Biology subjects

Wong, Y. T.

Publications and source records attributed to Wong, Y. T..

7 recordsLinked to original sources

bioRxiv2024

Direction-aware functional class scoring enrichment analysis of Infinium DNA methylation data

Infinium Methylation BeadChip arrays remain one of the most popular platforms for epigenome-wide association studies, but tools for downstream pathway analysis have their limitations. Functional class scoring (FCS) is a group of pathway enrichment techniques that involve the ranking of genes and evaluation of their collective regulation in biological systems, but the implementations described for Infinium methylation array data do not retain direction information, which is important for mechanistic understanding of genomic regulation. Here, we evaluate several candidate FCS methods that retain directional information. According to simulation results, the best-performing method involves the mean aggregation of probe limma t-statistics by gene followed by a rank-ANOVA enrichment test using the mitch package. This method, which we call "LAM", outperformed an existing over-representation analysis method in simulations, and showed higher sensitivity and robustness in an analysis of real lung tumour-normal paired datasets. Using matched RNA-seq data we examine the relationship of methylation differences at promoters and gene bodies with RNA expression at the level of pathways in lung cancer. To demonstrate the utility of our approach, we apply it to three other contexts where public data were available. Firstly, we examine differential pathway methylation associated with chronological age. Secondly, we investigate pathway methylation differences in infants conceived with in vitro fertilisation. Lastly, we analyse differential pathway methylation in 19 disease states, identifying hundreds of novel associations. These results show LAM is a powerful method for the detection of differential pathway methylation as compared to existing methods. A reproducible vignette is provided to illustrate how to implement this method.

genomics↗

bioRxiv2023

Naturalistic Movies and Encoding Analysis Redefine Areal Borders in Primate Visual Cortex

Accurate definition of the borders of cortical visual areas is essential for the study of neuronal processes leading to perception. However, data used for definition of areal boundaries has suffered from issues related to resolution, uniform coverage, or suitability for objective analysis, leading to ambiguity. Here, we present a novel approach that combines widefield optical imaging, presentation of naturalistic movies, and encoding model analysis, to objectively define borders in the primate extrastriate cortex. We applied this method to test conflicting hypotheses about the third-tier visual cortex, where areal boundaries have remained controversial. The results support a hypothesis whereby an area contains representations of both the upper and lower contralateral quadrants (DM) is located immediate anterior to V2, and unveil pronounced tuning preferences in the third-tier areas. High-density electrophysiological recordings with a Neuropixels probe confirm these findings. Our encoding-model approach offers a powerful, objective way to disambiguate areal boundaries.

neuroscience↗

bioRxiv2022

XPD protects CTCF-Cohesin binding sites from somatic mutagenesis

Xeroderma pigmentosum group D (XPD) is a DNA helicase with critical functions in transcription initiation and nucleotide excision repair. Missense mutations in XPD are putative drivers in around 10% of bladder cancers (BLCA), but the associated mutational process remains poorly understood. Here, we examine the somatic mutational landscape of XPD wild-type (n=343) and mutant (n=39) BLCA whole genomes. The genome-wide distribution of somatic mutations is significantly altered in XPD mutants, affecting both APOBEC and non-APOBEC associated mutational processes. Specifically, XPD mutants are enriched in T[C>T]N mutations (SBS2) with altered correlation with replication timing. At a locoregional genomic level, mutant XPD BLCA had striking T>G mutation hotspots at CTCF-cohesin binding sites (CBS) with evidence linking XPD to genomic uracil repair. Leveraging differential distribution of somatic mutations, we developed a machine-learning model for predicting pathogenic XPD mutations, which we validated in an independent TCGA cohort with 100% accuracy. Our model enabled the discovery of missed XPD mutation calls and uncovered pathogenic non-hotspot XPD mutations in bladder cancer. Our study reveals how XPD mutations redistribute somatic mutations in cancer genomes and provides a genome sequencing approach to differentiate driver and passenger XPD mutations.

molecular biology↗

bioRxiv2020

Long-range neural coherence encodes stimulus information in primate visual cortex

In the primary visual cortex, neurons with similar receptive field properties are bound together through widespread networks of horizontal connections that span orientation columns. How connectivity across the cortical surface relates to stimulus information is not fully understood. We recorded spiking activity and the local field potential (LFP) from the primary visual cortex of marmoset monkeys and examined how connectivity between distant orientation columns affect the encoding of visual orientation. Regardless of their spatial separation, recording sites with similar orientation preferences have higher coherence between spiking activity and the local field potential than sites with different preferred orientation. Using information theoretic methods, we measured the amount of stimulus information that is shared between pairs of sites. More stimulus information can be decoded from pairs with the same preferred stimulus orientation than the pairs with a different preferred orientation, and the amount of information is significantly correlated with the magnitude of beta-band spike-LFP coherence. These effects remained after controlling for firing rate differences. Our results thus show that spike-LFP synchronization in the beta-band is associated with the encoding of stimulus information within the primary visual cortex of marmoset monkeys. Significance StatementA fundamental step in processing images in the visual cortex is coordinating the neural activity across distributed populations of neurons. Here, we demonstrate that populations of neurons in the primary visual cortex of marmoset monkeys with the same stimulus orientation preference temporally coordinate their activity patterns when presented with a visual stimulus. We find maximum synchronization in the beta range depends on the similarity of orientation preference at each pair of the neural population.

