Biology subjects

Chan, S.

Publications and source records attributed to Chan, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Non-canonical IL-2 signaling facilitates peripheral regulatory T cell differentiation

Non-canonical IL-2 signaling, termed Monoclonal antibody or Matrix-directed Alternative Cytokine Signaling (MACS), is mediated by a CD25-chemokine receptor complex and operates in concert with the canonical JAK-STAT5 pathway; however, its role in T cell homeostasis remains poorly defined. Here, we uncover a role for MACS in regulatory T cell (Treg) differentiation and functional specification. We generated Il2E66K/E66K mice in which CD25-CCR7 assembly is disrupted and IL-2-induced STAT5 phosphorylation is preserved. Immunophenotyping analysis by flow cytometry revealed that MACS deficiency reduces the accumulation of Nrp1- Foxp3+ Tregs in gut-associated lymphoid tissues from 24-weeks-old Il2E66K/E66K mutant mice. Single-cell transcriptomics, functional suppression assays, and in vitro differentiation revealed that MACS engagement drives Treg differentiation and sustains effector Treg programs - marked by robust IL-10 expression - in part via an AP-1-dependent transcriptional network. These findings establish IL-2 MACS as a distinct signal directing peripheral immune tolerance and highlight a potential node for targeted immunomodulation.

immunology↗

bioRxiv2026

GALE-dependent glycoproteome remodelling is a determinant of oncogenic RAS transformation

Oncogenic transformation is accompanied by extensive remodelling of the cellular glycosylation landscape, yet the mechanisms linking oncogenic signalling to glycoproteome reprogramming remain poorly defined. We used site-resolved intact glycoproteomics to systematically map oncogenic RAS-dependent changes across the N- and O-linked glycoproteome. Integrating multiomics profiling with functional approaches, we identify UDP-glucose 4-epimerase (GALE) as a transcriptional target of oncogenic RAS that is induced through MAPK signalling and MYC-dependent transcription. GALE depletion selectively disrupted RAS-dependent glycoproteome remodelling, preferentially impairing sialylation of N-linked glycans and O-linked GalNAc-type glycosylation. Functionally, these glycosylation defects were accompanied by suppressed anchorage-independent growth and reduced in vivo tumorigenicity of KRAS-mutant cells, establishing GALE-dependent nucleotide-sugar interconversion as a requirement for malignant growth. Clinically, GALE expression was elevated in pancreatic ductal adenocarcinoma, wherein KRAS mutations are highly prevalent, and across a broad spectrum of human cancers. Collectively, our findings define a regulatory axis that connects oncogenic signalling to nucleotide-sugar precursor availability and diversification of the cellular glycan repertoire, revealing GALE as a metabolic dependency in RAS-driven cancer.

Cancer Biology↗

bioRxiv2026

Mapping immune cellular landscapes and vaccine responses across a spectrum of health and immunodeficiency.

Immune responses to infection and vaccination exhibit diversity between individuals that can be shaped by differences in their immune cell landscapes and the signalling, transcriptional, and genetic mechanisms that coordinate immune cell function. Specific antibody deficiency (SAD) and common variable immunodeficiency (CVID) are common forms of predominantly antibody deficiencies that result in poor responses to vaccination. While molecular and cellular causes of the immune dysfunction and poor vaccination responses for individuals with CVID have been reported, immune cell or molecular defects have not yet been identified in SAD. Here, we have used single-cell multi-omics to define the cellular landscapes, transcriptional states, adaptive immune repertoires and protein expression of patients with SAD and CVID before and after polysaccharide vaccination. We discovered that while SAD and CVID exhibit overlapping immune defects, including accumulation of exhausted NK memory cells and dysregulated expression of genes that mediate lipopolysaccharide sensing and clearance by monocytes, individuals with SAD have a unique expansion of cytotoxic CD4+ T cells that correlates with reduced regulatory T cells. In response to vaccination, we observed rapid changes in gene expression associated with lipopolysaccharide responses by monocytes and NF-kB pathway activation in B cells, and an apparent expansion of a CD95+ class-switched memory B cell population that does not occur in patients with lower antigen-specific responses. Together, our findings reveal cellular and molecular factors that underpin variability in vaccine responses and define SAD in a broader spectrum of immune dysfunction.

