Biology subjects

Tran, U.

Publications and source records attributed to Tran, U..

11 recordsLinked to original sources

bioRxiv2026

Amyloid/RNA Condensates with Germ Granule Characteristics Are Present in Rat Epididymal Spermatozoa and Exhibit Prion-Like Propagation Activity

Environmental exposures to the germline can alter its epigenome resulting in new traits being acquired by offspring. While the epigenetic carrier in mammalian spermatozoa remains unknown, studies in C.elegans show that amyloids and sperm-specific populations of germ granules, phase-separated biomolecular condensates enriched in RNA-binding proteins and small noncoding RNAs, transmit heritable epigenetic phenotypes to descendant cells. Here we discovered that rat epididymal spermatozoa contain germ granule-like condensates in the head perforatorium, a cytoplasmic derived structure that participates in early post-fertilization events. The perforatoria condensates contain evolutionarily conserved germ granule markers and small noncoding RNAs and are enriched in amyloid, including those of the clinically relevant amyloidogenic proteins androgen receptor (AR) and TDP43. Further, perforatoria extracts exhibit prion-like propagation behavior by functioning as molecular seeds to template amyloid assembly in recombinant AR and TDP43. We propose that nature has conserved sperm germ granule-like structures throughout evolution to allow an organism to respond and adapt to a changed environment by passing environmentally encoded information to the embryo via a non-Mendelian protein-based mechanism of inheritance.

cell biology↗

bioRxiv2026

Biocompatible designated Resin-3D-printed polymers exhibit reproductive toxicity prevented by Parylene-C

Resin three-dimensional (3D) printing is an increasingly popular manufacturing and prototyping method used to create microphysiological systems (MPS), but resin cytotoxicity significantly hinders its adoption, especially when sensitive cell models are incorporated. The mammalian oocyte and early preimplantation embryo consist of cells that are highly sensitive to toxicants and thus represent stringent cell-based models for biocompatibility testing. We developed a Multi-Endpoint Oocyte Safety Assay (MEIOSA) to evaluate the biocompatibility of four ISO 10993 biocompatible BioMed resins (Clear, Durable, Elastic 50A, and Flex 80A). MEIOSA assesses the viability, morphology, meiotic stage, and meiotic spindle morphology of the oocyte after in vitro maturation (IVM). Oocytes were in vitro matured in plate inserts 3D printed with the four BioMed resins. Oocytes cultured in rigid resins (Clear and Durable) or elastomeric resins (Elastic 50A, and Flex 80A) exhibited impaired meiotic progression and complete oocyte degeneration, respectively, relative to controls cultured in polystyrene which matured normally. To determine whether such cytotoxicity could be prevented, we coated the resin inserts with a 5 {micro}m impermeable Parylene-C (PC) barrier. PC coating completely rescued the degeneration and meiotic maturation defect phenotypes for all resins. Remarkably, when the most cytotoxic material (Flex 80A) was coated with PC, the resulting eggs were fertilization-competent and produced embryos capable of normal preimplantation development via in vitro fertilization. Our findings demonstrate that standardized viability-based biocompatibility tests do not identify cytotoxic effects for all cell types and establish MEIOSA as a high sensitivity test model to robustly evaluate biomaterial biocompatibility. Furthermore, PC coating prevents the toxic effects of all resin-3D-printed materials tested, opening up a new toolbox to create MPS compatible with reproductive, and by extension, other sensitive cell cultures. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/730268v1_ufig1.gif" ALT="Figure 1"> View larger version (71K): org.highwire.dtl.DTLVardef@18fab44org.highwire.dtl.DTLVardef@1352e5forg.highwire.dtl.DTLVardef@77889forg.highwire.dtl.DTLVardef@1aabd89_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Inflammatory Stromal Aging in Ulcerative Colitis and Colitis-Associated Cancer

