Biology subjects

Lau, E.

Publications and source records attributed to Lau, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Subcellular spatiotemporal proteomics delineates distinct phases of ER stress proteostatic response

Endoplasmic reticulum (ER) stress is associated with many human diseases, but current understanding of how ER stress responses reshape the stressed proteome over time is still emerging. Specifically, how organellar protein quality control and clearance pathways coordinate to maintain proteostasis in early and prolonged ER stress is unclear. Here we describe a spatiotemporal proteomic strategy termed simultaneous proteome localization and turnover analysis with time resolution (SPLAT-TR) to interrogate the synthesis, degradation, and localization changes of over 4,000 proteins in early (1-4 hours) and prolonged (16-24 hours) ER stress. As ER stress progresses, each time point is distinguished by distinct protein translocation and clearance regulations, coupled to differential organellar proteostasis and usage of protein degradation pathways. Mitochondria show a bimodal response, with a shift from early activation of respiratory protein towards protein quality control pathways in prolonged stress, coinciding with energetics decline. In the Golgi, the increased clearance of collagen proteins is paradoxically coupled to an increased synthesis of secretory pathway components, suggesting removal by secretion. In the ER, the proteome remodels under prolonged stress via increased synthesis of UFMylation and ER-phagy-related proteins coupled to the selective degradation of ER membrane and microdomain proteins. Inhibition of UFMylation alters ER-phagy receptor usage and synergistically induces stress-induced cell death. These results present a systematic delineation of cell compartment proteostasis under unfolded protein response and highlight the utility of SPLAT-TR to investigate time-dependent cellular events.

biochemistry↗

bioRxiv2026

Tracking cellular biomolecular condensate dynamics under proteostatic stress with middle-down phosphoproteomics

Coordination of biological function requires the partition of cellular components including into biomolecular condensates, but an overall landscape of how protein compartmentalize into higher-order assemblies under stress is still emerging. We apply proteome-wide solubility profiling to compare the compositions of NP-40-insoluble proteins and their phosphorylation status, using a new mass spectrometry-based hybrid bottom-up and chemical middle-down proteomics approach to analyze the solubility behavior of 8,740 proteins and 31,647 phosphopeptides under normal and ER stress conditions. Cell stress induces a pervasive differential partition of proteins in and out of detergent-insoluble cellular compartments. This differential partition is partially orthogonal to stress-induced abundance changes and comprises both phosphorylation-dependent and phosphorylation-independent mechanisms. Whereas phosphorylation-independent partition changes involve largely secretory pathway proteins and implicate higher-order assemblies of chaperones and clients, phosphorylation-based partitions suggest a dynamic rearrangement of biomolecular condensate compositions across cytoplasmic and nuclear ribonucleoprotein assemblies. The accumulation of serine/arginine rich (SR) proteins and other annotated nuclear speckle members in the condensate-rich proteome fractions emerges as a central feature of stress-induced remodeling. Our results establish global solubility dynamics as an integral component of proteome stress response and implicates broad involvements of splice factor spatial reorganization as a prominent facet of ER stress response.

biochemistry↗

bioRxiv2026

Proteogenomic analysis of the differential stability of cardiac protein isoforms

Alternative splicing is an important regulatory layer in gene expression, but knowledge on the isoform protein molecules continue to lag their canonical counterparts. An open question is whether alternative protein isoforms feature different half-life than the canonical counterpart, which could indicate differential usage and functional diversification. Here we combined a proteogenomics approach with heavy water-based protein turnover analysis to survey 24 pairs of canonical-alternative protein isoforms in the mouse heart. The results provide a reference on their numerical half-life and also reveal widespread differences in isoform stability.

biochemistry↗

bioRxiv2026

Body Mass Index-Specific Nanoparticle Protein Corona Signatures in Late Pregnancy