immunology↗

bioRxiv2026

Recovering biological structure in sparse single-cell proteomics with GIRAFI

Single-cell proteomics (SCP) based on liquid-chromatography mass-spectrometry resolves protein-level cellular heterogeneity, but interpretation remains limited by detection-linked sparsity. SCP profiles continuous, peptide-derived intensities and has lower throughput than single-cell RNA sequencing, making denoising methods for large-scale, count-based transcriptomics difficult to apply. Here we present GIRAFI, a graph-informed statistical learning framework that imputes missing values and reveals reproducible cell states by constraining inference to dataset-aware, prior-knowledge-informed protein neighborhoods. We evaluated GIRAFI across SCP datasets spanning diverse biological/technical contexts. In masking-based recovery experiments and cell-type-specific protein-protein interaction inference, GIRAFI outperformed existing methods, and matched bulk proteomics comparisons corroborated recovery accuracy and ablations supported the graph-informed design. Beyond reduced replicate- and source-associated technical structure, GIRAFI recovered ground-truth cell-type annotations, improved cell state-resolved pathway analysis, and enabled trajectory inference consistent with known time courses. These results establish graph-constrained imputation as an effective strategy for improving SCP robustness, biological structure, interpretation, and cross-dataset comparability.

bioinformatics↗

bioRxiv2026

Telomere Dysfunction in Human Astrocytes Drives Acrocentric Chromosome Instability and Nucleolar Reorganization

Loss of p53 and Rb enables continued cell division despite progressive telomere erosion, ultimately triggering telomere crisis. While recent work has clarified mechanisms of chromatin bridge resolution, the longitudinal dynamics of structural damage through crisis remain incompletely understood. We transduced normal human astrocyte (NHA) cells with HPV18 E6/E7 and tracked them across extended population doublings. NHA E6/E7 cells showed progressive telomere shortening, anaphase bridges, and a growth plateau consistent with crisis. Multicolor FISH revealed subclonal chromosomal abnormalities largely invisible to short-read sequencing, with acrocentric chromosomes disproportionately affected: chromosome 13 was abnormal in over 92% of metaphases, and chromosomes 21 and 22 were similarly enriched. Translocations involving chromosome 13 were transient, replaced at later passages, while numerical aberrations persisted. Immunofluorescence revealed compact spherical nucleoli replaced by dispersed necklace-like structures, indicating a large-scale reorganization of nucleolar structure in response to telomere dysfunction. To determine whether these changes reflected altered chromosomal organization in the nucleus, we performed Hi-C and deployed KaryoScope, our alignment-free k-mer-based approach that recovers trans-chromosomal signal from repetitive acrocentric short arms. Inter-chromosomal contacts among nucleolar organizing region-bearing acrocentric chromosomes were markedly and persistently depleted in E6/E7 cells. Together, cytogenetic, imaging, and chromatin-contact data identify the nucleolus as a structural nexus linking telomere dysfunction to large-scale genomic rearrangement.

cancer biology↗

bioRxiv2026

Spatiotemporal profiling reveals the role of inflammatory niche in driving prostate cancer

Prostate cancer (PCa) is a lethal malignancy that displays profound resistance to immune checkpoint blockade (ICB), via mechanisms that are poorly understood. Here, we investigate the causes of CD8 T cell exhaustion and mechanisms of tumor progression in a PCa animal model, by single cell and spatial profiling, along a time course, following orthotopic transplantation of RB1/TP53/PTEN-deficient mouse organoids, competent to express neoantigens. The resulting tumors were castration resistant, consisting of largely basal and L2 malignant cells with upregulated inflammatory gene programs, and a specific spatial distribution of macrophages, cancer associated fibroblast (CAF) subtypes, and CD8 T-cells that was not previously reported. Using Zman-seq, we demonstrate that the effector function of tumor-infiltrating CD8 T cells was rapidly impaired as early as 24hrs after their infiltration, likely driven by signals from proinflammatory macrophages, Ccl2-Jak2+ inflammatory CAFs, and malignant basal cells, thus driving resistance to ICB. Interestingly, dual blockade of JAK1/2 and PD1 induced potent anti-tumor effects in tumor epithelial cells, decreased malignant epithelial cells and pro-inflammatory macrophages, and increased the proportion of normal (Pi16+) fibroblasts in the TME. Our results underscore the therapeutic potential of targeting JAK1/2 to enhance the efficacy of ICB, providing a rationale for clinical investigation of this combination in PCa.

