Biology subjects

Yu, V.

Publications and source records attributed to Yu, V..

13 recordsLinked to original sources

bioRxiv2026

Mesothelial Plasticity Specifies a Pleural Immune Circuit that Orchestrates Lung Regeneration

Following injury, predisposition towards regenerative repair and away from degenerative remodeling is central to organismal health, yet the upstream determinants that instruct this fate choice remain poorly understood. Here, we identify mesothelial cell plasticity as a central determinant between regeneration and degeneration by comparing mouse models of pneumonectomy (PNX) versus chronic lung allograft dysfunction (CLAD). While mesothelial cells expand in both settings, following PNX, these cells undergo differentiation through multiple transitional states, culminating in an inflammatory population that orchestrates monocyte recruitment and subsequent tissue regeneration. In contrast, in CLAD, mesothelial cells enrich in an extracellular matrix-enriched state that lacks pro-regenerative signaling capacity. Using single cell epigenomic profiling and in vivo genetics, we define a mesothelium-specific TWIST1-CCL2 axis that governs mesothelium plasticity and signaling, monocyte recruitment and lung regrowth. Together, these findings demonstrate that context-dependent reprogramming of a pleural population, known to protect organs, can be leveraged to drive regeneration.

Developmental Biology↗

bioRxiv2026

Profilin-1 Deficiency Activates STING to Drive T Cell-Mediated Anti-Tumor Immunity in Breast Cancer

Dysregulation of actin-binding protein Profilin1 (Pfn1) in tumor cells has prominent impacts on the tumor-intrinsic aspects of tumor progression. However, whether and how modulation of Pfn1 expression in tumor cells influences immune surveillance in cancer is not known. We utilized an inducible CRISPR/Cas9 knockout (KO) model to first demonstrate that triggering Pfn1 depletion in breast cancer cells leads to features of genomic instability (polyploidy, micronuclei, and DNA damage) and intrinsic defects in both homologous-recombination- and non-homologous end-joining-mediated double-stranded DNA repair. Pfn1-deficient breast cancer cells exhibit nuclear envelope abnormality and the accumulation of cytosolic DNA. This leads to activation of the nucleic acid-sensing cGAS-STING pathway and the type-I interferon (IFN) response including STING-mediated upregulation of pro-inflammatory chemokines. In an immunocompetent mouse model of breast cancer, triggering Pfn1 loss selectively in tumor cells promotes an immunogenic tumor microenvironment marked by a striking increase in intratumoral presence of CD8 T cells, leading to a robust tumor regression. Pfn1 knockout-induced tumor regression requires an intact immune system and can also be reversed by CD8+ T cell depletion. Based on these findings, we conclude that Pfn1 loss in tumor cells leverages a type I IFN response to drive a T-cell-mediated anti-tumor response in breast cancer. These findings for the first time reveal promising therapeutic opportunities in targeting Pfn1-driven pathways to enhance immunotherapeutic outcomes in breast cancer. Significance StatementExpression of actin-binding protein Profilin-1 is frequently altered in cancer; yet how these changes impact the immune response against tumors is unclear. Here we show that triggering Profilin-1 depletion in breast cancer cells promotes features of genomic instability, defects in DNA repair, and cytosolic release of DNA. This activates the cGAS-STING pathway, triggering a type I interferon response and immune-cell-attracting signals that drive a CD8+ T cell-mediated anti-tumor immune response and tumor regression in vivo. Therefore, Profilin-1 could be a novel actionable target for achieving immunological benefit in breast cancer. On a broader level, our studies establish a conceptual framework of how dysregulation of actin cytoskeletal proteins can harness nuclear damage-sensing signaling to augment anti-tumor immune response in cancer.

cancer biology↗

bioRxiv2025

Assessing the Effectiveness of 3D-Printed Ceramic Structures for Coral Restoration: Growth, Survivorship, and Biodiversity Using Visual Surveys and eDNA

