Biology subjects

Dufresne, M.

Publications and source records attributed to Dufresne, M..

7 recordsLinked to original sources

bioRxiv2026

Multimodal Molecular Mapping of the Vasculature in Human Cortex Reveals Lipid Markers of Cerebral Amyloid Angiopathy

Cerebral amyloid angiopathy (CAA) commonly co-occurs with Alzheimers disease (AD), yet the molecular changes that accompany vascular {beta}-amyloid deposition in human tissue remain incompletely defined. Herein, we use a novel imaging approach that combines matrix-assisted laser desorption/ionization imaging mass spectrometry (IMS) with immunofluorescence microscopy on the same sections of postmortem human frontal cortex to map the lipid microenvironment of leptomeningeal vasculature in cases with and without CAA. Autofluorescence-guided regions-of-interest were imaged by IMS in both negative and positive ion modes and registered to post-IMS-acquired microscopy images. Immunofluorescence microscopy using collagen IV, -smooth muscle actin (SMA), and thiazine red enabled automated segmentation of total, amyloidpositive, and amyloid-negative vasculature regions. A CAA index, the ratio of amyloid-positive area to total vasculature area in a region imaged by IMS, was used to define vasculature and classify each case into having CAA, or CAA-present and not having CAA, or CAA-absent. An interpretable machine learning approach (XGBoost models with Shapley additive explanations for interpretation) was trained on pixel-level spectra and identified lipid signatures of vascular identity shared across groups as well as class-specific marker candidates that distinguished CAA-present from CAA-absent vasculature. CAA-present vessels were enriched for gangliosides (e.g., GM1), whereas CAA-absent vessels were characterized by higher contributions from phosphatidylserines (e.g., long-chain polyunsaturated PS species). Univariate differences were inconsistent between the two groups, but multivariate models in negative mode yielded stable discriminatory features. These results define spatial lipid correlates of vascular amyloid pathology in the human brain and establish a multimodal framework for mechanistically linking lipid metabolism, vascular integrity, and CAA in AD.

neuroscience↗

bioRxiv2025

IsoSpace: Chemistry-Informed Dimensionality Reduction and Automated Isotope Candidate Detection in Imaging Mass Spectrometry

Imaging mass spectrometry (IMS) experiments simultaneously map thousands of ion species throughout tissue. Its high-dimensionality makes human interpretation difficult and dimensionality reduction (DR) methods are common to facilitate exploration. Traditional DR methods, such as principal component analysis (PCA), are general approaches, designed to work across application domains. They are usually unaware of, and unable to exploit correlations specific to a particular measurement type. Compression-focused, such blind methods often deliver physically impossible latent patterns or make feature combinations that confuse rather than aid human understanding. We introduce a novel chemistry-informed DR method, IsoSpace, with built-in awareness of mass spectrometry-relevant patterns. Although generalizable, IsoSpace substantiates chemistry-informed as sensitive to potential isotopic relation-ships. Like traditional DR methods, IsoSpace groups mass-over-charge (m/z)-features to deliver a low-dimensional representation of IMS data. Unlike traditional methods, IsoSpace ensures that retrieved latent patterns constitute potential isotopic families. IsoSpaces decomposition facilitates IMS interpretation at the molecular species rather than ion species level, implicitly automating isotope candidate detection. Most de-isotoping techniques ignore spatial relationships or rely on molecular class assumptions, making them less suitable for molecularly diverse tissue environments. IsoSpace avoids such assumptions, integrating spatial and spectral cues to empirically detect potential isotopic peaks. IsoSpace uses non-negative matrix factorization and an m/z -pattern matrix to uncover isotopic-like sequences, evaluating them by intra-pattern correlation. In a mouse pup example with 879 m/z -peaks, IsoSpace identified 71 potential isotopic patterns, substantially reducing data complexity while preserving chemical un-derstanding. IsoSpace o!ers chemical-interpretation-permissive DR with unsupervised isotope candidate detection for heterogeneous samples. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/691393v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@5e8977org.highwire.dtl.DTLVardef@93150eorg.highwire.dtl.DTLVardef@4b7aa4org.highwire.dtl.DTLVardef@160aa43_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 0:C_FLOATNO Graphical abstract for IsoSpace, chemistry-informed dimensionality reduction and au-tomated isotope candidate detection in imaging mass spectrometry. C_FIG

bioinformatics↗

bioRxiv2025

Culmorin inhibits detoxification of the mycotoxin deoxynivalenol by plant UDP-glucosyltransferases

