated heart regeneration following heart injury in neonatal and adult mice. However, Mettl3 overexpression decreased cardiomyocyte proliferation and suppressed heart regeneration in postnatal mice. Conjoint analysis of methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA-seq identified Fgf16 as a downstream target of Mettl3-mediated m6A modification during postnatal heart regeneration. RIP-qPCR and luciferase reporter assays revealed that Mettl3 negatively regulates Fgf16 mRNA expression in an m6A-Ythdf2-dependent manner. The silencing of Fgf16 suppressed the proliferation of cardiomyocytes. However, the overexpression of {Delta}Fgf16, in which the m6A consensus sequence was mutated, significantly increased cardiomyocyte proliferation and accelerated heart regeneration in postnatal mice compared with wild-type Fgf16. Our data demonstrate that Mettl3 post-transcriptionally reduces Fgf16 mRNA levels through an m6A-Ythdf2-dependen pathway, thereby controlling cardiomyocyte proliferation and heart regeneration.

cell biology↗

bioRxiv2022

Omicron-specific mRNA vaccine induced potent neutralizing antibody against Omicron but not other SARS-CoV-2 variants

The emerging SARS-CoV-2 variants of concern (VOC) harbor mutations associated with increasing transmission and immune escape, hence undermine the effectiveness of current COVID-19 vaccines. In late November of 2021, the Omicron (B.1.1.529) variant was identified in South Africa and rapidly spread across the globe. It was shown to exhibit significant resistance to neutralization by serum not only from convalescent patients, but also from individuals receiving currently used COVID-19 vaccines with multiple booster shots. Therefore, there is an urgent need to develop next generation vaccines against VOCs like Omicron. In this study, we develop a panel of mRNA-LNP-based vaccines using the receptor binding domain (RBD) of Omicron and Delta variants, which are dominant in the current wave of COVID-19. In addition to the Omicron- and Delta-specific vaccines, the panel also includes a "Hybrid" vaccine that uses the RBD containing all 16 point-mutations shown in Omicron and Delta RBD, as well as a bivalent vaccine composed of both Omicron and Delta RBD-LNP in half dose. Interestingly, both Omicron-specific and Hybrid RBD-LNP elicited extremely high titer of neutralizing antibody against Omicron itself, but few to none neutralizing antibody against other SARS-CoV-2 variants. The bivalent RBD-LNP, on the other hand, generated antibody with broadly neutralizing activity against the wild-type virus and all variants. Surprisingly, similar cross-protection was also shown by the Delta-specific RBD-LNP. Taken together, our data demonstrated that Omicron-specific mRNA vaccine can induce potent neutralizing antibody response against Omicron, but the inclusion of epitopes from other variants may be required for eliciting cross-protection. This study would lay a foundation for rational development of the next generation vaccines against SARS-CoV-2 VOCs.

microbiology↗

bioRxiv2021

Impacts on the structure-function relationship of SARS-CoV-2 spike by B.1.1.7 mutations

The UK variant of the severe acute respiratory syndrome coronavirus (SARS-CoV-2), known as B.1.1.7, harbors several point mutations and deletions on the spike (s) protein, which potentially alter its structural epitopes to evade host immunity while enhancing host receptor binding. Here we report the cryo-EM structures of the S protein of B.1.1.7 in its apo form and in the receptor ACE2-bound form. One or two of the three receptor binding domains (RBDs) were in the open conformation but no fully closed form was observed. In the ACE-bound form, all three RBDs were engaged in receptor binding. The B.1.1.7-specific A570D mutation introduced a salt bridge switch that could modulate the opening and closing of the RBD. Furthermore, the N501Y mutation in the RBD introduced a favorable {pi}-{pi} interaction manifested in enhanced ACE2 binding affinity. The N501Y mutation abolished the neutralization activity of one of the three potent neutralizing antibodies (nAbs). Cryo-EM showed that the cocktail of other two nAbs simultaneously bound to all three RBDs. Furthermore, the nAb cocktail synergistically neutralized different SARS-CoV-2 pseudovirus strains, including the B.1.1.7.

biochemistry↗

bioRxiv2020

DNMT3b Dysfunction Promotes DNA cleavages at Centromeric R-loops to Increase Centromere Instability

This study investigates how DNA methyltransferase 3b (DNMT3b) dysfunction causes genome instability. We showed that in DNMT3b deficient cells, R-loops contribute to prominent {gamma}H2AX signal, which was mapped to repetitive satellite sequences including centromere regions. By ChIP and DRIP analyses, our data revealed that centromeric R-loops in DNMT3b deficient cells are removed by XPG/XPF, thus generating DNA breaks in centromeres to increase mitotic aberration. In immunodeficiency-centromeric instability-facial anomalies (ICF) patient cells carrying the loss-of-function mutation at DNMT3b, knockdown of XPG/XPF in ICF cells also reduces DNA breaks in centromere while bringing up centromeric R-loop to the level similar to that in wild-type cells. These results suggest that DNMT3b has a critical function in preventing XPG/XPF-mediated cleavages at centromeric R-loop sites. Finally, we showed the involvement of non-homologous end-joining repair at centromeric sites in ICF cells. Thus, DNA cleavages at centromeric R-loops with error-prone repair undermine centromere stability in ICF cells.

molecular biology↗