cancer biology↗

bioRxiv2026

Intratumoral expression of JAML on NK cells is controlled by tumor microenvironment and MHC class I interaction

Junctional adhesion molecule-like (JAML) is an adhesion molecule known to promote T cell activation and T cell-mediated tumor rejection. In the current study, we show that JAML expression is enriched on mouse intratumoral NK cells compared with splenic NK cells. JAML+ NK cells were associated with tissue residency and co-expressed the immune checkpoints PD-1 and LAG3. JAML expression could be induced on splenic NK cells by IL-2 and further enhanced by IL-21. JAML levels were inversely correlated with inhibitory signaling, as NK cells expressing self-recognizing Ly49 receptors had reduced JAML expression, suggesting regulation of JAML expression by MHC class I molecules. Interaction with the JAML ligand CXADR also reduced JAML surface expression, indicating that tumor-mediated membrane stripping may represent a mechanism of immunoediting. Although JAML RNA transcripts were detectable in human NK cells, JAML protein was found only intracellularly. Together, these findings identify the JAML-CXADR interaction as a potential regulatory pathway in NK cell-mediated killing of tumors.

immunology↗

bioRxiv2026

Reduction of Complex Dynamic Touch information to a single stable perceptual feature

Dynamic touch requires the perceptual system to extract stable material properties from complex, evolving signals. We show that the tactile system relies on total spectral energy, the overall vibratory power of contact-induced transients, rather than waveform details or dominant frequency. Using a spectral energy compensation method, we conducted five psychophysical experiments in two degraded feedback scenarios: soft finger interfaces, where fingertip stiffness was reduced by an inflatable silicone bubble, and soft surface interactions, where participants tapped compliant foam surfaces. In both, participants reliably discriminated hardness and identified materials only when natural spectral energy profiles were preserved, independent of signal type. Judgments scaled systematically with energy level, and under conflicting cues, spectral energy dominated over frequency or compliance. These findings establish spectral energy as a governing cue in tactile perception, revealing a simple and robust computation akin to estimating mechanical work. This principle offers a generalizable framework for restoring touch in prosthetics, teleoperation, and immersive virtual environments. TeaserTotal spectral energy - not frequency - is the behaviorally relevant feature driving material perception through dynamic touch.

neuroscience↗

bioRxiv2026

Evolutionary rewiring of the DNM2 proline-rich domain drives lineage-specific constraints in erythropoiesis

Dynamin-2 (DNM2) is a ubiquitously expressed GTPase essential for membrane trafficking, yet how its evolution shapes tissue-specific functions remains unclear. Here, we generated a humanized mouse model in which murine Dnm2 is fully replaced by human DNM2. Human DNM2 rescues the embryonic lethality of Dnm2 deletion but cannot sustain postnatal hematopoiesis, leading to fatal hemolytic anemia, erythroblast maturation arrest, reticulocytosis, and macrothrombocytosis. The defect emerges selectively during postnatal bone marrow erythropoiesis and is associated with impaired transferrin receptor turnover, despite normal fetal liver hematopoiesis. Comparative proteomics reveals extensive species-specific rewiring of the DNM2 proline-rich domain (PRD) interactome, with GRB2 as the sole conserved partner. Dnm2 haploinsufficiency phenocopies the erythroid defect with reduced severity, indicating a dosage-sensitive loss-of-function mechanism. These findings identify PRDs as rapidly evolving context-dependent adaptors that tune ubiquitous proteins to tissue-specific demands, and highlight regulatory domains compatibility as a key consideration for humanized models and gene-replacement strategies.

