Biology subjects

Si, K.

Publications and source records attributed to Si, K..

12 recordsLinked to original sources

bioRxiv2026

Small molecules targeting BRCA1-deficient cancer cells

BRCA1 mutation-carriers frequently develop triple-negative breast cancers that are resistant to cancer therapies. We used our established luciferase-expressing BRCA1-deficient human mammary epithelial-derived cell line series with stable shRNA-mediated BRCA1-knockdown, H-RasG12V-mediated transformation, and TP53-deficiency (PMID: 20038817) to perform a high-throughput-screen using the National Cancer Institute (NCI) chemical library Diversity Set II of 1,440 small molecules and noninvasive bioluminescence imaging. We selected five (NSC667251, NSC636948, NSC21683, NSC281383, and NSC136513) compounds that reproducibly induced cell death in engineered BRCA1-knockdown cells and in BRCA1-deficient human cancer cell lines. In p53-mutant MDA-MB-231 and SKBr3 lines, the compounds induced apoptosis and PARP cleavage by 12 hours. Sub-G1 flow cytometric analysis demonstrated maximal apoptosis induction by 48 hours of drug exposure. p53 protein stabilization and phosphorylation were observed with the selected compounds in BRCA1-deficient wild-type TP53-expressing cells. Drug-treated BRCA1-knockdown MCF10A cells and BRCA1-mutant HCC-1937 breast cancer cells showed gamma-H2AX foci and phospho-H2AX by immunoblotting indicating genotoxicity and DNA damage as contributing factors for apoptosis. NSC636948 was previously characterized as an inhibitory ligand of peroxisome proliferator-activated beta, delta; (PPAR beta, delta) and both NSC636948 and NSC667251 act as inverse agonists of PPAR beta, delta. Kaplan Meier survival analysis of a combined breast cancer cohort (n = 1,959) derived from the METABRIC, demonstrated that patients with high PPARD expression exhibited significantly worse overall survival compared with those with low PPARD expression (log-rank p = 0.008). The selected compounds provide candidate therapeutic leads as well as insights into molecular targets for further evaluation in BRCA1-deficient tumor models and for assessment in combination therapy strategies.

cancer biology↗

bioRxiv2026

Dissecting inter-focal heterogeneity and convergent immunosuppressive ecosystems in multifocal hepatocellular carcinoma through single-cell and spatial multi-omics

Background Multifocal hepatocellular carcinoma (HCC) comprises spatially separated tumor foci with distinct evolutionary trajectories, posing a major therapeutic challenge. Whether divergent lesions retain shared immune-evasion mechanisms beyond lesion-specific heterogeneity and offer cross-focal therapeutic opportunities remains unknown. Objective To resolve malignant and microenvironmental heterogeneity across tumor foci and identify conserved immunosuppressive programs underlying multifocal HCC progression. Design Matched tumour foci and peritumoural tissues from patients with multifocal HCC underwent integrated single-cell and spatial multi-omics profiling, including scFAST-seq (n=15), scATAC-seq (n=12), and Stereo-seq (n=14). In-house RNA-seq (n=13), public scRNA-seq (HRA001748) and RNA-seq datasets (TCGA-LIHC, OEP000321) were used for validation. Multiplex immunohistochemistry (n=96) and functional assays validated key findings. Results Multifocal HCC exhibited extensive inter-focal heterogeneity in malignant genomic, transcriptional, epigenetic, and evolutionary states, accompanied by diverse immune and stromal landscapes. Despite this divergence, spatially separated tumor foci converged on shared malignant states marked by elevated TMED2 expression and conserved immunosuppressive ecosystems characterized by regulatory T-cell (Treg) and SPP1+/SPRED1+ macrophage enrichment, impaired cytotoxic CD8+ T-cell immunity, and recurrent stromal-vascular remodeling. Mechanistically, malignant hepatocytes engaged SPP1+/SPRED1+ macrophages through C3/C5 complement signaling across divergent tumor foci, while macrophages and Tregs contributed to CD8+ T-cell dysfunction through CD274-PDCD1, CD80/CD86-CTLA4/CD28, and MHC-I-CD8 interactions. A tumor-intrinsic TMED2-ADAR1-dependent A-to-I RNA editing program promoted C3/C5 complement expression and secretion, linking malignant heterogeneity to conserved tumor-immune signaling. Conclusions Despite divergent malignant evolution, multifocal HCC converges on shared immunosuppressive ecosystems. The TMED2-ADAR1-C3/C5 complement axis represents a conserved tumor-immune vulnerability that may enable therapeutic strategies targeting common immune-evasion mechanisms across heterogeneous tumor foci.

