Biology subjects

Coronel, J.

Publications and source records attributed to Coronel, J..

8 recordsLinked to original sources

bioRxiv2025

Comprehensive Multimodal Profiling of Atherosclerosis Reveals Bhlhe40 as a Potential Regulator of Vascular Smooth Muscle Cell Phenotypic Modulation

BackgroundVascular smooth muscle cells (VSMCs) play a central role in atherosclerosis by undergoing phenotypic modulation from a quiescent, contractile state to a range of synthetic phenotypes, including fibroblast-like, macrophage-like, and lipid-laden foam cell-like states. However, a comprehensive multimodal characterization and understanding of the transcriptional programs driving these transitions remain incomplete. MethodsTo comprehensively define the phenotypic diversity of VSMCs during atherosclerosis progression, we performed in-depth profiling using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and bulk RNA sequencing in a VSMC lineage-tracing atherosclerotic mouse model. Insights from these datasets guided the design of targeted in vitro experiments to investigate candidate regulatory mechanisms. ResultsSingle-cell multi-omics revealed extensive cellular heterogeneity within atherosclerotic plaques, including a rare population of VSMC-derived macrophage-like cells, whose presence was confirmed by histological analysis. These studies also identified a substantial population of VSMC-derived foam cells, comprising approximately 70% of all foam cells in the lesions. These cells exhibited activation of gene programs associated with lipid metabolism, proliferation, and tumor-like features. The transcription factor Bhlhe40 emerged as a key regulator of this phenotypic transition, with elevated expression in VSMC-derived foam cells during disease progression. Functional knockdown of Bhlhe40 suppressed VSMC phenotypic switching and foam cell characteristics, underscoring its potential role as a driver of VSMC modulation. ConclusionsThese findings advance our understanding of VSMC phenotypic modulation in atherosclerosis and highlight Bhlhe40 as a key regulator of this process. Elucidating the mechanisms governing VSMC plasticity may offer new therapeutic opportunities to reduce cardiovascular risk by targeting disease-driving cellular transitions.

molecular biology↗

bioRxiv2025

Single-Cell Multimodal Profiling Reveals a Novel CD26+ Fibroblast Subpopulation in Atherosclerosis

BackgroundAtherosclerosis involves complex interactions between lipids, immune cells, vascular smooth muscle cells (VSMCs), and fibroblasts within the arterial wall. While significant advances in single-cell technologies have shed light on the roles of immune cells and VSMCs in plaque development, fibroblasts remain underexplored, leaving critical gaps in understanding their contributions to disease progression and plaque stability. Comprehensive characterization of fibroblast phenotypes in atherosclerosis is essential to unravel their diverse functions and to distinguish between subsets that may play protective versus pathogenic roles in the disease process. MethodsHere, we utilized CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) to comprehensively profile fibroblast diversity in a mouse model of atherosclerosis. Mice were fed an atherogenic diet for 0, 8, 19, and 26 weeks, representing distinct stages of disease progression, enabling a detailed phenotypic characterization of fibroblasts throughout the course of atherosclerosis development. ResultsWe identified four distinct fibroblast subpopulations, including a myofibroblast population closely resembling VSMC-derived chondromyocytes. The proportions of these fibroblast subsets exhibited a modest decline as atherosclerosis progressed. Through multimodal analysis, we identified CD26 as a highly expressed and specific marker for one of these fibroblast subpopulations, distinguishing it from other subsets. Using a combination of flow cytometry and immunohistochemistry, we demonstrated that CD26+ fibroblasts predominantly reside in the adventitia of healthy arteries. During atherosclerosis progression, these cells expand into the intima and primarily localize within the fibrous cap of the lesion. ConclusionsOur multi-omic analysis highlights the phenotypic diversity and dynamic changes of fibroblasts during atherosclerosis progression. Among these, CD26+ fibroblasts emerge as a distinct subpopulation that expands within atherosclerotic lesions and may play a critical role in promoting plaque stability through their migration into the fibrous cap.

