Biology subjects

Noel, T.

Publications and source records attributed to Noel, T..

8 recordsLinked to original sources

bioRxiv2025

EZH2-TTP-mTORC1 Axis Drives Phenotypic Plasticity and Therapeutic Vulnerability in Lethal Prostate Cancer

Phenotypic plasticity is a recognized mechanism of therapeutic resistance in prostate cancer (PCa), however current knowledge of driver mechanisms and therapeutic interventions are limited. Using genetically engineered mouse models (GEMMs) devoid of Pten and Rb1, we previously demonstrated the chromatin reprogramming factor enhancer of zeste homolog 2 (EZH2) as an important regulator of alternative transcription programs promoting phenotypic plasticity. Here, using a multi-omics approach we demonstrate that EZH2 regulates multilineage cell states dependent on the RNA binding protein Tristetraprolin (TTP) that mediates RNA stability and activation of translation. Combined chemical inhibition of EZH2 and PI3K/mTORC1 resulted in superior anti-tumor activity in murine and human phenotypic plastic models and was most significant when this combination was used with castration or enzalutamide. Together, these data indicate phenotypic plasticity dependence on coordination between EZH2, TTP and mTORC1 signaling that represent novel therapeutic dependencies for this lethal PCa phenotype. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/669104v1_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@5ef713org.highwire.dtl.DTLVardef@af402forg.highwire.dtl.DTLVardef@19eedcforg.highwire.dtl.DTLVardef@10ee421_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance StatementEZH2 plays a key role in driving cell state transitions in neuroendocrine prostate cancer (NEPC), guiding cancer cells towards a more aggressive, therapy-resistant cell type. This transformation creates a specific vulnerability, as NEPC cells become highly reliant on both EZH2 and PI3K/mTORC1-translation signaling. Targeting this dependency, we demonstrate that combining EZH2 with PI3K/mTORC1 inhibition provides effective suppression of NEPC cell growth, offering a promising therapeutic strategy for treating this challenging and aggressive prostate cancer subtype.

cancer biology↗

bioRxiv2025

Engineering Large-Scale and Innervated Functional Human Gut for Transplantation

A confined culture system (CCS) establishes methods to generate complex functional human gastrointestinal tissues. This approach yields large-scale innervated small intestinal, colonic and gastric organoids with an elongated tubular shape for both in vitro and in vivo studies. Transcriptomic and electrophysiological data demonstrate the co-development of a functional de novo enteric nervous system, which is absent from conventional organoids. When compared to traditional methods, CCS derived small intestinal, colonic and gastric organoids reached maturation supporting transplantation in half of the time, resulting in enhanced engraftment rates and sizes. Murine luminal content exposure within CCS organoids in vivo further augmented function, supporting the potential translational benefits required to model complex intestinal diseases. In summary, the CCS methodology simplifies current protocols while adding complexity and expediting the generation of clinically relevant functional gut tissues.

bioengineering↗

bioRxiv2024

Single RNA molecule resolution spatial imaging of immunotherapy response in triple negative breast tumors harboring tertiary lymphoid structures

Cancer immunotherapy trials have had variable success, prompting a search for biomarkers of response. Tertiary lymphoid structures (TLS) have emerged as prognostic for multiple tumor types. These ectopic immunological bodies resemble secondary lymphoid organs with segregated B and T cell zones, but they are heterogeneous in their organization and cellular composition. These features have consequences in terms of prognostication and disease clearance, so there is interest in what drives TLS heterogeneity and corresponding immunological responses. We applied single RNA molecule resolution imaging to study biopsies from triple negative breast tumors harboring TLS where the biopsies were taken longitudinally, prior to therapy, after pembrolizumab and after pembrolizumab with radiation therapy. We developed a computational framework to identify TLS and tumor beds and to align spatial trajectories between the immune and malignant structures for systematic analyses. We identified two tumor types based on immune infiltration profiles in the tumor bed. Immune "infiltrated" tumors were eliminated after pembrolizumab, while "non-infiltrated" tumors saw gains in effector T cells and myeloid cells after pembrolizumab and were cleared after pembrolizumab with RT. TLS from infiltrated tumors had better separation of B and T cell zones and had higher expression of immunoreactivity gene pathways in most cell types. Further, malignant cell MHC expression was higher in the tumor beds of infiltrated tumors, providing one plausible mechanism for the groupings. In non-infiltrated tumors, classical dendritic cells enter the tumor bed from TLS proximal zones after pembrolizumab and bring transcription of the CXCL9 chemokine, which can recruit T cells and promote T cell effector phenotypes and was higher in infiltrated tumors at baseline.

genomics↗

bioRxiv2023

Rapamycin and caspofungin show synergistic antifungal effects in caspofungin-susceptible and caspofungin-resistant Candida strains in vitro

ObjectivesCaspofungin is an echinocandin antifungal agent that inhibits synthesis of glucan required for the fungal cell wall. Resistance is mediated by mutation of Fks1 glucan synthase, among which S645P is the most common resistance-associated polymorphism. Rapamycin is a macrolide that inhibits the mechanistic target of rapamycin (mTOR) protein kinase activity. This study investigated the interaction between rapamycin and caspofungin in inhibiting the growth of wild type Candida albicans and Fks1 S645P mutant clinical isolate and wild type Candida lusitaniae and genetically engineered isogenic strain with Fks1 S645P mutation at equivalent position. MethodsInteractions between caspofungin and rapamycin were evaluated using the microdilution checkerboard method in liquid medium. The results were analysed using the fractional inhibitory concentration (FIC) index and the response surface (RS) analysis according to the Bliss model. ResultsSynergy between rapamycin and caspofungin was shown for C. albicans and C. lusitaniae strains by RS analysis of the checkerboard tests. Synergy was observed in strains sensitive and resistant to caspofungin. Weak subinhibitory concentrations of rapamycin were sufficient to restore caspofungin susceptibility. ConclusionsWe report here for the first time synergy between caspofungin and rapamycin in Candida species. Synergy was shown for strains susceptible and resistant to caspofungin. This study highlights the role of the TOR pathway in sensing antifungal-mediated cell wall stress and in modulating the cellular response to echinocandins in Candida yeasts.