genetics↗

bioRxiv2025

Using a wearable EEG device to examine age trends in sleep macro- and micro-architecture across adolescence

Adolescence is a period of distinct maturational changes in sleep physiology. Age-related trends in sleep physiology have been captured using laboratory-based polysomnography, a method limited by logistical burden and high cost. We tested the ability of the accessible Dreem3 sleep EEG headband to replicate established age effects in sleep physiology from late childhood through early adulthood. Typically developing youth (N=100, 9-26 years) completed 3-4 consecutive nights of at-home sleep recording. We estimated age-related trends across eight macro-architecture and 15 micro-architecture variables with known age effects, and conducted exploratory analyses of 24 additional variables. Dreem replicated established age trends, including increases in non-rapid eye movement (NREM) stage 2, and decreases in N3, time in bed, NREM delta and theta power with increasing age. Exploratory analysis revealed age effects in twelve variables, including decreases in spindle activity with increasing age. Sleep EEG wearables offer an accessible way to characterize sleep physiology development.

neuroscience↗

bioRxiv2025

How Ikaros and Aiolos homo- and heterodimers drive gene expression to ensure B cell development

Ikaros family transcription factors (TF) are major regulators of cell differentiation and function. They function as homo- and heterodimers, but the contribution of specific dimers to gene regulation is unknown. We investigated the function of Ikaros-Ikaros, Ikaros-Aiolos and Aiolos-Aiolos in B cell development, and show that the dimers are not equivalent. Ikaros homodimers are required in proB and large preB cells where they bind and regulate the expression of a surprisingly small number of genes related to cell adhesion and migration, predominantly as transcriptional repressors. In contrast, Ikaros-Aiolos heterodimers and Aiolos homodimers are required in small preB and immature IgM+ B cells to regulate 10-fold larger target gene repertoires involved in B cell receptor signaling and immune functions. Aiolos-containing dimers act mainly as repressors in small preB cells but activators in immature B cells, where Aiolos-Aiolos antagonizes Ikaros-Ikaros. Mechanistically, Aiolos binds more GGAA motifs with different flanking nucleotides than Ikaros, which depends on a single amino acid difference in zinc finger 3 of its DNA binding domain. These results illustrate how homo- and heterodimerization of homologous TF proteins can markedly impact binding specificity, target gene response and pathway modulation in cells of the same lineage.

immunology↗

bioRxiv2025

A Multivalent Pan-Ebolavirus Nanoparticle Vaccine Provides Protection in Rodents from Lethal Infection by Adapted Zaire and Sudan Viruses

Both Zaire ebolavirus (EBOV) and Sudan ebolavirus (SUDV) are members of the family Filoviridae, first discovered in 1976 during outbreaks of hemorrhagic fever in northern Zaire and southern Sudan. Ebola virus disease outbreaks are major public health events because of their potential for human-to-human transmission with high case fatality rates. Filoviral surface glycoproteins (GPs) are known to be the primary targets of neutralizing antibodies for protection from disease, and are the relevant immunogens in the two approved EBOV vaccines. Here we describe the design, electron microscopy-based structural characterization, and efficacy testing of a series of icosahedral I53-50 nanoparticles displaying prefusion trimeric EBOV and SUDV GP antigens. Mice and guinea pigs vaccinated with either a cocktail of EBOV-GP-I53-50 plus SUDV-GP-I53-50 or mosaic EBOV / SUDV-GP-I53-50 nanoparticles were protected from death or severe clinical signs of disease and weight loss, respectively, when challenged with either mouse-adapted EBOV or guinea pig-adapted SUDV.

immunology↗

bioRxiv2024

The farnesyl transferase inhibitor KO-2806 re-sensitizes relapsing tumors to RAS inhibition