Coral reef degradation has spurred the development of artificial structures to mitigate losses in coral cover. These structures serve as substrates for coral transplantation, with the expectation that growing corals will attract reef-associated taxa -- while the substrates ability to directly support biodiversity is often neglected. We evaluated a novel 3D-printed modular tile made of porous terra cotta, designed with complex surface structures to enhance micro- and cryptic biodiversity, through a restoration project in Hong Kong. Over four years, we monitored 378 outplanted coral fragments using diver assessments and photography, while biodiversity changes were assessed through visual surveys and eDNA metabarcoding. Coral survivorship was high, with 88% of transplants surviving by the studys end. The restoration site exhibited greater fish and macroinvertebrate abundance compared to a nearby unrestored area. eDNA analyses revealed 23.5% higher eukaryote ASV richness at the restoration site than the unrestored site and a 13.3% increase relative to a natural reference coral community. This study highlights the tiles dual functionality: (1) supporting coral growth and (2) enhancing cryptic biodiversity, an aspect often neglected in traditional reef restoration efforts. Our findings underscore the potential of 3D-printed ceramic structures to improve both coral restoration outcomes and broader reef ecosystem recovery.

ecology↗

bioRxiv2025

Single-cell transcriptomic analysis of HPV-related multiphenotypic sinonasal carcinoma uncovers MYB-HPV association

Human papillomavirus (HPV)-related multiphenotypic sinonasal carcinoma (HMSC) is a rare tumor that morphologically resembles high grade adenoid cystic carcinoma (ACC), yet exhibits indolent clinical behavior. Both demonstrate MYB proto-oncogene upregulation, but HMSC lacks the MYB translocation typically seen in ACC. Transcriptional changes in HMSC tumors remain uncharacterized. We performed single-cell RNA sequencing (scRNA-seq) on a human HMSC tumor and compared expression profiles with published ACC and oropharyngeal squamous cell carcinoma (OPSCC) scRNA-seq datasets. Primary malignant cells from HMSC (n=134) and ACC (n=980) clustered separately, and HMSC lacked bicellular differentiation into luminal and myoepithelial cells, distinguishing it from ACC. A greater proportion of HMSC cells expressing HPV-related genes (HPVon) expressed MYB (83% vs. 62%, p=0.022) and MYB targets (p=6.4*10-6), suggesting an HPV-MYB association. This finding was validated in HPV-positive OPSCC, with 7/10 tumors showing MYB upregulation in HPVon versus HPVoff cells (p<0.05). A 264-gene signature from HPVon HMSC cells was also associated with worse prognosis in HPV+ OPSCC (p<0.003), suggesting an alternate role for HPV that has not been well characterized. Further validation of the HPV-MYB association and prognostically relevant HPV gene signature may improve patient stratification and therapeutic strategies in HPV-related malignancies.

cancer biology↗

bioRxiv2024

Discovery and engineering of the antibody response against a prominent skin commensal

The ubiquitous skin colonist Staphylococcus epidermidis elicits a CD8+ T cell response pre-emptively, in the absence of an infection1. However, the scope and purpose of this anti-commensal immune program are not well defined, limiting our ability to harness it therapeutically. Here, we show that this colonist also induces a potent, durable, and specific antibody response that is conserved in humans and non-human primates. A series of S. epidermidis cell-wall mutants revealed that the cell surface protein Aap is a predominant target. By colonizing mice with a strain of S. epidermidis in which the parallel {beta}-helix domain of Aap is replaced by tetanus toxin fragment C, we elicit a potent neutralizing antibody response that protects mice against a lethal challenge. A similar strain of S. epidermidis expressing an Aap-SpyCatcher chimera can be conjugated with recombinant immunogens; the resulting labeled commensal elicits high titers of antibody under conditions of physiologic colonization, including a robust IgA response in the nasal mucosa. Thus, immunity to a common skin colonist involves a coordinated T and B cell response, the latter of which can be redirected against pathogens as a novel form of topical vaccination.

microbiology↗

bioRxiv2023

MRTF promotes breast cancer cell motility through SRF-dependent upregulation of DIAPH3 expression

Dysregulated actin cytoskeleton gives rise to aberrant cell motility and metastatic spread of tumor cells. This study evaluates the effect of overexpression of wild-type vs functional mutants of MRTF-A on migration and invasion of breast cancer (BC) cells. Our studies indicate that SRFs interaction is critical for MRTF-A-induced promotion of both 2D and 3D cell migration, while the SAP-domain function is important selectively for 3D cell migration. Increased MRTF-A activity is associated with more effective membrane protrusion, a phenotype that is attributed predominantly to SRFs interaction of MRTF. We demonstrate formin-family protein mDia2 as an important mediator of MRTF-stimulated actin polymerization at the leading edge and cell migration. Multiplexed quantitative immunohistochemistry and transcriptome analyses of clinical BC specimens further demonstrate a positive correlation between nuclear localization of MRTF with malignant traits of cancer cells and enrichment of MRTF-SRF gene signature in pair-matched distant metastases vs primary tumors. In conclusion, this study establishes a novel mechanism of MRTF-dependent regulation of cell migration and provides evidence for the association between MRTF activity and increased malignancy in human breast cancer, justifying future development of a specific small molecule inhibitor of the MRTF-SRF transcriptional complex as a potential therapeutic agent in breast cancer. SIGNIFICANCEO_LIActin cytoskeletal dysregulation gives rise to metastatic dissemination of cancer cells. This study mechanistically investigates the impact of specific functional disruption of MRTF (a transcriptional co-factor of SRF) on breast cancer cell migration. C_LIO_LIThis study establishes a novel mechanism linking mDia2 to MRTF-dependent regulation of cell migration and provides clinical evidence for the association between MRTF activity and increased malignancy in human breast cancer. C_LIO_LIFindings from these studies justify future exploration of specific small molecule inhibitor of the MRTF-SRF transcriptional complex as a potential therapeutic agent in breast cancer. C_LI