The protein corona (PC) formed on the surface of nanoparticles (NPs) upon exposure to human biofluids is a dynamic interface that reflects the physiological and pathological status of the host. In this study, we investigated how maternal body mass index (BMI) influences the composition of the NPs PC during late pregnancy. Polystyrene NPs were incubated with plasma samples collected from third-trimester pregnant individuals across normal weight, overweight, and obese BMI categories. Comprehensive characterization using dynamic light scattering (DLS), zeta potential measurements, and transmission electron microscopy (TEM) confirmed BMI-dependent differences in PC thickness and colloidal stability. SDS-PAGE and label-free quantitative proteomics revealed distinct molecular compositions: PCs from obese individuals were enriched in inflammatory and lipid metabolism-associated proteins (e.g., APOE, CRP), while normal weight-derived PCs showed higher levels of complement regulators and extracellular matrix proteins. Principal component analysis (PCA) demonstrated clear clustering of proteomic profiles by BMI group, suggesting BMI-specific PC fingerprints. These findings indicate that maternal metabolic phenotype shapes nano-bio interactions at the proteomic level and highlight the potential of PC profiling as a non-invasive approach for assessing maternal health and metabolic status. This work lays the foundation for integrating NP-based proteomics into precision nanomedicine for maternal-fetal health monitoring.

biophysics↗

bioRxiv2026

MXene Protein Corona Interfaces for Molecular Profiling of Alzheimers Disease

The protein corona (PC) that forms on the surface of nanomaterials upon contact with biological fluids provides a molecular snapshot of the hosts physiological and pathological state. Here, we investigate two-dimensional (2D) titanium carbide (Ti3C2Tx) MXene nanosheets as nanobiointerfaces for capturing Alzheimers disease (AD)-associated plasma protein signatures. Ti3C2Tx MXene flakes were incubated with plasma from clinically diagnosed AD patients and age-matched healthy controls (HC), leading to the formation of Ti3C2Tx MXene-PC complexes. Physicochemical characterization using dynamic light scattering, zeta potential analysis, and transmission electron microscopy revealed disease-dependent changes in hydrodynamic size, surface charge, and PC profile. Proteomic analysis of the isolated PC layers quantified 1,611 proteins without prior fractionation, demonstrating effective enrichment of low-abundance plasma components. Principal component analysis (PCA) revealed consistent separation between AD- and HC-derived Ti3C2Tx MXene-PC proteomes despite inter-individual heterogeneity. Differential abundance analysis identified selective enrichment of heterogeneous nuclear ribonucleoproteins (hnRNPs), annexins, and inflammatory mediators in AD-derived PC, implicating dysregulated RNA metabolism, membrane stress responses, and immune activation, hallmark processes in AD pathology. Our findings demonstrate that Ti3C2Tx MXene-PC interfaces act as selective molecular filters that reshape the detectable plasma proteome, enabling disease-associated molecular phenotyping and establishing a versatile nanointerface-driven framework for uncovering AD-related plasma signatures, providing a foundation for future translational diagnostic development.

biophysics↗

bioRxiv2025

Micro- and macro- heterogeneity of N-glycoproteome remodeling in endoplasmic reticulum stress

N-glycosylation plays essential roles in the folding, trafficking, and maturation of proteins in the secretory pathways, but how individual protein and residue glycosylation rewires under endoplasmic reticulum (ER) stress is unknown. Particularly, intact glycopeptide data that retain the connectivity between glycosylation sites and the attached glycans are needed to reveal the micro- and macro- heterogeneity of N-glycosylation sites and their permutations in stressed cells. Here, we developed an optimized magnetic polyethyleneimine boronic acid-containing scaffold (mPBA) enrichment workflow to achieve sensitive and broad enrichment of intact glycoproteins for mass spectrometry analysis, quantifying 13759 unique protein-, site-, and glycoform combinations, termed glycopeptidoforms, in normal and stressed cells while requiring only 0.1 to 0.5 mg total peptide input. The data reveals a systems-level shift in the fate of hundreds of glycoproteins. N-glycosylation changes are highly dynamic, with magnitude far exceeding protein expression changes, and showing complex protein-, site-, and glycan-specific granularity. Individual glycoform reconfigurations can be observed that suggest lesions within specific steps in protein maturation and trafficking pathways. Mannose trimming is disrupted across multiple proteins and cell states, suggesting a central feature of ER stress mediated glycoproteome remodeling. Together, these results reveal molecular details into the remodeling of protein secretory pathways upon ER stress and highlight the utility of mPBA for sensitive N-glycoproteomics studies.