cancer biology↗

bioRxiv2026

The Spatiotemporal Proteome Landscape of Aging: Structural determinants of age-sensitive proteome remodeling

Aging is marked by a decline in cellular functions accompanied by widespread changes in mRNA and protein abundance, yet whether aging broadly remodels subcellular protein localization and concentration--and why some proteins change while others remain stable--remains unclear. This gap matters because cellular function depends not only on expression levels but also on correct spatial organization. Using yeast replicative aging as a model, we built a robotic pipeline to enrich old cells from 5,661 strains, acquired 90 million single-cell 3D images, and applied machine learning to map proteome-wide changes in localization, concentration, and aggregation throughout aging. This age-resolved single-cell atlas uncovers widespread proteome remodeling and rewiring of protein interaction networks. Moreover, structural analysis reveals biophysical determinants of age-sensitive proteome remodeling across ages and species. Together, these results reveal a structure-encoded intrinsic principle underlying spatial proteome breakdown during aging and provide a resource to dissect mechanistic links among aging hallmarks.

systems biology↗

bioRxiv2026

p62 protein pleomorphism confers tissue-specific function

Protein structure dictate function, and proteins often perform the same function in different cell/tissue-type environments. Here, we report that in Drosophila melanogaster, the broadly expressed protein p62/SQSTM1 instead performs mutually exclusive functions across tissues - autophagy in midgut and mitochondria-associated proteostasis in muscle. These functional differences arise from tissue-specific secondary and tertiary structures adopted by the same p62 polypeptide, rather than protein abundance, isoforms, post-translational modification, or binding-partner availability. The tissue-specific structures are cell autonomous and resistant to environmental perturbation. Deletion of a short intrinsically disordered region converts muscle p62 to a midgut-like structural and functional state, but this forced switch causes muscle dysfunction, linking tissue-specific physiology to alternative structural states of the same polypeptide. We posit that Drosophila p62 exemplifies a mechanism for tissue-specificity in which intrinsic structural plasticity and the physiochemical/molecular environment of a tissue enable a broadly expressed protein to adopt tissue-specific structure and function.

cell biology↗

bioRxiv2025

A Spatially Resolved Atlas of Alternative Polyadenylation Across 18 Human Tissues and 76 Disease States

Alternative polyadenylation (APA) is a key regulator of gene expression and cellular dynamics, yet systematic investigations of spatially resolved APA across diverse human tissues remain limited. Here, we developed SpatialAPA (https://github.com/Omicslab-Zhang/spatialAPA), a framework that benchmarks multiple APA identification methods and integrates spatial APA data with gene expression and cellular dynamics at spatial resolution. Applying SpatialAPA to 363 spatial transcriptomic data from 56 projects across 18 human tissues and 76 diseases, we constructed a spatially resolved APA atlas comprising 346,932 APA events across 52,175 genes. This atlas reveals organ-specific APA patterns and provides new insights into how APA regulates tissue homeostasis and disease progression beyond transcriptional control. To ensure cross-sample comparability, we applied batch correction, while spatial cell deconvolution uncovered cell-type-specific dynamics and interactions. In triple-negative breast cancer, integrated spatial and single-cell analyses identified TSPAN8-positive epithelial subpopulations whose distinct APA regulation and transcriptional programs drive differentiation and malignant progression. To facilitate community access, we developed an online platform (http://www.biomedical-web.com/spatialAPAdb/home) for exploring APA, gene expression, and cellular dynamics in health and disease. Together, this study establishes the first comprehensive spatial APA atlas, providing a valuable resource and analytical framework for investigating molecular mechanisms and therapeutic targets.