Resistance remains a key issue limiting the clinical benefit from RAS-targeting therapeutic agents and necessitates combination approaches. We identify persistent mTORC1 activity in preclinical KRAS-mutant NSCLC and CRC models as a frequent, nongenetic driver of inherent and adaptive resistance to RAS inhibition. This vulnerability is targetable with the farnesyl transferase inhibitor KO-2806, which blocks mTORC1 activation via RHEB while sparing mTORC2 and its associated toxicities. The addition of KO-2806 to NSCLC or CRC tumors progressing on mutant-selective RAS inhibitors led to rapid and durable tumor regression. In contrast, switching from mutant-selective to pan-RAS inhibitor monotherapy resulted in only stasis of NSCLC tumors and had no effect on CRC tumor progression. Further, the addition of KO-2806 rescued sensitivity of progressing tumors to the pan-RAS inhibitor RMC-6236. Our results establish mTORC1 as an important mediator of escape from RAS inhibition and highlight KO-2806 as a promising RAS companion inhibitor in patients with prior RAS inhibitor exposure. SignificanceUtilizing in vivo models of tumor relapse, we define a subset of RAS inhibitor-resistant tumors in which vertical inhibition of MAPK is insufficient to restore sensitivity. By controlling parallel mTORC1 activity, KO-2806 may expand utility of RAS inhibitors in patients that have progressed on RAS-targeted therapy, regardless of inhibitor class.

cancer biology↗

bioRxiv2024

Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma

High-Grade Serous Ovarian Cancer (HGSOC) originates from fallopian tube (FT) precursors. However, the molecular changes that occur as precancerous lesions progress to HGSOC are not well understood. To address this, we integrated high-plex imaging and spatial transcriptomics to analyze human tissue samples at different stages of HGSOC development, including p53 signatures, serous tubal intraepithelial carcinomas (STIC), and invasive HGSOC. Our findings reveal immune modulating mechanisms within precursor epithelium, characterized by chromosomal instability, persistent interferon (IFN) signaling, and dysregulated innate and adaptive immunity. FT precursors display elevated expression of MHC-class I, including HLA-E, and IFN-stimulated genes, typically linked to later-stage tumorigenesis. These molecular alterations coincide with progressive shifts in the tumor microenvironment, transitioning from immune surveillance in early STICs to immune suppression in advanced STICs and cancer. These insights identify potential biomarkers and therapeutic targets for HGSOC interception and clarify the molecular transitions from precancer to cancer. STATEMENT OF SIGNIFICANCEThis study maps the immune response in fallopian tube precursors of high-grade serous ovarian cancer, highlighting localized interferon signaling, CIN, and competing immune surveillance and suppression along the progression axis. It provides an explorable public spatial profiling atlas for investigating precancer mechanisms, biomarkers, and early detection and interception strategies.

cancer biology↗

bioRxiv2024

Integrating spatial profiles and cancer genomics to identify immune-infiltrated mismatch repair proficient colorectal cancers

Predicting the progression of solid cancers based solely on genetics is challenging due to the influence of the tumor microenvironment (TME). For colorectal cancer (CRC), tumors deficient in mismatch repair (dMMR) are more immune infiltrated than mismatch repair proficient (pMMR) tumors and have better prognosis following resection. Here we quantify features of the CRC TME by combining spatial profiling with genetic analysis and release our findings via a spatially enhanced version of cBioPortal that facilitates multi-modal data exploration and analysis. We find that [~]20% of pMMR tumors exhibit similar levels of T cell infiltration as dMMR tumors and that this is associated with better survival but not any specific somatic mutation. These T cell-infiltrated pMMR (tipMMR) tumors contain abundant cells expressing PD1 and PDL1 as well as T regulatory cells, consistent with a suppressed immune response. Thus, like dMMR CRC, tipMMR CRC may benefit from immune checkpoint inhibitor therapy. SIGNIFICANCEpMMR tumors with high T cell infiltration and active immunosuppression are identifiable with a mid-plex imaging assay whose clinical deployment might double the number of treatment-naive CRCs eligible for ICIs. Moreover, the low tumor mutational burden in tipMMR CRC shows that MMR status is not the only factor promoting immune infiltration.