The Fusarium metabolite culmorin (CUL) frequently co-occurs with the mycotoxin deoxynivalenol (DON) on cereals. While DON is recognized as a major Fusarium virulence factor on plants, the function of CUL is still unclear. Herein, we show that CUL-deficient F. graminearum mutants created by CLM1 deletion are less aggressive on wheat than the wild-type, accompanied by increased DON-3-glucoside/DON ratios in infected wheat ears. In root elongation assays with wheat and Brachypodium distachyon, CUL had no effect alone but significantly increased the toxicity of DON. Analysis of DON/CUL-treated roots further indicated that both wheat and B. distachyon are able to glucosylate CUL and that its presence impedes DON-glucosylation in both species. We identified two B. distachyon UDP-glucosyltransferases (UGT) able to glucosylate CUL and further investigated the effect of CUL on the kinetics of validated DON-glucosylating plant UGTs (BdUGT5g03300, HvUGT13248, OsUGT79). This suggested that CUL inhibits DON-glucosylation either by serving as competitive substrate with DON or by unproductive binding. Especially BdUGT5g03300 was strongly inhibited by CUL and even its glucosides. Our results indicate that CUL contributes to Fusarium virulence by weakening plant-defenses related to UGT-catalyzed DON-detoxification. As even CUL-glucosides are potentially inhibitory to UGTs, this implies a complex synergy of CUL with DON. HighlightWe present biochemical evidence that the Fusarium metabolite culmorin contributes to Fusarium virulence on plants by suppressing detoxification of the virulence factor deoxynivalenol by glucosyltransferases.

biochemistry↗

bioRxiv2025

Autophagy driven by VPS34 enables differentiated cell plasticity and cancer initiation

Differentiated cell plasticity and autophagy are fundamental mechanisms of tissue repair. To investigate their integration to maintain tissue homeostasis, we developed a unique model in which VPS34, the highly conserved class III PI3K that promotes autophagic flux, was inactivated in pancreatic exocrine cells, recognised study models. Using scRNAseq, we found that VPS34-null acinar cells evolved towards a transcriptional identity present at low levels in mouse and human pancreas. Functionally, it unexpectedly prevented transdifferentiation, chronic pancreatitis and precancer initiation triggered by stressors. Mechanistically, the newly differentiated cell state was less susceptible to cancer promotion by oncogenic KRAS, through reduced class I PI3K and increased lysosomal degradation of pro-inflammatory REG3A. This result opens the so far unreachable possibility of strategies for protection from environmentally induced cancer initiation.

pathology↗

bioRxiv2025

A Multimodal Imaging Pipeline for the Discovery of Molecular Markers of Cellular Neighborhoods

Insights into tissue microenvironments are constrained by profiling cellular and molecular components independently. To address this, we developed an integrated, multimodal workflow combining imaging mass spectrometry and highly multiplexed immunofluorescence on the same sample. Custom computational pipelines enable precise spatial co-registration, facilitating direct integration of cellular and molecular profiles. CODEX-derived cellular and neighborhood masks enable mining of IMS-derived lipid data to identify molecular markers of cell types and spatial neighborhoods in human kidney tissue. We discovered distinct carnitine distributions in cortical and medullary regions, indicating metabolic heterogeneity driven by microenvironment-specific oxygen levels and energy demands. Glomerular cell-type-specific analysis found ether-linked phosphatidylcholine and sphingomyelin, species associated with slit diaphragm integrity, localized to podocytes. Immune cell neighborhoods exhibited molecular signatures consistent with cell signaling and activation pathways in damaged tissue regions. This multi-omic framework links cellular organization with molecular signatures to unveil cellular and molecular relationships underlying tissue function and pathology.

molecular biology↗

bioRxiv2023

PI3Kα activity in PHGDH-low pancreatic epithelial cells limits tissue proliferative regeneration in cancer promoting conditions