bioinformatics↗

bioRxiv2025

Engineering gene expression dynamics via self-amplifying RNA with drug-responsive non-structural proteins

The design of gene therapies with drug-regulatable expression of therapeutic payloads is of interest for diverse applications. We hypothesized that a regulated expression system based on alphavirus-derived self-amplifying RNAs (saRNAs), which encode 4 non-structural proteins (nsPs) that copy the RNA backbone to enable sustained expression, would have advantages in safety and simplicity of delivery. Here we designed saRNAs where payload expression is regulated by the FDA-approved drug trimethoprim (TMP), by fusing TMP-responsive degradation domains (DDs) to nsPs to regulate RNA self-amplification. Screening a library of nsP-DD fusions, we identified an optimal design with DDs fused to nsP2, nsP3, and the payload, achieving a high fold-change in expression level in response to TMP and low expression in the off state. In mice, this saRNA circuit enabled diverse dynamic expression patterns in response to oral TMP. Implementing this circuit for controlled expression of an HIV antigen, an escalating TMP regimen significantly enhanced germinal center responses critical for B cell affinity maturation. This drug- regulated RNA technology holds potential for vaccines, immunotherapies, and gene therapies.

bioengineering↗

bioRxiv2025

High-throughput 3D super-resolution imaging in deep tissue

Fluorescence images obtained with optical microscopes intrinsically suffer from blur and noise, which can be partially reversed by the deconvolution process. However, the deconvolution process is ill-conditioned, leading to a trade-off between detail preservation and noise suppression. Here, we develop 3D-FUDIP to fully decouple the deconvolution process into two parts: deblurring and denoising, achieving an 8-fold improvement in spatial resolution. By adopting the Poisson model, which obeys the quantum nature of photons, our 3D-FUDIP can be successfully applied to various noise conditions, especially low-light conditions where the photon number is generally extremely small. The results show that our 3D-FUDIP improves the SNR by up to 6-fold with only a one-fifth photon budget. Besides, 3D-FUDIP boosts the spatial bandwidth product (SBP) by one order of magnitude, allowing more spine details to be resolved within a larger imaging volume. By synergizing deep learning with these advances, we propose 3D-FUDIPn to further improve the imaging resolution. We demonstrate 3D-FUDIPs performance in various imaging systems, including confocal, two-photon, and light-sheet microscopes, showing compatibility and potential applications in biological science.

neuroscience↗

bioRxiv2024

Separated attractors in neural landscape of motor cortex encoding motor learning

Animals gain motor learning via decrease of variation through repeated training. The secondary motor (M2) cortex shows an indispensable role in the learning process of the rotarod-learning task. Yet, it remains unclear how population decoding in M2 cortex guides the repetitive training to transform into motor enhancement. We recorded neuronal population activity using Ca2+ imaging during this enhancement revealing that neuronal population correlates of the persistent internal learning state evolves in the process of motor learning. With the behavioral micro-states analysis, we identify the growing periodicity, stability, and consistency with two gradually clearer point attractor in the M2 neural state space. The results show the evolution of attractors in M2 participate in decrease of training-acquisition behavior variation and provide a general framework for the mapping between arbitrary non-task motor learning and neural topological structure.

neuroscience↗

bioRxiv2022

Multi-Domain Characterization and Rapid Detection Technology for Cocaine and Methamphetamine Acute Abuse based on EEG