ABSTRACTUlcerative colitis is a chronic inflammatory bowel disease that can progress from dysplasia to cancer. Inflammatory responses are critical drivers in this process, typically triggered by epithelial lesions and the ensuing infiltration of microbiota into the interstitial layer. Here, we focus on the pro-inflammatory state of the interstitial fibroblasts, which promotes immune infiltration and augments disease progression. The study aims to provide a mechanistic link how fibroblasts of the colitis-associated microenvironment integrate inflammatory signals, microbial infiltration and cellular memory. To this end, we investigated a large number of primary colon fibroblasts obtained from normal, colitis and colon cancer samples using a range of in vitro approaches and an in vivo co-inoculation cancer model. mRNA sequencing analysis identified that the disease-associated fibroblasts are exhibit a cellular inflammatory status, which involves the injury-induced senescence pathway. Using CXCL8, a potent chemokine upregulated in colitis and cancer colon fibroblasts, as a paradigm, this inflammatory status is triggered by the activation of the NF{kappa}B signaling via immune-derived cytokines (TNF, IL-1{beta}), bacterial signals (LPS) and the microbiome itself using mycoplasma as a paradigm. Finally, iPSC reprogramming studies indicate that fibroblasts from ulcerative colitis retain an epigenetic memory that sustains elevated CXCL8 expression. Together, our findings demonstrate that the senescence associated secretory phenotype of colon fibroblasts is a robust indicator for inflammation-driven colon tumorigenesis.

cancer biology↗

bioRxiv2026

SPATIALLY PATTERNED PODOCYTE STATE TRANSITIONS COORDINATE AGING OF THE GLOMERULUS

BackgroundWith the US population living longer, the risk, incidence, prevalence and severity for chronic kidney diseases become more abundant. Glomerular diseases are the leading cause for chronic and end-stage kidney disease. Yet, the cellular responses and the underlying mechanisms of progressive glomerular disease, which ultimately leads to glomerulosclerosis and loss of kidney function with advancing age, are poorly understood. MethodsKidneys of young (4 months-old), middle-aged (20 months-old) and aged (24 months-old) mice were separated into outer cortex and juxta-medullary region and processed for single nuclei transcriptomics. Focusing on the aging glomerulus data were analyzed using a state-of-the-art analysis pipeline dissecting out the cellular age- and kidney region-specific responses. ResultsGlobal analysis of the transcriptome reveals regional-specific differences that are detectable across multiple cell types exemplified by the expression of Napsa as a bona-fide juxta-medullary marker. In contrast aging led to rather cell type-specific responses. In the glomerulus, healthy podocytes were characterized by expression of canonical podocyte genes; conversely the senescent, aged podocytes were characterized by the down-regulation of canonical podocyte genes and the emergence of inflammatory and senescent signatures. Interestingly, these senescent podocytes were primarily located in the juxtamedullary region suggesting that juxtamedullary podocytes are more sensitive. Yet, instead of aging being defined by distinct cell states, the profiles, as well as ligand-receptor and pseudotime analyses suggest that podocytes aging is selective and coordinated, not universal degeneration. This was different to the other glomerular cell types, parietal epithelial cells, glomerular endothelial cells and mesangial cells. While they also as existed in different subpopulations, they exhibited little regional-, or age-depended changes. Finally proximal tubular aging manifested itself as discrete cellular states. ConclusionsThe single nuclei transcriptomics of the aging kidney provides a mechanistic explanation for regional susceptibility of nephrons and suggests that the future therapeutic strategies need to consider the cellular and spatial complexity of the glomerulus.

bioinformatics↗

bioRxiv2026

A single cell atlas of mouse podocytes upon injury identifies kidney zone-dependent responses.

There are regional differences in the kidney in focal segmental glomerulosclerosis (FSGS) where podocyte injury is more severe in the juxta-medulla (JM) compared to the outer cortex (OC). Single nuclear RNA-sequencing was performed to determine any regional transcriptomic differences. 1055 differentially expressed genes (DEGs) were identified between healthy OC and JM podocytes. Of 53 podocyte canonical genes, only Magi1 and Mapt, and Npnt were higher in healthy OC and JM podocytes respectively. Hallmark pathway analysis showed that in normal mice, healthy JM podocytes are enriched for oxidative phosphorylation, glycolysis and fatty acid metabolism compared to OC podocytes. At day 7 in an experimental FSGS model induced in mice with a cytopathic anti-podocyte antibody, 226 and 225 DEGs were higher in OC and JM podocytes respectively, and 166 overlapped. Five podocyte subclusters were identified, of which the most severe (subcluster 4) was enriched for a senescence phenotype, including the p53 pathway. Inducing FSGS in mice in which p53 was deleted specifically in podocytes had lower glomerular injury compared to diseased wildtype mice. These results are consistent with differences in podocytes in the OC and JM, which might underlie regional differences in FSGS.