microbiology↗

bioRxiv2021

High Resolution Slide-seqV2 Spatial Transcriptomics Enables Discovery of Disease-Specific Cell Neighborhoods and Pathways

High resolution spatial transcriptomics is a transformative technology that enables mapping of RNA expression directly from intact tissue sections; however, its utility for the elucidation of disease processes and therapeutically actionable pathways remain largely unexplored. Here we applied Slide-seqV2 to mouse and human kidneys, in healthy and in distinct disease paradigms. First, we established the feasibility of Slide-seqV2 in human kidney by analyzing tissue from 9 distinct donors, which revealed a cell neighborhood centered around a population of LYVE1+ macrophages. Second, in a mouse model of diabetic kidney disease, we detected changes in the cellular organization of the spatially-restricted kidney filter and blood flow regulating apparatus. Third, in a mouse model of a toxic proteinopathy, we identified previously unknown, disease-specific cell neighborhoods centered around macrophages. In a spatially-restricted subpopulation of epithelial cells, we also found perturbations in 77 genes associated with the unfolded protein response (UPR). Our studies illustrate and experimentally validate the utility of Slide-seqV2 for the discovery of disease-specific cell neighborhoods. One-Sentence SummaryHigh resolution Slide-seqV2 spatial transcriptomics in human and mouse kidneys.

molecular biology↗

bioRxiv2020

HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes

Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of up to 100 chosen genes in single cells. HyPR-seq involves hybridizing DNA probes to RNA, distributing cells into nanoliter droplets, amplifying the probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects nonpolyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome scRNA-seq, making HyPR-seq a powerful method for targeted RNA profiling in single cells.

genomics↗

bioRxiv2018

Hexokinase and glucokinases are essential for fitness and virulence in the pathogenic yeast Candida albicans

Metabolic flexibility promotes infection and commensal colonization by the opportunistic pathogen Candida albicans. Yeast cell survival depends upon assimilation of fermentable and non-fermentable locally available carbon sources. Physiologically relevant sugars like glucose and fructose are present at low level in host niches. However, because glucose is the preferred substrate for energy and biosynthesis of structural components, its efficient metabolization is fundamental for the metabolic adaptation of the pathogen. We explored and characterized the C. albicans hexose kinase system composed of one hexokinase (CaHxk2) and two glucokinases (CaGlk1 and CaGlk4). Using a set of mutant strains, we found that hexose phosphorylation is mostly assured by CaHxk2, which sustains growth on hexoses. Our data on hexokinase and glucokinase expression point out an absence of cross regulation mechanisms at the transcription level and different regulatory pathways. In the presence of glucose, CaHxk2 migrates in the nucleus and contributes to the glucose repression signaling pathway. In addition, CaHxk2 participates to oxidative, osmotic and cell wall stress responses, while glucokinases are overexpressed under hypoxia. Hexose phosphorylation is a key step necessary for filamentation, that is affected in the hexokinase mutant. Virulence of this mutant is clearly impacted in the Galleria mellonella and macrophage models. Filamentation, glucose phosphorylation and stress response defects of the hexokinase mutant prevent host killing by C. albicans. By contributing to metabolic flexibility, stress answer response and morphogenesis, hexose kinase enzymes play an essential role in the virulence of C. albicans.\n\nAuthor summaryThe pathogenic yeast C. albicans is both a powerful commensal and pathogen of humans that can infect wide range of organs and body sites. To grow in its host and establish an infection, the pathogen must assimilate carbon from these heterogenous environments. C. albicans regulates central carbon metabolism in a niche-specific manner, activating alternatively gluconeogenesis, glyoxylate cycle and the glycolytic metabolism. For yeast and other microorganisms, glucose is the preferred carbon and energy source and its accurate detection and metabolism is essential. However, the glycolytic hexose kinase system has not been investigated yet in C. albicans. In this report, we showed that hexokinase and glucokinases contribute to the fitness and virulence of C. albicans. We revealed the main metabolic role of the hexokinase CaHxk2 which impacts on growth, glucose signalling, morphological transition and virulence. However, glucokinases contribute to the anoxic response and their implication in regulation processes is suggested.

microbiology↗

bioRxiv2018

Dual RNAseq of human leprosy lesions identifies bacterial determinants linked to host immune response

To understand how the interaction between an intracellular bacterium and the host immune system contributes to outcome at the site of infection, we studied leprosy, a disease that forms a clinical spectrum, in which progressive infection by the intracellular bacterium Mycobacterium leprae is characterized by the production of type | IFNs and antibody production. We performed dual RNAseq on patient lesions, identifying a continuum of distinct bacterial states that are linked to the host immune response. The bacterial burden, represented by the fraction of bacterial transcripts, correlates with a host type | IFN gene signature, known to inhibit antimicrobial responses. Second, the bacterial transcriptional activity, defined by the bacterial mRNA/rRNA ratio, links bacterial heat shock proteins with the BAFF-BCMA host antibody response pathway. Our findings provide a platform for interrogation of host and pathogen transcriptomes at the site of infection, allowing insight into mechanisms of inflammation in human disease.

microbiology↗