Multi-domain characterization and a new fast detection method for acute illegal psychostimulants abuse detection based on waking-state EEG of mice is proposed in this paper. To get corftical electroencephalogram (EEG), three groups of mice were injected with cocaine (Coca), methamphetamine (Meth), and saline (Sali) respectively following the experimental paradigm of drug abuse. The EEG features were extracted out by multi-domain views, including time, frequency, complexity, dynamics, and independent domains to obtain acute drug abuse effects on the brain. New strategy combing time domain with frequency domain is developed as multi-domain input and by means of dimension transformation approach preserving temporal information, the performance of drug abuse detection is greatly improved with deep learning models of ResNet50. Results show that comparing to support vector machine (SVM), k nearest neighbor (kNN), random forest (RF), and long short-term memory fully convolutional networks (LSTM-FCN), ResNet50 based on our proposed multi-domain features has best F1-score of 95.10%. This promising method provides a low-cost, fast, and widely assisted technology for psychostimulants abuse identification.

bioinformatics↗

bioRxiv2022

Two-photon patterned photostimulation with low-power, high-efficiency and reliable single-cell optogenetic control

Two-photon optogenetics enables selectively stimulating individual cells for manipulating neuronal ensembles. As the general photostimulation strategy, the patterned two-photon excitation has enabled millisecond-timescale activation for single or multiple neurons, but its activation efficiency is suffered from high laser power due to low beam-modulation efficiency. Here, we develop a high- efficiency beam-shaping method based on the Gerchberg-Saxton (GS) algorithm with spherical-distribution initial phase (GSSIP) to reduce the patterned two-photon excitation speckles and intensity. It can well control the phase of shaped beams to attain speckle-free accurate patterned illumination with an improvement of 44.21% in the modulation efficiency compared with that of the traditional GS algorithm. A combination of temporal focusing and the GSSIP algorithm (TF-GSSIP) achieves patterned focusing through 500-m-thickness mouse brain slices, which is 2.5 times deeper than the penetration depth of TF-GS with the same signal-to-noise ratio (SNR). With our method, the laser power can be reduced to only 55.56% of that with traditional method (the temporal focusing with GS, TF-GS) to reliably evoke GCaMP6s response in C1V1-expressing cultured neurons with single-cell resolution. Besides, the photostimulation efficiency is remarkably increased by 80.19% at the same excitation density of 0.27 mW/m2. This two-photon stimulation method with low-power, reliable and patterned illumination may pave the way for analyzing neural circuits and neural coding and decoding mechanism.

neuroscience↗

bioRxiv2021

Proteome plasticity in response to persistent environmental change

Temperature is a variable component of the environment and all organisms must deal with or adapt to temperature change. Acute temperature change activates cellular stress responses resulting in the refolding or removal of damaged proteins. However, how organisms adapt to long-term temperature change remains largely unexplored. Here, we report that budding yeast responds to long-term high temperature challenge by switching from chaperone induction to the reduction of temperature sensitive proteins and re-localizing a portion of its proteome. Surprisingly, we also find many proteins adopt an alternative conformation. Using Fet3p as an example, we find that the temperature-dependent conformational difference is accompanied by distinct thermostability, subcellular localization, and importantly, cellular functions. We postulate that in addition to the known mechanisms of adaptation, conformational plasticity allows some polypeptides to acquire new biophysical properties and functions when environmental change endures.

molecular biology↗

bioRxiv2018

Antimicrobial peptides modulate long-term memory

Antimicrobial peptides act as a host defense mechanism and regulate the commensal microbiome. To obtain a comprehensive view of genes contributing to long-term memory we performed mRNA sequencing from single Drosophila heads following behavioral training that produces long-lasting memory. Surprisingly, we find that two immune peptides with antimicrobial activity, Diptericin B and Gram-Negative Bacteria Binding Protein like 3, regulate long-term but not short-term memory or instinctive behavior in Drosophila. The cellular requirement of these two peptides is distinct: head fat body for DptB, and neurons for GNBP-like3. That antimicrobial peptides influence memory provides a novel example of the emerging link between the immune and nervous systems and reveals that some immune peptides may have been repurposed in the nervous system.

neuroscience↗