genomics↗

bioRxiv2024

Tiled Amplicon Sequencing Enables Culture-free Whole-Genome Sequencing of Pathogenic Bacteria From Clinical Specimens

Pathogen sequencing is an important tool for disease surveillance and demonstrated its high value during the COVID-19 pandemic. Viral sequencing during the pandemic allowed us to track disease spread, quickly identify new variants, and guide the development of vaccines. Tiled amplicon sequencing, in which a panel of primers is used for multiplex amplification of fragments across an entire genome, was the cornerstone of SARS-CoV-2 sequencing. The speed, reliability, and cost-effectiveness of this method led to its implementation in academic and public health laboratories across the world and adaptation to a broad range of viral pathogens. However, similar methods are not available for larger bacterial genomes, for which whole-genome sequencing typically requires in vitro culture. This increases costs, error rates and turnaround times. The need to culture poses particular problems for medically important bacteria such as Mycobacterium tuberculosis, which are slow to grow and challenging to culture. As a proof of concept, we developed two novel whole-genome amplicon panels for M. tuberculosis and Streptococcus pneumoniae. Applying our amplicon panels to clinical samples, we show the ability to classify pathogen subgroups and to reliably identify markers of drug resistance without culturing. Development of this work in clinical settings has the potential to dramatically reduce the time of diagnosis of drug resistance for multiple drugs in parallel, enabling earlier intervention for high priority pathogens.

genomics↗

bioRxiv2023

Highly pathogenic avian influenza H5N1 virus infections in pinnipeds and seabirds in Uruguay: a paradigm shift to virus transmission in South America

The highly pathogenic avian influenza viruses of the clade 2.3.4.4b have caused unprecedented deaths in South American wild birds, poultry, and marine mammals. In September 2023, pinnipeds and seabirds appeared dead on the Uruguayan Atlantic coast. Sixteen influenza virus strains were characterized by real-time reverse transcription PCR and genome sequencing in samples from sea lions (Otaria flavescens), fur seals (Arctocephalus australis), and terns (Sterna hirundinacea). Phylogenetic and ancestral reconstruction analysis showed that these strains have pinnipeds as the most likely ancestral host, representing a recent introduction of the clade 2.3.4.4b in Uruguay. The Uruguayan and closely related strains from Peru (sea lions) and Chile (sea lions and a human case) carry mammalian adaptative residues 591K and 701N in the viral polymerase basic protein 2 (PB2). Our findings suggest that the clade 2.3.4.4b strains in South America may have spread from mammals to mammals and seabirds, revealing a new transmission route.

microbiology↗

bioRxiv2023

β-carotene accelerates resolution of atherosclerosis by promoting regulatory T cell expansion in the atherosclerotic lesion

{beta}-carotene oxygenase 1 (BCO1) catalyzes the cleavage of {beta}-carotene to form vitamin A. Besides its role in vision, vitamin A regulates the expression of genes involved in lipid metabolism and immune cell differentiation. BCO1 activity is associated with the reduction of plasma cholesterol in humans and mice, while dietary {beta}-carotene reduces hepatic lipid secretion and delays atherosclerosis progression in various experimental models. Here we show that {beta}-carotene also accelerates atherosclerosis resolution in two independent murine models, independently of changes in body weight gain or plasma lipid profile. Experiments in Bco1-/- mice implicate vitamin A production in the effects of {beta}-carotene on atherosclerosis resolution. To explore the direct implication of dietary {beta}-carotene on regulatory T cells (Tregs) differentiation, we utilized anti-CD25 monoclonal antibody infusions. Our data show that {beta}-carotene favors Treg expansion in the plaque, and that the partial inhibition of Tregs mitigates the effect of {beta}-carotene on atherosclerosis resolution. Our data highlight the potential of {beta}-carotene and BCO1 activity in the resolution of atherosclerotic cardiovascular disease.

immunology↗

bioRxiv2022

Evaluation of the broth microdilution methodology for susceptibility testing of Mycobacterium tuberculosis in Peru