bioinformatics↗

bioRxiv2025

A poly(A) isoform-aware single-cell and spatial atlas defines fibroblast niches in the human bladder

Bladder function relies on coordinated interactions among epithelial, stromal, vascular, and neural compartments, but high-resolution molecular and spatial features remain undefined. We generated a publicly accessible, poly(A) isoform-aware single-nucleus and spatial reference of the adult human bladder spanning four anatomical regions and both sexes. Integrating 74,694 snRNA-seq profiles with 168,476 Xenium-resolved cells, we identified 22 cell types and 23,489 polyadenylation sites, with isoform usage improving stromal resolution beyond gene expression alone. Spatial mapping revealed layered fibroblast niches aligned with epithelial, vascular, and neural structures, supported by Visium data. This multimodal reference links isoform regulation to anatomical context and provides a reusable framework for cell-type annotation, cross-study integration, and analyses of bladder physiology and disease.

molecular biology↗

bioRxiv2025

Senescence-Linked Fibrosis in the Aging Human Ovary Revealed by p16-Based Histological Profiling and Spatial Transcriptomics

Cellular senescence is implicated as a driver of ovarian aging, but senescent cells in the human postmenopausal ovary remain poorly defined. Using spatially resolved p16INK4a protein expression, a canonical senescence marker, we identified and mapped senescent cells in postmenopausal ovaries. We integrated p16 immunohistochemistry, multiplexed immunofluorescence, spatial transcriptomics, and AI-guided digital pathology to map senescent microenvironments. p16-positive cells formed discrete stromal, vascular, and cyst-associated clusters that increased with age and were enriched for macrophages and myofibroblast-like cells. Wholetranscriptome profiling of 92 spatial regions uncovered a 32-gene p16-associated signature, BuckSenOvary, that distinguished p16-positive regions across cortex and medulla. BuckSenOvary is characterized by suppression of cell-cycle regulators and activation of inflammatory and extracellular-matrix remodelling genes. AI-based collagen matrix analysis confirmed that p16-positive regions exhibit more architecturally complex collagen, demonstrating that focal senescent microenvironments are fibro-inflammatory. These findings position senescent ovarian niches as therapeutic targets to preserve ovarian function.

cell biology↗

bioRxiv2025

Lysine acetylation plays a role in RNA binding protein-regulated alternative pre-mRNA splicing.

Alternative pre-mRNA splicing allows one gene to encode multiple spliced messenger RNAs and, in turn, multiple proteins from a single gene transcript. This process is tightly regulated by cis elements within the pre-mRNA and trans-acting RNA binding proteins that recognize and bind to these elements, thus influencing the spliceosome assembly at adjacent splice sites. Thus, chemical modifications in either the cis-elements or trans factors or both can significantly alter splicing patterns and, thereby, the cellular proteome. Recent studies highlight that many RNA binding proteins (RBPs) are modified at multiple lysine side chains via acetylation, which neutralizes the formal positive charge and disrupts RPBs ability to participate in RNA recognition, binding and protein-protein interactions. This suggests that lysine acetylation of RPBs may be a novel mode of eukaryotic gene regulation during pre-mRNA processing. To test this, we used the well-characterized polypyrimidine tract binding protein (which is acetylated at several lysine side chains) as a model system to investigate the role of reversible RBP acetylation in regulating alternative-pre mRNA splicing. Using multiple sequence analysis, structure-based electrostatic modeling of RNA-protein interactions, and multi-site glutamine (acetyllysine mimic) and arginine (deacetyllysine mimic) mutants, we show for the first time that for a subset of PTBP1-regulated exons, acetylation at RNA-interacting lysine side chains significantly alters PTBP1 splicing activity.

