Biology subjects

Prieto, C.

Publications and source records attributed to Prieto, C..

6 recordsLinked to original sources

bioRxiv2026

NucleiSky enables cross-scale multimodal registration of microscopy data using nuclei constellations

Integrating tissue-level organisation with sub-cellular resolution and molecular information often requires combining multiple microscopy modalities and scales. However, aligning images acquired with different modalities, settings, or instruments remains challenging. Here, we introduce NucleiSky, a microscopy image registration framework that utilises the spatial arrangement of nuclei or other landmarks as an intrinsic biological fingerprint. NucleiSky represents images as constellations of centroids and aligns them using geometric algorithms and spatial consensus scoring. In benchmark datasets, NucleiSky could localise query regions within larger reference images using as few as five nuclei. We show that NucleiSky can locate high-magnification fields of view within low-magnification overview scans, map these alignments to additional channels, support live brightfield-to-fixed registration using synthetic nuclear labels, and guide microscope retargeting. We further show that the same constellation-matching principle can be extended to 3D localisation and to non-nuclear landmarks. These findings establish local landmark geometry as an intrinsic spatial fingerprint that enables localisation and registration across imaging scales, modalities and microscopy platforms. NucleiSky is available as an open-source Python package and as notebook-based applications.

Cell Biology↗

bioRxiv2025

TL1A-activated T cells remodel the rectal mucosa in Crohn's disease patients with perianal fistulizing disease

BackgroundPerianal fistulizing disease (PFD) is a complication that affects about 20% of Crohns disease (CD) patients whose etiology remains unknown. ObjectivesTo identify predisposing events driving fistula formation. DesignRectal biopsies from CD patients with or without PFD (CD+PFD and CD, respectively; n=31) were collected and subjected to single-cell RNA sequencing (scRNA-seq). Functional analyses were conducted using peripheral CD3+ T cells, intestinal tissue explants, primary fibroblasts and 2D-epithelial monolayer cell cultures. ResultsThe rectal mucosa of CD+PFD patients is imprinted with cellular and transcriptomic alterations specific to PFD and independent of luminal inflammation, potentially driven by TL1A activation in CD4+ T cells. We identified lymphotoxin beta (LTB or its functional heterotrimer LT1{beta}2) as a novel mediator downstream of TL1A that, along with IL-22, induces a PFD-associated signature in rectal fibroblast and epithelial cells, respectively. This signature includes an increased abundance of fibroblasts, an induction of matrix-degrading enzymes, transcriptomic rewiring of the lamina propria S1 fibroblasts, and an anti-bacterial and immune responses in epithelial cells. Notably, the induction of LT1{beta}2 and IL-22 occurs independently of TNF signaling, revealing a new TL1A-LT1{beta}2/IL-22 axis that remains active under anti-TNF therapy. ConclusionOur findings revealed unique cellular alterations in the rectum of CD patients with PFD, highlighting the previously unrecognized involvement of TL1A in mediating this signature and supporting the need for exploring the role of TL1A inhibition as a therapeutic approach for PFD.

immunology↗

bioRxiv2023

Myeloperoxidase activity predicts atherosclerotic plaque disruption and atherothrombosis

BackgroundUnstable atherosclerotic plaque is characterized by increased myeloperoxidase (MPO) activity. As unstable plaque is vulnerable to disruption and ensuing thrombosis, we examined whether plaque MPO activity predicts atherothrombosis in a pre-clinical model and correlates with ruptured human atheroma. MethodsTo assess if plaque MPO activity predicts atherothrombosis, rabbits were subjected to aortic endothelial denudation, cholesterol feeding, in vivo magnetic resonance imaging (MRI) of MPO activity using MPO-Gd (gadolinium), followed by pharmacological triggering of atherothrombosis, histology, and MPO activity determined by liquid chromatography tandem mass spectrometry (LC-MSMS) by quantifying the MPO-specific product of hydroethidine, 2-chloroethidium. To correlate plaque MPO activity to ruptured human atheroma, ex vivo determination of MPO activity by MPO-Gd retention in carotid endarterectomy (CEA) specimens was correlated with in vivo MRI plaque phenotyping in patients, histology, and MPO activity determined by LC-MSMS. ResultsIn rabbits, pre-trigger in vivo MPO activity, validated by LC-MSMS and histology, was higher in thrombosis-prone than thrombosis-resistant plaques and lesion-free segments (R1 relaxation rate = 2.2 {+/-} 0.4 versus 1.6 {+/-} 0.2 and 1.5 {+/-} 0.2 s-1, respectively, p<0.0001), and it predicted atherothrombosis. In CEA specimens, MPO-Gd retention was greater in histologic and MRI-graded American Heart Association (AHA) type VI than types III, IV and V plaques ({Delta}R1 relaxation rate from baseline = 48 {+/-} 6 versus 16 {+/-} 7, 17 {+/-} 8 and 23 {+/-} 8%, respectively, p<0.0001). This association was confirmed by comparing AHA grade to MPO activity determined by LC-MSMS (277 {+/-} 338 versus 7 {+/-} 6, 11 {+/-} 12 and 42 {+/-} 39 pmol 2-chloroethidium/mg protein for type VI versus type III-V plaques, respectively, p=0.0008). ConclusionsMPO activity is elevated in thrombosis-prone rabbit and ruptured human atheroma. Non-invasive molecular imaging of MPO activity predicts atherothrombosis, highlighting the potential of arterial MPO activity to detect vulnerable, destabilized atherosclerosis.