biochemistry↗

bioRxiv2025

Neural recordings of continuous speech reveal robust signatures of prediction in second language learners of English

When listening to speech in their native language, speakers use prior context to anticipate upcoming phonemes, words, and concepts, integrating information at the sublexical, lexical, and sentence level. While it has been suggested that late second language learners do not predict to the same extent as native listeners, adequately evaluating this claim requires measurement of predictions at these multiple levels of representation simultaneously in natural speech. We recorded magnetoencephalography (MEG) responses from native Mandarin and Sinhala speakers listening to continuous narrative English speech. We used multivariate temporal response function (mTRF) analysis to investigate whether second language listeners demonstrate the same markers of prediction in neural data as native English speakers listening to the same stimuli. We demonstrate that late second language listeners exhibit strikingly similar responses to native speakers in sensitivity to phoneme surprisal and entropy with respect to sublexical, lexical, and sentence-level context. The few small response differences we observed appear most likely to arise from specific properties of the native languages, rather than general differences between native and second-language listening. These results provide evidence that late second-language listeners indeed leverage prediction in similar ways as native listeners in understanding continuous speech. This suggests that multivariate analyses of neural data from naturalistic listening may be vital in carefully evaluating the differences and similarities in speech prediction across populations. Significance StatementMuch is still unknown about how people listening to a second language predict upcoming words and sounds. Here, we leverage neuroimaging during continuous speech and analyze responses to multiple speech language features in the signal to study the neural encoding of prediction simultaneously at multiple levels of linguistic context. We observe robust encoding of statistical properties tied to prediction at all context levels in second-language learners of English and that responses are strikingly similar between native and second language listeners. Speech language features are encoded similarly in both groups of language learners, with few differences between the native and second language listeners, indicating that second language listeners predict upcoming input similarly to native listeners.

neuroscience↗

bioRxiv2025

SALVE: prediction of interorgan communication with transcriptome latent space representation

Massive transcriptomics data allow gene relationships to be discovered from their correlated expression. We describe SALVE, a method to infer the associations between secretome-encoding transcripts and gene modules in a distal organ from RNA sequencing data. This method builds upon similar bioinformatics approaches by introducing transcriptome latent space representations and transfer learning to simultaneously increase discovery power and predict downstream functional associations. Applied to GTEx v8 data, we show the method readily recapitulates canonical endocrine relationships, including insulin and adiponectin signaling, while inferring new candidate organokines and their signaling modality. We also explore its utility for generating new hypotheses on cardiokine candidates and finding distal factors that may affect cardiac protein synthesis and metabolism. The predictions suggest a potential role of circulating galectin-3 (LGALS3) in regulating cardiac protein synthesis and homeostasis, which can be recapitulated in part in human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes. This method may aid in ongoing efforts to delineate interorgan communications and endocrine networks in various areas of study. New & NoteworthyWe describe a bioinformatics strategy to find associations between the secretome-coding genes and functional pathways of two organs. This approach may be used to find crosstalk signals between the heart, adipose, liver, and other tissues. Applied to GTEx data, it suggests a potential role of circulating galectin-3 in regulating cardiac protein synthesis and homeostasis pathways.

bioinformatics↗

bioRxiv2025

Features fade, pointers persist: dissociable parietal mechanisms in visual working memory formation and maintenance