biochemistry↗

bioRxiv2024

BICC1 Interacts with PKD1 and PKD2 to Drive Cystogenesis in ADPKD

Autosomal dominant polycystic kidney disease (ADPKD) is primarily of adult-onset and caused by pathogenic variants in PKD1 or PKD2. Yet, disease expression is highly variable and includes very early-onset PKD presentations in utero or infancy. In animal models, the RNA-binding molecule Bicc1 has been shown to play a crucial role in the pathogenesis of PKD. To study the interaction between BICC1, PKD1 and PKD2 we combined biochemical approaches, knockout studies in mice and Xenopus, genetic engineered human kidney cells carrying BICC1 variants as well as genetic association studies in a large ADPKD cohort. We first demonstrated that BICC1 physically binds to the proteins Polycystin-1 and -2 encoded by PKD1 and PKD2 via distinct protein domains. Furthermore, PKD was aggravated in loss-of-function studies in Xenopus and mouse models resulting in more severe disease when Bicc1 was depleted in conjunction with Pkd1 or Pkd2. Finally, in a large human patient cohort, we identified a sibling pair with a homozygous BICC1 variant and patients with very early onset PKD (VEO-PKD) that exhibited compound heterozygosity of BICC1 in conjunction with PKD1 and PKD2 variants. Genome editing demonstrated that these BICC1 variants were hypomorphic in nature and impacted disease-relevant signaling pathways. These findings support the hypothesis that BICC1 cooperates functionally with PKD1 and PKD2, and that BICC1 variants may aggravate PKD severity highlighting RNA metabolism as an important new concept for disease modification in ADPKD.

genetics↗

bioRxiv2021

Ureter single-cell and spatial mapping reveal cell types, architecture, and signaling networks

Tissue engineering offers a promising treatment strategy for ureteral strictures, but its success requires an in-depth understanding of the architecture, cellular heterogeneity, and signaling pathways underlying tissue regeneration. Here we define and spatially map cell populations within the human ureter using single-cell RNA sequencing, spatial gene expression, and immunofluorescence approaches. We focused on the stromal and urothelial cell populations to enumerate distinct cell types composing the human ureter and inferred potential cell-cell communication networks underpinning the bi-directional crosstalk between these compartments. Furthermore, we analyzed and experimentally validated the importance of Sonic Hedgehog (SHH) signaling pathway in adult stem cell maintenance. The SHH-expressing basal cells supported organoid generation in vitro and accurately predicted the differentiation trajectory from basal stem cells to terminally differentiated umbrella cells. Our results highlight essential processes involved in adult ureter tissue homeostasis and provide a blueprint for guiding ureter tissue engineering.

developmental biology↗

bioRxiv2021

Upregulated PD-1 Signaling is an Important Antagonist to Glomerular Health in Aged Kidneys

Kidney aging and its contribution to disease and its underlying mechanisms are not well understood. With an aging population, kidney health becomes an important medical and socioeconomic factor. We previously showed that podocytes isolated from aged mice exhibit increased expression of Programed Cell Death Protein 1 (PD-1) surface receptor and its two ligands (PD-L1, PD-L2). PDCD1 transcript increases with age in micro-dissected human glomeruli, which correlates with lower eGFR, and higher segmental glomerulosclerosis and vascular arterial intima to lumen ratio. In vitro studies in podocytes demonstrate a critical role for PD-1 signaling in cell survival and induction of a Senescence-Associated Secretory Phenotype (SASP). To prove PD-1 signaling is critical to podocyte aging, aged mice were injected with anti-PD-1 antibody (aPD-1ab). Treatment significantly improved the aging phenotype in both kidney and liver. In the glomerulus, it increased the life-span of podocytes, but not parietal epithelial, mesangial or endothelial cells. Transcriptomic and immunohistochemistry studies demonstrate that anti-PD-1 treatment improved the health-span of podocytes. It restored the expression of canonical podocyte genes, transcription factors and gene regulatory networks, increased cellular metabolism signatures and lessened SASPs. These results suggest a critical contribution for increased PD-1 signaling towards both kidney and liver aging.

cell biology↗