biochemistry↗

bioRxiv2023

Intermediate molecular phenotypes to identify genetic markers of anthracycline-induced cardiotoxicity risk

Cardiotoxicity due to anthracyclines (CDA) affects cancer patients, but we cannot predict who may suffer from this complication. CDA is a complex disease whose polygenic component is mainly unidentified. We propose that levels of intermediate molecular phenotypes in the myocardium associated with histopathological damage could explain CDA susceptibility; so that variants of genes encoding these intermediate molecular phenotypes could identify patients susceptible to this complication. A genetically heterogeneous cohort of mice generated by backcrossing (N = 165) was treated with doxorubicin and docetaxel. Cardiac histopathological damage was measured by fibrosis and cardiomyocyte size by an Ariol slide scanner. We determine intramyocardial levels of intermediate molecular phenotypes of CDA associated with histopathological damage and quantitative trait loci (ipQTLs) linked to them. These ipQTLs seem to contribute to the missing heritability of CDA because they improve the heritability explained by QTL directly linked to CDA (cda-QTLs) through genetic models. Genes encoding these molecular subphenotypes were evaluated as genetic markers of CDA in three cancer patient cohorts (N = 517) whose cardiac damage was quantified by echocardiography or Cardiac Magnetic Resonance. Many SNPs associated with CDA were found using genetic models. LASSO multivariate regression identified two risk score models, one for pediatric cancer patients and the other for women with breast cancer. Molecular intermediate phenotypes associated with heart damage can identify genetic markers of CDA risk, thereby allowing a more personalized patient management. A similar strategy could be applied to identify genetic markers of other complex trait diseases.

genetics↗

bioRxiv2021

Screening of CHO-K1 endogenous promoters for expressing recombinant proteins in mammalian cell cultures

For the production of recombinant protein therapeutics in mammalian cells, a high rate of gene expression is desired and hence strong viral-derived promoters are commonly used. However, they usually induce cellular stress and can be susceptible to epigenetic silencing. Endogenous promoters, which coordinates their activity with cellular and bioprocess dynamics while at the same time they maintain high expression levels, may help to avoid such drawbacks. In this work, endogenous promoters were identified based on high expression levels in RNA-seq data of CHO-K1 cells cultured in high density. The promoters of Actb, Ctsz, Hmox1, Hspa5, Vim and Rps18 genes were selected for generating new expression vectors for the production of recombinant proteins in mammalian cells. The in silico-derived promoter regions were experimentally verified and the majority showed transcriptional activity comparable or higher than CMV. Also, stable expression following a reduction of culture temperature was investigated. The characterized endogenous promoters (excluding Rps18) constitute a promising alternative to CMV promoter due to their high strength, long-term expression stability and integration into the regulatory network of the host cell. These promoters may also comprise an initial panel for designing cell engineering strategies and synthetic promoters, as well as for industrial cell line development.

cell biology↗

bioRxiv2019

Faster 3D saturation-recovery based myocardial T1 mapping using a reduced number of saturation points and denoising

PurposeTo accelerate the acquisition of free-breathing 3D saturation-recovery-based (SASHA) myocardial T1 mapping by acquiring fewer saturation points in combination with a novel post-processing 3D denoising technique to maintain high accuracy and precision.\n\nMethods3D SASHA T1 mapping acquires nine T1-weighted images along the saturation recovery curve, resulting in long acquisition times. In this work, we propose to accelerate conventional cardiac T1 mapping by reducing the number of saturation points. High T1 accuracy and precision is maintained by applying a 3D denoising technique to the T1-weighted images prior to pixel-wise T1 fitting. The proposed approach was evaluated on a T1 phantom and 20 healthy subjects, by varying the number of T1-weighted images acquired between three and nine, both prospectively and retrospectively. Three patients with suspected cardiovascular disease were acquired using five T1-weighted images. T1 accuracy and precision was determined for all the acquisitions before and after denoising.\n\nResultsIn the T1 phantom, no statistical difference was found in terms of accuracy and precision for the different number of T1-weighted images before or after denoising (P=0.99 and P=0.99 for accuracy, P=0.64 and P=0.42 for precision, respectively). In vivo, both prospectively and retrospectively, the precision improved considerably with the number of T1-weighted images employed before denoising (P<0.05) but was independent on the number of T1-weighted images after denoising.\n\nConclusionWe demonstrate the feasibility of accelerating 3D SASHA T1 mapping by reducing the number of acquired T1-weighted images in combination with an efficient 3D denoising, without affecting accuracy and precision of T1 values.

bioengineering↗