An emerging body of work has adopted the theoretical construct of pointers: an object is mentally represented by a content-free pointer binding the corresponding features together. Indeed, fMRI studies have highlighted dissociable parietal regions sensitive to pointer and feature load respectively. Specifically, while the superior IPS (intraparietal sulcus) is sensitive to feature load, inferior IPS is only sensitive to the number of pointers - i.e., the number of objects. However, the spatiotemporal dynamics remain unclear, and therefore it is unknown whether these effects reflect visual working memory (VWM) formation, maintenance, or both, especially given limited temporal resolution of fMRI. In our current MEG (magnetoencephalography) study, participants memorized visual arrays with different numbers of objects (object/pointer load: two, four), as well as different features and feature-per-object (color, orientation, bifeatural) in a VWM task. We observed a dissociation between inferior and superior IPS in the temporal dynamics of feature-sensitive and pointer-sensitive responses. While pointer-sensitive signals persisted across VWM formation and maintenance in inferior IPS, feature-sensitivity was only transiently manifested during VWM formation in superior IPS. This spatiotemporal dissociation may reflect a representational architecture optimized for efficiency, reducing the need for sustained neural activity to maintain features once they are bound to pointers. In revealing the spatiotemporal profile of pointer and feature representations, our results provide novel evidence on how pointers underlie energy-efficient neural representations in VWM.

neuroscience↗

bioRxiv2025

Non-visually-derived mental objects tax "visual" pointers

In daily life, we can construct mental objects from various modalities: we can create a cat in the mind from visual experience, or from what someone says or signs linguistically. Do mental objects derived from different input sources share the same set of "slots" (or pointers, indexicals)? Employing a novel imagine-one-then-more paradigm in a large EEG sample (N = 52) across two recording sites, we found that increasing the number of imagined objects derived from a non-visual source--auditory speech during eye closure--led to greater suppression of left posterior alpha power. This observation closely mirrors effects previously observed for visually-derived representations. Our results support the existence of a domain-general pointer system that functions as a modality-independent object register in moment-to-moment cognition.

neuroscience↗

bioRxiv2025

Unleashing the potential of OPM-MEG to study event-related fields against low-frequency artifacts: the case of sentence processing

OPM-MEG (optically pumped magnetometers-magnetoencephalography) offers unprecedented opportunity in its proximity to the brain and in mobility, outperforming other human MEG systems. However, movements induce low-frequency artifacts (up to [~] 3 Hz) in this system, calling for pipelines that could efficiently reduce these low-frequency noises. Although a high-pass filter of e.g., 4 Hz may minimize these artifacts, it may also eliminate many event-related field (ERF) components, such as the N400 response in sentence processing studies. Moreover, as an emerging technology with expensive sensors, many labs are starting with an experimental setup with fewer sensors (e.g., [~] 10), making it challenging to reject principal components based on visually inspecting the topographic field maps. In the current paper, we show that a combination of moderate high-pass filtering (1 Hz) and evoked-biased denoising source separation (evoked-biased DSS) can effectively reveal typical N400 deflections and effects (between nouns and verbs), with a nine-sensor OPM-MEG setup. Our current pipeline paves the way to studying ERFs with OPM-MEG in more budget-friendly setups with a small number of sensors.

neuroscience↗

bioRxiv2025

Deuterium labeling enables proteome wide turnover kinetics analysis in cell culture

The half-life of proteins is tightly regulated and underlies many cellular processes. It remains unclear the extent to which proteins are dynamically synthesized and degraded in different cell types and cell states. We introduce an improved D2O labeling workflow and apply it to examine the landscape of protein turnover in pluripotent and differentiating human induced pluripotent stem cells (hiPSC). The majority of hiPSC proteins show minimal turnover beyond cell doubling rates, but we also identify over 100 new fast-turnover proteins not previously described as short-lived. These include proteins that function in cell division and cell cycle checkpoints, that are enriched in APC/C and SPOP degrons, and that are depleted upon pluripotency exit. Differentiation rapidly shifts the set of fast-turnover proteins toward including RNA binding and splicing proteins. The ability to identify fast-turnover proteins in different cell cultures also facilitates secretome analysis, as exemplified by studies of hiPSC-derived cardiac myocytes and primary human cardiac fibroblasts. The presented workflow is broadly applicable to protein turnover studies in diverse primary, pluripotent, and transformed cells.