cancer biology↗

bioRxiv2024

Computationally designed mRNA-launched protein nanoparticle vaccines

Both protein nanoparticle and mRNA vaccines were clinically de-risked during the COVID-19 pandemic1-6. These vaccine modalities have complementary strengths: antigen display on protein nanoparticles can enhance the magnitude, quality, and durability of antibody responses7-10, while mRNA vaccines can be rapidly manufactured11 and elicit antigen-specific CD4 and CD8 T cells12,13. Here we leverage a computationally designed icosahedral protein nanoparticle that was redesigned for optimal secretion from eukaryotic cells14 to develop an mRNA-launched nanoparticle vaccine for SARS-CoV-2. The nanoparticle, which displays 60 copies of a stabilized variant of the Wuhan-Hu-1 Spike receptor binding domain (RBD)15, formed monodisperse, antigenically intact assemblies upon secretion from transfected cells. An mRNA vaccine encoding the secreted RBD nanoparticle elicited 5- to 28-fold higher levels of neutralizing antibodies than an mRNA vaccine encoding membrane-anchored Spike, induced higher levels of CD8 T cells than the same immunogen when delivered as an adjuvanted protein nanoparticle, and protected mice from vaccine-matched and -mismatched SARS-CoV-2 challenge. Our data establish that delivering protein nanoparticle immunogens via mRNA vaccines can combine the benefits of each modality and, more broadly, highlight the utility of computational protein design in genetic immunization strategies.

immunology↗

bioRxiv2024

A microglia-containing cerebral organoid model to study early life immune challenges

Prenatal infections and activation of the maternal immune system have been proposed to contribute to causing neurodevelopmental disorders (NDDs), chronic conditions often linked to brain abnormalities. Microglia are the resident immune cells of the brain and play a key role in neurodevelopment. Disruption of microglial functions can lead to brain abnormalities and increase the risk of developing NDDs. How the maternal as well as the fetal immune system affect human neurodevelopment and contribute to NDDs remains unclear. An important reason for this knowledge gap is the fact that the impact of exposure to prenatal risk factors has been challenging to study in the human context. Here, we characterized a model of cerebral organoids (CO) with integrated microglia (COiMg). These organoids express typical microglial markers and respond to inflammatory stimuli. The presence of microglia influences cerebral organoid development, including cell density and neural differentiation, and regulates the expression of several ciliated mesenchymal cell markers. Moreover, COiMg and organoids without microglia show similar but also distinct responses to inflammatory stimuli. Additionally, IFN-{gamma} induced significant transcriptional and structural changes in the cerebral organoids, that appear to be regulated by the presence of microglia. Specifically, interferon-gamma (IFN-{gamma}) was found to alter the expression of genes linked to autism. This model provides a valuable tool to study how inflammatory perturbations and microglial presence affect neurodevelopmental processes.

neuroscience↗

bioRxiv2024

The Jag2/Notch1 signaling axis promotes sebaceous gland differentiation and controls progenitor proliferation

The sebaceous gland (SG) is a vital appendage of the epidermis, and its normal homeostasis and function is crucial for effective maintenance of the skin barrier. Notch signaling is a well-known regulator of epidermal differentiation, and has also been shown to be involved in postnatal maintenance of SGs. However, the precise role of Notch signaling in regulating SG differentiation in the adult homeostatic skin remains unclear. While there is evidence to suggest that Notch1 is the primary Notch receptor involved in regulating the differentiation process, the ligand remains unknown. Using monoclonal therapeutic antibodies designed to specifically inhibit of each of the Notch ligands or receptors, we have identified the Jag2/Notch1 signaling axis as the primary regulator of sebocyte differentiation in homeostatic skin. Mature sebocytes are lost upon specific inhibition of the Jag2 ligand or Notch1 receptor, resulting in the accumulation of proliferative stem/progenitor cells in the SG. Strikingly, this phenotype is reversible, as these stem/progenitor cells re-enter differentiation when the inhibition of Notch activity is lifted. Thus, Notch activity promotes correct sebocyte differentiation, and is required to restrict progenitor proliferation.

developmental biology↗