cell biology↗

bioRxiv2023

Single Cell Transcriptomics-informed Induced Pluripotent Stem Cells Differentiation to Tenogenic Lineage

During vertebrate embryogenesis, axial tendons develop from the paraxial mesoderm and differentiate through specific developmental stages to reach the syndetome stage. While the main roles of signaling pathways in the earlier stages of the differentiation have been well established, pathway nuances in syndetome specification from the sclerotome stage have yet to be explored. Here, we show stepwise differentiation of human iPSCs to the syndetome stage using chemically defined media and small molecules that were modified based on single cell RNA-sequencing and pathway analysis. We identified a significant population of branching off-target cells differentiating towards a neural phenotype overexpressing Wnt. Further transcriptomics post-addition of a WNT inhibitor at the somite stage and onwards revealed not only total removal of the neural off-target cells, but also increased syndetome induction efficiency. Fine-tuning tendon differentiation in vitro is essential to address the current challenges in developing a successful cell-based tendon therapy.

developmental biology↗

bioRxiv2023

The Expression of Vesicular Glutamate Transporter 1 (VGLUT1) in the Rat Larynx and Implications for Laryngeal Proprioception

Proprioception plays a crucial role in laryngeal function. Further, dysfunctional proprioception likely contributes to disorders such as laryngeal dystonia, dysphagia and vocal fold paresis. Despite this, the physiology of laryngeal proprioception is not well-understood. Controversy remains over whether canonical proprioceptive organs, like muscle spindles (MS) even exist in the intrinsic laryngeal muscles (ILM). Vesicular Glutamate Transporter 1 (VGLUT1) expression has been described in the sensory afferents of MS. This studys primary aim is to determine whether the ILM contain MS using VGLUT1. This is a novel approach, as prior studies have relied on morphology and myosin composition to study this question. Secondarily, we describe the pattern of VGLUT1 expression in the rat larynx, Larynges of 62 Sprague-Dawley rats distributed across 5 age groups (P3, P8, P11, P14-15, and adult), were sectioned and immunostained for VGLUT1 and beta-tubulin III. Other markers (S46, GNAT3, PLC{beta}2, S100b, CGRP) were used to further characterize identified afferent innervation. Of 62 rats, MS were identified in the lateral thyroarytenoid muscles of just three P8 rats, and no golgi tendon organs (GTO) were seen. VGLUT1-positive intramuscular receptor-like entities were observed ILM, and VGLUT1-positive nerve endings were observed in the laryngeal mucosa, concentrated around the arytenoid cartilage. Employing VGLUT1 immunostaining, this study shows that rat intrinsic laryngeal muscles rarely express MS and do not express GTO. This leaves open the possibility that the larynx exhibits a unique proprioceptive apparatus. VGLUT1-positive intramuscular and mucosal structures provide candidates for an alternative system. Further defining the role of these sensory organs will increase our understanding of vocal fold function and ultimately lead to better treatment of vocal fold disorders. KEY POINTSO_LIDysfunctional laryngeal proprioception likely contributes to disorders such as laryngeal dystonia, dysphagia, and vocal fold paresis. Unlike proprioception of skeletal muscles, proprioception of the intrinsic laryngeal muscles is poorly understood. C_LIO_LIIn the present study we demonstrate that canonical proprioceptive organs (muscles spindles and Golgi tendon organs) are rarely expressed in the rat larynx, by studying the expression pattern of VGLUT1. C_LIO_LIWe also demonstrate the presence of other sensory innervation and structures which may contribute to an alternative proprioceptive circuitry, which requires further study. C_LI

neuroscience↗

bioRxiv2023

Establishment of beta cell heterogeneity via differential CpG methylation at Nnat

