Biology subjects

Chan, K. S.

Publications and source records attributed to Chan, K. S..

7 recordsLinked to original sources

bioRxiv2026

Metastable Dimeric Intermediate Drives Native-like Spidroin Fibrillogenesis, while Dehydration Promotes Cross-β Transition

The exceptional mechanical properties of spider dragline silk originate from hierarchical spidroin self-assembly, yet mimicking this process to generate native-like structures remains challenging. Here, we report a metastable dimeric intermediate as an essential molecular factor for fibrillogenesis. Small-angle X-ray scattering (SAXS) and atomic force microscopy (AFM) revealed a compact core stabilized by solvent-excluded "dry interfaces" surrounded by extended random coil regions. Within the core, a subset of the polyalanine blocks is held by side-chain packing rather than by main-chain {beta}-sheets; the majority remain exposed in the surrounding coil regions. Upon lowering the denaturant concentration, these exposed polyalanine segments pair with their counterparts at a fibril end, forming intermolecular {beta}-sheets that act as linkers and drive the stepwise end-to-end polymerization of the dimeric particles. In solution, the resulting fibrils exhibit an ordered {beta}-structure in which the polypeptide chains run parallel to the fibril axis, in contrast to amyloid-like cross-{beta}, in which the strands lie perpendicular to it; this matches key features of native silk nanofibril architecture. However, X-ray diffraction (XRD) analysis demonstrates that these native-like nanofibrils undergo an effectively irreversible transition toward amyloid-like cross-{beta} structures upon drying. Native-like fibrils are thus achievable by self-assembly, but structural control is lost during the final dehydration step. Accordingly, we propose a general principle for decoupling self-assembly from dehydration: native-like nanofibrils are formed first, then dried under conditions that restrict molecular-chain mobility (for example, mechanical constraint or immobilization on a surface), which we expect to suppress thermodynamic relaxation into cross-{beta} structures.

biophysics↗

bioRxiv2026

Ferrous Iron Accumulation Is a Hallmark and Therapeutic Vulnerability of Therapy-Induced Senescence

Chemotherapy and radiation reduce tumor burden but leave behind residual cells that survive via therapy-induced senescence (TIS). These cells constitute a latent reservoir fueling recurrence, yet strategies for their selective elimination are lacking. Here, we identify lysosomal ferrous iron accumulation as a conserved hallmark and actionable vulnerability of TIS tumor cells. Across diverse models, senescent tumor cells exhibit marked hypersensitivity to ferroptosis induction. In breast cancer PDX models, sequential ferroptosis induction following chemotherapy significantly delays recurrence, while dual inhibition of GPX4 and FSP1 produces durable, often complete, eradication of residual tumors without overt toxicity. Mechanistically, activation of the TFEB-HO-1 axis in TIS tumor cells drives ferrous iron accumulation, thereby priming cells for ferroptosis. Together, these findings establish ferrous iron accumulation as a defining feature of TIS and position ferroptosis induction as a potent senolytic strategy to eliminate therapy-refractory residual disease. Statement of significanceSenescent tumor cells remaining after treatment can drive cancer recurrence yet remain poorly understood and therapeutically intractable. Here, we identify lysosomal ferrous iron accumulation as a universal hallmark of therapy-induced senescence and demonstrate that ferroptosis induction functions as an effective senolytic strategy. Our findings provide mechanistic and translational support for the "one-two punch" therapeutic paradigm.

cancer biology↗

bioRxiv2026

UniST: A Unified Computational Framework for 3D Spatial Transcriptomics Reconstruction

Spatial transcriptomics (ST) enables the measurement of gene expression in its native spatial context, yet most ST datasets are acquired as two-dimensional (2D) sections. Consequently, the underlying three-dimensional (3D) organization of tissues is only partially observed, and 3D ST data generated from serial sections are typically sparse and heterogeneous, with substantial tissue loss and missing measurements. These limitations pose major analytical challenges for reconstructing coherent 3D tissue architecture, rather than issues of experimental scalability alone. Here, we present UniST, a unified generative artificial intelligence (AI) framework designed to computationally reconstruct dense and continuous 3D ST landscapes from sparse serial sections, without altering the underlying experimental ST technologies. UniST integrates three complementary modules: kernel point convolution with cross-attention layers for point cloud upsampling, optical flow-based interpolation for continuous slice reconstruction, and a graph autoencoder with implicit neural representations for gene expression imputation. Together, these components densify sparse slices, resolve discontinuities, and map spatial coordinates to high-dimensional transcriptomics. Across multiple ST platforms and tissue contexts, UniST accurately restored structural continuity and biologically meaningful expression patterns. In a mouse embryo dataset, UniST reconstructed a dense 3D heart architecture from sparsely sampled slices. In two 3D human cancer tissues, UniST recovered critical spatial features, including tumor-immune boundaries and tertiary lymphoid structures, that were fragmented in the original data. By providing a generalizable computational solution that complements existing ST acquisition protocols, UniST facilitates cost-efficient and scalable reconstruction of 3D ST landscapes, enabling more faithful investigation of tissue organization and disease biology.