neuroscience↗

bioRxiv2020

Mechanisms of Feature Selectivity and Invariance in Primary Visual Cortex

Visual object identification requires both selectivity for specific visual features that are important to the objects identity and invariance to feature manipulations. For example, a hand can be shifted in position, rotated, or contracted but still be recognised as a hand. How are the competing requirements of selectivity and invariance built into the early stages of visual processing? Typically, cells in the primary visual cortex are classified as either simple or complex. They both show selectivity for edge-orientation but complex cells develop invariance to edge position within the receptive field (spatial phase). Using a data-driven model that extracts the spatial structures and nonlinearities associated with neuronal computation, we show that the balance between selectivity and invariance in complex cells is more diverse than thought. Phase invariance is frequently partial, thus retaining sensitivity to brightness polarity, while invariance to orientation and spatial frequency are more extensive than expected. The invariance arises due to two independent factors: (1) the structure and number of filters and (2) the form of nonlinearities that act upon the filter outputs. Both vary more than previously considered, so primary visual cortex forms an elaborate set of generic feature sensitivities, providing the foundation for more sophisticated object processing.

neuroscience↗

bioRxiv2018

Coherent neuronal dynamics driven by optogenetic stimulation in the primate brain

Coherent neuronal dynamics play an important role in complex cognitive functions. Optogenetic stimulation promises to provide new ways to test the functional significance of coherent neural activity. However, the mechanisms by which optogenetic stimulation drives coherent dynamics remain unclear, especially in the non-human primate brain. Here, we perform computational modeling and experiments to study the mechanisms of optogenetic-stimulation-driven coherent neuronal dynamics in non-human primates. Neural responses arise from stimulation-evoked temporal windows of excitatory and inhibitory activity. The temporal properties of the E-I windows generate coherent neuronal dynamics at varied frequencies and depend on optogenetic stimulation parameters. Experimental results agree with parameter dependent predictions from the computational models. These results demonstrate that responses to optogenetic stimulation are governed by local circuit properties that alter the timing of E-I activity. Transient imbalances in excitatory and inhibitory activity may provide a general mechanism for generating coherent neuronal dynamics.

neuroscience↗

bioRxiv2017

Cholecystokinin release triggered by presynaptic NMDA receptors produces LTP and sound-sound associative memory formation

Memory is stored in neural networks via changes in synaptic strength mediated in part by NMDA-dependent long-term potentiation (LTP). There is evidence that entorhinal cortex enables neocortical neuroplasticity through cholecystokinin (CCK)-containing neocortical projections. Here we show that a CCKB antagonist blocks high-frequency stimulation (HFS)-induced LTP in the auditory cortex, whereas local infusion of CCK induces LTP. CCK-/- mice lacked neocortical LTP and showed deficits in a cue-cue associative learning paradigm; administration of CCK rescued associative learning. HFS of CCK-containing entorhino-neocortical projection neurons in anesthetized mice enabled cue-cue associative learning. Furthermore, when one cue was pre-conditioned to footshock, the mouse showed a freezing response to the other cue, indicating that the mice had formed an association. HFS-induced neocortical LTP was completely blocked by either NMDA antagonist or CCK-BR antagonist, while application of either NMDA or CCK induced LTP after low-frequency stimulation (LFS). Moreover, in the presence of CCK LTP was still induced, even after blockade of NMDA receptors. Local application of NMDA induced CCK release in the neocortex. To identify how NMDA receptor switches LTP, a stimulation protocol of 25 pulse-pairs was adopted to replace HFS; NMDA-dependent LTP was induced with the inter-pulse intervals between 10 and 100 ms, but not with those of 5 and 200 ms. LTP-mediated plasticity was linked to localization of the NMDA receptor subunit NR2a on cortical CCK terminals originating in the entorhinal cortex. These novel findings suggest that presynaptic NMDA receptors on CCK terminals control the release of CCK, which enables neocortical LTP and formation of cue-cue associative memory.\n\nOne Sentence SummaryPresynaptic NMDA receptors switches the release of CCK from entorhinal neurons, which enables neocortical LTP and formation of sound-sound associative memory.

neuroscience↗