Aims/hypothesisBeta cells within the pancreatic islet represent a heterogenous population wherein individual sub-groups of cells make distinct contributions to the overall control of insulin secretion. These include a subpopulation of highly-connected hub cells, important for the propagation of intercellular Ca2+ waves. Functional subpopulations have also been demonstrated in human beta cells, with an altered subtype distribution apparent in type 2 diabetes. At present, the molecular mechanisms through which beta cell hierarchy is established are poorly understood. Changes at the level of the epigenome provide one such possibility which we explore here by focussing on the imprinted gene neuronatin (Nnat), which is required for normal insulin synthesis and secretion. MethodsSingle cell RNA-seq datasets were examined using Seurat 4.0 and ClusterProfiler running under R. Transgenic mice expressing eGFP under the control of the Nnat enhancer/promoter regions were generated for fluorescence-activated cell (FAC) sorting of beta cells and downstream analysis of CpG methylation by bisulphite and RNA sequencing, respectively. Animals deleted for the de novo methyltransferase, DNMT3A from the pancreatic progenitor stage were used to explore control of promoter methylation. Proteomics was performed using affinity purification mass spectrometry and Ca2+ dynamics explored by rapid confocal imaging of Cal-520 and Cal-590. Insulin secretion was measured using Homogeneous Time Resolved Fluorescence Imaging. ResultsNnat mRNA was differentially expressed in a discrete beta cell population in a developmental stage- and DNA methylation (DNMT3A)-dependent manner. Thus, pseudo-time analysis of embryonic data sets demonstrated the early establishment of Nnat-positive and negative subpopulations during embryogenesis. NNAT expression is also restricted to a subset of beta cells across the human islet that is maintained throughout adult life. NNAT+ beta cells also displayed a discrete transcriptome at adult stages, representing a sub-population specialised for insulin production, reminiscent of recently-described "{beta}HI" cells and were diminished in db/db mice. Hub cells were less abundant in the NNAT+ population, consistent with epigenetic control of this functional specialization. Conclusions/interpretationThese findings demonstrate that differential DNA methylation at Nnat represents a novel means through which beta cell heterogeneity is established during development. We therefore hypothesise that changes in methylation at this locus may thus contribute to a loss of beta cell hierarchy and connectivity, potentially contributing to defective insulin secretion in some forms of diabetes. Research in contextWhat is already known about this subject? - Neuronatin (Nnat/NNAT) is an imprinted gene in humans and mice and is required for glucose-stimulated insulin secretion in vivo - Pancreatic beta cells are functionally heterogeneous with specific highly-connected subpopulations known to coordinate islet wide Ca2+ dynamics - Functional subpopulations have been described in human beta cells and their distribution is altered in type 2 diabetes What is the key question? - Does NNAT mark a discrete subpopulation of functional beta cells and which epigenetic pathways coordinate its formation and maintenance? What are the new findings? - A subpopulation of NNAT+ beta cells is established prior to the first week of postnatal life in mice via de novo DNA methylation at the Nnat promoter - NNAT+ beta cells are transcriptionally highly differentiated and appear to be functionally specialised for insulin production, possibly corresponding to recently-described "{beta}HI" and "CD63hi" beta cells. NNAT is expressed in a subset of beta cells across the human islet, and its deficiency in human beta cells diminishes glucose-stimulated insulin secretion - NNAT+ cells are likelier to belong to the population of follower, rather than hub cells, consistent with a role in insulin production rather than glucose detection How might this impact on clinical practice in the foreseeable future? - Epigenome-modifying compounds may provide a way of enhancing beta cell function and the ensemble behaviour of the islet to stimulate insulin secretion

cell biology↗

bioRxiv2021

Directing iPSC Differentiation into iTenocytes using Combined Scleraxis Overexpression and Cyclic Loading

Regenerative therapies for tendon are falling behind other tissues due to the lack of an appropriate and potent cell therapeutic candidate. This study aimed to induce cell tenogenesis using stable Scleraxis (Scx) overexpression in combination with uniaxial mechanical stretch of mesenchymal stromal cells (MSCs) of different origins. Scleraxis (Scx) is the single direct molecular regulator of tendon differentiation known to date. Mechanoregulation is known to be a central element guiding tendon development and healing. Cells explored were bone marrow-derived (BM-)MSCs as well as MSCs differentiated from induced pluripotent stem cells (iMSCs). Mechanical stimulation combined with Scx overexpression resulted in morphometric and cytoskeleton-related changes, upregulation of early and late tendon markers, increased ECM deposition and alignment, and tenomodulin perinuclear localization in iMSCs, which was greater compared to BM-MSCs and controls. Our findings suggest that these cells can be differentiated into tenocytes and may be a better candidate for tendon cell therapy applications than BM-MSCs.