biochemistry↗

bioRxiv2024

A finite set of content-free pointers in visual working memory: MEG evidence

Human visual working memory (VWM) is known to be capacity-limited, but the nature of this limit continues to be debated. Recent work has proposed that VWM is supported by a finite ([~] 3) set of content-free pointers, acting as stand-ins for individual objects and binding features together. Here, based on two visual working memory experiments (N=20 each) examining memory for simple and complex objects, we report a sustained MEG response over right posterior cortex whose magnitude tracks the core hypothesized properties of this system: load-dependent, capacity-limited and content-free. These results provide novel evidence for a finite set of content-free pointers underlying VWM.

neuroscience↗

bioRxiv2024

Improved determination of protein turnover rate with heavy water labeling by mass isotopomer ratio selection

The synthesis and degradation rates of proteins form an essential component of gene expression control. Heavy water labeling has been used in conjunction with mass spectrometry to measure protein turnover rates, but the optimal analytical approaches to derive turnover rates from the isotopomer patterns of deuterium labeled peptides continue to be a subject of research. Here we describe a method, which comprises a reverse lookup of numerically approximated peptide isotope envelopes, coupled to the selection of optimal isotopomer pairs based on peptide sequence, to calculate the molar fraction of new peptide synthesis in heavy water labeling mass spectrometry experiments. We validated this approach using an experimental calibration curve comprising mixtures of fully unlabeled and fully labeled proteomes. We then re-analyzed 17 proteome-wide turnover experiments from four mouse organs, and showed that the method increases the coverage of well-fitted peptides in protein turnover experiments by 25-82%. The method is implemented in the Riana software tool for protein turnover analysis, and may avail ongoing efforts to study the synthesis and degradation kinetics of proteins in animals on a proteome-wide scale. Whats newWe describe a reverse lookup method to calculate the molar fraction of new synthesis from numerically approximated peptide isotopomer profiles in heavy water labeling mass spectrometry experiments. Using an experimental calibration curve comprising mixtures of fully unlabeled and fully labeled proteomes at various proportions, we show that this method provides a straightforward way to calculate the proportion of new proteins in a protein pool from arbitrarily chosen isotopomer ratios. We next analyzed which of the isotopomer pairs within the peptide isotope envelope yielded isotopomer time courses that fit most closely to kinetic models, and found that the identity of the isotopomer pair depends partially on the number of deuterium accessible labeling sites of the peptide. We next derived a strategy to automatically select the isotopomer pairs to calculate turnover rates based on peptide sequence, and showed that this increases the coverage of existing proteome-wide turnover experiments in multiple data sets of the mouse heart, liver, kidney, and skeletal muscle by up to 25-82%.

biochemistry↗

bioRxiv2024

A Ratiometric Catalog of Protein Isoform Shifts in the Cardiac Fetal Gene Program

Pathological cardiac remodeling is associated with the reactivation of fetal genes, yet the extent of the hearts fetal gene program and its impact on proteome compositions remain incompletely understood. Here, using a new proteome-wide protein ratio quantification strategy with mass spectrometry, we identify pervasive isoform usage shifts in fetal and postnatal mouse hearts, involving 145 pairs of highly homologous paralogs and alternative splicing-derived isoform proteins. Proteome-wide ratio comparisons readily rediscover hallmark fetal gene signatures in muscle contraction and glucose metabolism pathways, while revealing novel isoform usage in mitochondrial and gene expression proteins, including PPA1/PPA2, ANT1/ANT2, and PCBP1/PCBP2 switches. Paralogs with differential fetal usage tend to be evolutionarily recent, consistent with functional diversification. Alternative splicing adds another rich source of fetal isoform usage differences, involving PKM M1/M2, GLS-1 KGA/GAC, PDLIM5 long/short, and other spliceoforms. When comparing absolute protein proportions, we observe a partial reversion toward fetal gene usage in pathological hearts. In summary, we present a ratiometric catalog of paralogs and spliceoform pairs in the cardiac fetal gene program. More generally, the results demonstrate the potential of applying the proteome-wide ratio test concept to discover new regulatory modalities beyond differential gene expression.