ObjectiveIncreased consumption of meat is an epidemiologically validated risk condition for pancreatic cancer development, but the underlying mechanisms and whether it is related to induction of epithelial cell plasticity are unknown. DesignExperimental protocol to test the influence of high consumption of meat was compared to pancreatic inflammation experimental models. To determine the molecular drivers promoting pancreatic cell plasticity, we compared transcriptomics data sets from human samples of pancreatic inflammation and pancreatic cancer (PDAC) prone to plasticity and validated in vivo, ex vivo and in vitro the main identified target. ResultsMeat-enriched diet promoted plasticity of pancreatic acinar cells, that transdifferentiated in duct-like cells, and presented PI3K activation. We identified a selective PI3K activation gene signature enriched with plasticity. In this signature, PHGDH, which encodes an enzyme responsible for amino acid serine synthesis, was differentially expressed. High level of PHGDH in acinar cells was necessary for the proliferative action of PI3K sustained by an increased maximal mitochondrial capacity and decreased cyclin-dependent inhibitor p27 level. PHGDH level was decreased in transdifferentiated acinar cells. In this context, active PI3K promoted cell plasticity but decreased the number of cycling cells. Both epithelial-restricted genetic inactivation of PI3K and full PI3K inhibition by pharmacological dosage reduced inflammation-induced tissue damage, while a pharmacological PI3K activator promoted PanIN precancer lesion development. ConclusionMeat-enriched diet promoted plasticity. Blockage of plasticity by PI3K inhibition provoked an increased rate of acinar cell proliferation that had a beneficial impact on the tissue microenvironment less prone to precancer lesion development. What is already known on this topicIt is now well accepted that inflammatory conditions predispose to pancreatic tumour development; increased consumption of red and processed meat is an epidemiologically validated risk condition, but the underlying mechanisms are unknown. What this study addsWe identify PI3K activation as a common molecular pathway activated by increased consumption of red and processed meat and by inflammatory condition to promote pancreatic plasticity and precancer lesion development. How this study might affect research, practice or policyAs we show that treatments with the clinically available PI3K inhibitor block pancreatic plasticity under inflammatory stress while maintaining pancreas mass and limiting inflammatory reaction damage, they may represent an efficient and safe preventive interception drug in patients at risk of developing pancreatic cancer. PI3K pro-cancer action is exacerbated by the loss of serine synthesis enzyme; hence, diets that alter amino acid synthesis should be tightly controlled in those patients.

pathology↗

bioRxiv2023

The Loss of the E3 ubiquitin ligase TRIP12 inhibits Pancreatic Acinar Cell Plasticity and Tumor Cell Metastatic Capacity

Background & AimsAlthough specialized and dedicated to the production of digestive enzymes, pancreatic acinar cells harbor a high plasticity and are able to modify their identity. They undergo reversible acinar-to-ductal cell metaplasia (ADM) through epigenetic silencing of the acinar lineage gene program mainly controlled by PTF1a (Pancreas Transcription Factor 1a). ADM becomes irreversible in the presence of oncogenic Kras mutations and leads to the formation of preneoplastic lesions. We investigated the role of the E3 ubiquitin ligase Thyroid hormone Receptor Interacting Protein 12 (TRIP12), involved in PTF1a degradation, in pancreatic carcinogenesis. MethodsWe used genetically engineered mouse models of pancreas-selective Trip12 deletion, mutant Kras (G12D) and mutant Trp53 (R172H). We performed RNA sequencing analysis from acinar cells and cell lines derived from mice models tumors. We investigated the impact of TRIP12 deficiency on acute pancreatitis, tumor formation and metastasis development. ResultsTRIP12 is overexpressed in human pancreatic preneoplastic lesions and tumors. We show that a conditional deletion of TRIP12 in the pancreas during murine embryogenesis alters pancreas homeostasis and acinar cell genes expression patterns in adults. EGF induced-ADM is suppressed in TRIP12-depleted pancreatic acini. In vivo, a loss of TRIP12 prevents acini to develop ADM in response to pancreatic injury, the formation of Kras-induced pancreatic preneoplastic lesions, and impairs tumors and metastasis formation in the presence of mutated Trp53. TRIP12 is required for Claudin18.2 isoform expression in pancreatic tumors cells. ConclusionsOur study identifies TRIP12 as a novel regulator of acinar fate in the adult pancreas with an important dual role in pancreatic carcinogenesis, in initiation steps and in metastatic behavior of tumor cells. SynopsisThis study shows that Thyroid hormone Receptor Interacting Protein 12 plays an important dual role in the initiation steps and invasion of pancreatic carcinogenesis. Moreover, expression of TRIP12 switches on the expression of Claudin-18, a targetable biomarker of pancreatic tumors.

cancer biology↗