cell biology↗

bioRxiv2020

A model of traumatic brain injury using human iPSC-derived cortical brain organoids

Traumatic brain injury confers a significant and growing public health burden and represents a major environmental risk factor for dementia. Previous efforts to model traumatic brain injury and elucidate pathologic mechanisms have been hindered by complex interactions between multiple cell types, biophysical, and degenerative properties of the human brain. Here, we use high-intensity focused ultrasound to induce mechanical injury in 3D human pluripotent stem cell-derived cortical organoids to mimic traumatic brain injury in vitro. Our results show that mechanically injured organoids recapitulate key hallmarks of traumatic brain injury, phosphorylation of tau and TDP-43, neurodegeneration, and transcriptional programs indicative of energy deficits. We present high-intensity focused ultrasound as a novel, reproducible model of traumatic brain injury in cortical organoids with potential for scalable and temporally-defined mechanistic studies.

neuroscience↗

bioRxiv2020

The genomes of invasive coral Tubastraea spp. (Dendrophylliidae) as tool for the development of biotechnological solutions

Corals have been attracting huge attention due to the impact of climate change and ocean acidification on reef formation and resilience. Nevertheless, some species like Tubastraea coccinea and T. tagusensis have been spreading very fast replacing the native ones which affect the local environment and decrease biodiversity of corals and other organisms associated with them. Despite some focal efforts to understand the biology of these organisms, they remain understudied at the molecular level. This knowledge gap hinders the development of cost-effective strategies for both conservation and management of invasive species. In this circumstance, it is expected that genome sequencing would provide powerful insights that could lead to better strategies for prevention, management, and control of this and other invasive species. Here, we present three genomes of Tubastraea spp. in one of the most comprehensive biological studies of corals, that includes flow cytometry, karyotyping, transcriptomics, genomics, and phylogeny. The genome of T. tagusensis is organized in 23 chromosomes pairs and has 1.1 Gb, the T. coccinea genome is organized in 22 chromosome pairs and has 806 Mb, and the Tubastraea sp. genome is organized in 21 chromosome pairs and has 795 Mb. The hybrid assembly of T. tagusensis using short and long-reads has a N50 of 227,978 bp, 7,996 contigs and high completeness estimated as 91.6% of BUSCO complete genes, of T. coccinea has a N50 of 66,396 bp, 17,214 contigs and 88.1% of completeness, and of Tubastraea sp. has a N50 of 82,672 bp, 12,922 contigs and also 88.1% of completeness. We inferred that almost half of the genome consists of repetitive elements, mostly interspersed repeats. We provide evidence for exclusive Scleractinia and Tubastraea gene content related to adhesion and immunity. The Tubastraea spp. genomes are a fundamental study which promises to provide insights not only about the genetic basis for the extreme invasiveness of this particular coral genus, but to understand the adaptation flaws of some reef corals in the face of anthropic-induced environmental disturbances. We expect the data generated in this study will foster the development of efficient technologies for the management of coral species, whether invasive or threatened.

evolutionary biology↗

bioRxiv2017

Role for Ribosome-Associated Complex and Stress-Seventy subfamily B (RAC-Ssb) in integral membrane protein translation

Targeting of most integral membrane proteins to the endoplasmic reticulum is controlled by the signal recognition particle (SRP), which recognizes a hydrophobic signal sequence near the protein N-terminus. Proper folding of these proteins is monitored by the unfolded protein response, and involves protein degradation pathways to ensure quality control. Here, we identify a new pathway for quality control of major facilitator superfamily transporters that occurs before the first transmembrane helix-the signal sequence recognized by SRP-is made by the ribosome. Increased rates of translation elongation of the N-terminal sequence of these integral membrane proteins can divert the nascent protein chains to the ribosome-associated complex (RAC) and Stress-Seventy Subfamily B (Ssb) chaperones. We also show that quality control of integral membrane proteins by RAC-Ssb couples translation rate to the unfolded protein response, which has implications for understanding mechanisms underlying human disease and protein production in biotechnology.

molecular biology↗