bioinformatics↗

bioRxiv2025

Targeting Endothelial PERK Accelerates Lymphoid Regeneration by Enhancing DLL4-NOTCH3 Signaling at the Pre-B Niche

Delayed immune recovery after hematopoietic stem cell (HSC) transplantation is associated with a poor clinical outcome, yet strategies to enhance lymphocyte regeneration are limited. We studied the role of unfolded protein response (ER stress) in hematopoietic regeneration within the bone marrow (BM) microenvironment. We revealed that PERK activation is a prominent feature of BM endothelium in leukemia patients and is a hallmark response in mouse BM following ionizing irradiation. Ablating endothelial Perk boosted Notch ligand DLL4 expression and promoted DLL4-dependent early HSC and B progenitor regeneration. Single-cell analysis shows that endothelial DLL4 activates NOTCH3 expressed by mesenchymal stroma cells, and that the PERK-DLL4 axis coordinates the regulation of lymphoid commitment and niche cytokine production. NOTCH3 is critical for the upregulation of IL7 following irradiation and for supporting the expansion of lymphoid progenitors in mesenchymal sphere cultures. These findings not only unveil a previously unrecognized ER stress-controlled vascular-stroma signaling mechanism in regenerative hematopoiesis but also highlight PERK blockade as a promising therapeutic strategy to improve immune recovery after myeloablative transplantation. SummaryZou et al unravel that the adaptive ER stress response in bone marrow blood vessels restricts the post-transplant regeneration of immune progenitor cells by attenuating the expression of Notch ligand DLL4. Targeting ER stress sensor PERK can accelerate immune recovery after transplantation by enhancing DLL4-NOTCH3 signaling and IL7 cytokine production.

cell biology↗

bioRxiv2025

A global genetic interaction map of a human cell reveals conserved principles of genetic networks

We generated a genome-scale, genetic interaction network from the analysis of more than 4 million double mutants in the haploid human cell line, HAP1. The network maps [~]90,000 genetic interactions, including thousands of extreme synthetic lethal and genetic suppression interactions. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes, pathways, biological processes, and cellular compartments. Comparative analyses showed that general principles of genetic networks are conserved from yeast to human cells. A genetic interaction network mapped in a single genetic background complements the DepMap gene co-essentiality network, recapitulating many of the same biological connections and also capturing unique functional information to reveal roles of uncharacterized genes and molecular determinants of specific cancer cell line genetic dependencies.

systems biology↗

bioRxiv2021

A cohesin traffic pattern genetically linked to gene regulation

Cohesin-mediated loop extrusion folds interphase chromosomes at the ten to hundreds kilobases scale. This process produces structural features such as loops and topologically associating domains. We identify three types of cis-elements that define the chromatin folding landscape generated by loop extrusion. First, CTCF sites form boundaries by stalling extruding cohesin, as shown before. Second, transcription termination sites form boundaries by acting as cohesin unloading sites. RNA polymerase II contributes to boundary formation at transcription termination sites. Third, transcription start sites form boundaries that are mostly independent of cohesin, but are sites where cohesin can pause. Together with cohesin loading at enhancers, and possibly other cis-elements, these loci create a dynamic pattern of cohesin traffic along the genome that guides enhancer-promoter interactions. Disturbing this traffic pattern, by removing CTCF barriers, renders cells sensitive to knock-out of genes involved in transcription initiation, such as the SAGA and TFIID complexes, and RNA processing such DEAD-Box RNA helicases. In the absence of CTCF, several of these factors fail to be efficiently recruited to active promoters. We propose that the complex pattern of cohesin movement along chromatin contributes to appropriate promoter-enhancer interactions and localization of transcription and RNA processing factors to active genes. HIGHLIGHTSO_LIAt least three types of chromatin boundaries regulate a cohesin traffic pattern. C_LIO_LIThe cohesin traffic pattern guides enhancer-promoter interactions. C_LIO_LIRemoving CTCF renders cells sensitive to deletion of RNA processing and gene regulation genes. C_LIO_LIDepleting CTCF affects localization of RNA processing and gene regulatory proteins. C_LI

genomics↗

bioRxiv2018

The consensus molecular classification of muscle-invasive bladder cancer

Muscle-Invasive Bladder Cancer (MIBC) is a molecularly diverse disease with heterogeneous clinical outcomes. Several molecular classifications have been proposed, yielding diverse sets of subtypes, which hampers the clinical implications of such knowledge. Here, we report the results of a large international effort to reach a consensus on MIBC molecular subtypes. Using 1750 MIBC transcriptomes and a network-based analysis of six independent MIBC classification systems, we identified a consensus set of six molecular classes: Luminal Papillary (24%), Luminal Non-Specified (8%), Luminal Unstable (15%), Stroma-rich (15%), Basal/Squamous (35%), and Neuroendocrine-like (3%). These consensus classes differ regarding underlying oncogenic mechanisms, infiltration by immune and stromal cells, and histological and clinical characteristics. This consensus system offers a robust framework that will enable testing and validating predictive biomarkers in future clinical trials.

cancer biology↗