Peru is amongst the 30 countries with the highest burden of multidrug-resistant tuberculosis worldwide. In the fight against drug-resistant tuberculosis, the UKMYC6 microtiter plate was developed and validated by the CRyPTIC project. Our objective was to evaluate the use of the broth microdilution UKMYC6 plate for susceptibility testing of drug-resistant Mycobacterium tuberculosis (MTB) strains in Peru. 496 nationally-representative MTB strains determined drug-resistant by the routine agar proportion method (APM) were selected. MICs of 13 anti-tuberculosis drugs were determined for each strain using the microdilution UKMYC6 plates and compared with the APM result. MIC distributions for APM-susceptible and APM-resistant strains were demonstrated for rifampicin, isoniazid, kanamycin, and levofloxacin, with reasonable agreement (0.64[≤]k[≤]0.79) for rifampicin, ethambutol, ethionamide and kanamycin and the best agreement for isoniazid and levofloxacin (k>0.8). No strain presented MICs higher than the CRyPTIC Epidemiological cut-off values for the new (bedaquiline, delamanid) or repurposed (clofazimine, linezolid) drugs. The microbroth dilution method using the UKMYC6 microtiter plate allowed the complete susceptibility characterization, through the determination of MICs, of drug-resistant Mycobacterium tuberculosis strains in Peru. This methodology showed a good diagnostic performance for the drugs rifampicin, isoniazid, kanamycin and levofloxacin drugs.

microbiology↗

bioRxiv2020

Low-cost 3D-printed inverted microscope to detect Mycobacterium tuberculosis in a MODS culture

BackgroundThe MODS is an important assay for early diagnosis of tuberculosis and drug susceptibility. MODS is based in the microscopic observation, underneath, of the characteristic cords of Mycobacterium tuberculosis colonies grown in liquid media. An inverted optical microscope is required to observe and interpret MODS cultures. Unfortunately, the cost of commercial inverted microscopes is not affordable in low resource settings in developing countries. MethodologyTo perform a diagnosis of tuberculosis using the MODS assay, images with modest quality are enough for proper interpretation. Therefore, the use of a high cost commercial inverted optical microscope is not indispensable. In this study, we designed a prototype of an optical inverted microscope created with a 3D printer and based on a smartphone. The system was evaluated by comparison of manual interpretations of 226 TB positive MODS culture images and 207 negative MODS culture images. SignificanceThe prototype resulted in a low-cost inverted optical microscope, with simple functioning, and whose parts have been manufactured using 3D printing techniques. The quality of the images was good enough and achieved a 100% concordance between the manual inspection with the developed microscope, and the standard diagnostics of MODS.

microbiology↗

bioRxiv2019

Deep learning reveals cancer metastasis and therapeutic antibody targeting in whole body

Reliable detection of disseminated tumor cells and of the biodistribution of tumor-targeting therapeutic antibodies within the entire body has long been needed to better understand and treat cancer metastasis. Here, we developed an integrated pipeline for automated quantification of cancer metastases and therapeutic antibody targeting, named DeepMACT. First, we enhanced the fluorescent signal of tumor cells more than 100-fold by applying the vDISCO method to image single cancer cells in intact transparent mice. Second, we developed deep learning algorithms for automated quantification of metastases with an accuracy matching human expert manual annotation. Deep learning-based quantifications in a model of spontaneous metastasis using human breast cancer cells allowed us to systematically analyze clinically relevant features such as size, shape, spatial distribution, and the degree to which metastases are targeted by a therapeutic monoclonal antibody in whole mice. DeepMACT can thus considerably improve the discovery of effective therapeutic strategies for metastatic cancer. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/541862v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@ffe1b9org.highwire.dtl.DTLVardef@13c55eborg.highwire.dtl.DTLVardef@2ccb6corg.highwire.dtl.DTLVardef@df55e9_HPS_FORMAT_FIGEXP M_FIG C_FIG Supplementary Movies and deep learning algorithms of DeepMACT are available at http://discotechnologies.org/DeepMACT/

cancer biology↗