biochemistry↗

bioRxiv2024

Electrophysiological responses to syntactic and 'morphological' structures: evidence from Mandarin Chinese

Although psycho-/neuro-linguistics has assumed a distinction between morphological and syntactic structure building as in traditional theoretical linguistics, this distinction has been increasingly challenged by theoretical linguists in recent years. Opposing a sharp, lexicalist distinction between morphology and syntax, non-lexicalist theories propose common morpho-syntactic structure building operations that cut across the realms of "morphology" and "syntax", which are considered distinct territories in lexicalist theories. Taking advantage of two pairs of contrasts in Mandarin Chinese with desirable linguistic properties, namely compound vs. simplex nouns (the "morphology" contrast, differing in morphological structure complexity per lexicalist theories) and separable vs. inseparable verbs (the "syntax" contrast, differing in syntactic structure complexity per lexicalist theories), we report one of the first pieces of evidence for shared neural responses for morphological and syntactic structure complexity in language comprehension, supporting a non-lexicalist view where shared neural computations are employed across morpho-syntactic structure building. Specifically, we observed that the two contrasts both modulated neural responses in left anterior and centro-parietal electrodes in an a priori 275:400 ms time window, corroborated by topographical similarity analyses. These results serve as preliminary yet prima facie evidence towards shared neural computations across morphological and syntactic structure building in language comprehension.

neuroscience↗

bioRxiv2023

Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart

A computational analysis of mass spectrometry data was performed to uncover alternative splicing derived protein variants across chambers of the human heart. Evidence for 216 non-canonical isoforms was apparent in the atrium and the ventricle, including 52 isoforms not documented on SwissProt and recovered using an RNA sequencing derived database. Among non-canonical isoforms, 29 show signs of regulation based on statistically significant preferences in tissue usage, including a ventricular enriched protein isoform of tensin-1 (TNS1) and an atrium-enriched PDZ and LIM Domain 3 (PDLIM3) isoform 2 (PDLIM3-2/ALP-H). Examined variant regions that differ between alternative and canonical isoforms are highly enriched in intrinsically disordered regions, and over two-thirds of such regions are predicted to function in protein binding and/or RNA binding. The analysis here lends further credence to the notion that alternative splicing diversifies the proteome by rewiring intrinsically disordered regions, which are increasingly recognized to play important roles in the generation of biological function from protein sequences.

biochemistry↗

bioRxiv2023

Electrophysiological hallmarks for event relations and event roles in working memory

The ability to maintain events (i.e. interactions between/among objects) in working memory is crucial for our everyday cognition, yet the format of this representation is poorly understood. The current ERP study was designed to answer two questions: How is maintaining events (e.g., the tiger hit the lion) neurally different from maintaining item coordinations (e.g., the tiger and the lion)? That is, how is the event relation (present in events but not coordinations) represented? And how is the agent, or initiator of the event encoded differently from the patient, or receiver of the event during maintenance? We used a novel picture-sentence match-across-delay approach in which the working memory representation was pinged during the delay, in two ERP experiments with Chinese and English materials. First, we found that maintenance of events elicited a long-lasting late sustained difference in posterior-occipital electrodes relative to non-events. This effect resembled the negative slow wave reported in previous studies of working memory, suggesting that the maintenance of events in working memory may impose a higher cost compared to coordinations. Second, in order to elicit a hallmark for agent vs. patient representation in working memory, we pinged agent or patient characters during the delay. Although planned comparisons did not reveal significant differences in the ERPs elicited by the agent pings vs. patient pings, we found that the ping appeared to dampen the ongoing sustained difference, suggesting a shift from sustained activity to activity silent mechanisms. These results represent one of the uses of ERPs to elucidates the format of neural representation for events in working memory.

neuroscience↗