Biology subjects

Combes, A.

Publications and source records attributed to Combes, A..

13 recordsLinked to original sources

bioRxiv2025

Spatial Transcriptomics Reveals CXCL12+ Fibroblasts as Central Immune Organizers through CXCR4 Signaling in Abdominal Aortic Aneurysm

BACKGROUNDAbdominal aortic aneurysm (AAA) is characterized by sterile inflammation, immune cell infiltration, and stromal remodeling that progressively weaken the aortic wall, leading to life-threatening aortic rupture. The molecular mechanisms and spatial organization of immune-stromal interactions in human tissue are poorly understood, limiting the potential to develop effective pharmacological therapy for AAA. METHODSIn this observational cross-sectional study, formalin-fixed, paraffin-embedded tissues from 11 AAA patients and 12 controls were analyzed by Xenium spatial transcriptomics. Cellular states and localization within tissue architecture were mapped to identify cellular neighborhoods and infer cell-cell communication. RESULTSWe generated a high-resolution spatial transcriptomics atlas of 581,664 cells in 26 clusters. AAAs showed a significant loss of contractile smooth muscle cells, expansion of pro-angiogenic endothelial subsets, and broad infiltration of immune cells. These inflammatory changes were accompanied by expansion of activated, universal, and CXCL12 adventitial fibroblasts. Spatial transcriptomic analysis revealed fibroblast-immune colocalization and adventitial tertiary lymphoid organs. Inferred signaling pathway analysis identified increased interactions between CXCL12 fibroblasts and CXCR4 T and B cells in the adventitia of AAAs. Fibroblasts that expressed CXCL12 had significantly more immune cell neighbors than fibroblasts that did not, suggesting that they serve as stromal hubs for adaptive immune clustering. Genome-wide association analysis linked AAA heritability to fibroblasts, modulated smooth muscle cells, and foamy macrophages. CONCLUSIONOur novel high-resolution spatial transcriptomic atlas of human AAAs revealed coordinated pathogenic reprogramming of stromal and immune cells, defined by smooth muscle cell depletion, fibroblast activation, endothelial remodeling, and disproportionate expansion of immune cells. Through CXCR4 signaling, CXCL12 fibroblasts serve as central organizers of immune niches, suggesting stromal-immune crosstalk as a therapeutic target in AAA. CLINICAL PERSPECTIVESWhat Is New? O_LIWe generated the first subcellular-resolution spatial transcriptomic atlas of human abdominal aortic aneurysm (AAA), with >580,000 cells identified from aortic tissue sections C_LIO_LIWe identified CXCL12+ fibroblasts as central stromal hubs that organize adaptive immune niches through CXCR4-mediated crosstalk with B and T cells C_LIO_LIWe discovered that stromal populations carry the strongest genetic enrichment for AAA risk, notably fibroblast and modulated smooth muscle cell populations C_LI What Are The Clinical Implications? O_LIThese findings position stromal-immune interactions, particularly the CXCL12-CXCR4 axis, as a potential therapeutic target to slow AAA progression C_LIO_LIThe spatial atlas provides a framework for mechanistic studies and drug-discovery efforts, guiding future interventions aimed at modifying the microenvironment that destabilizes the aneurysmal aortic wall C_LI

cell biology↗

bioRxiv2025

Single-Cell Profiling Reveals Altered Endometrial Cellular Features Across the Menstrual Cycle in Endometriosis Patients

Endometriosis is a chronic, estrogen-dependent condition affecting over 190 million women globally, characterized by the ectopic presence of endometrial-like tissue that leads to inflammation, pain, and infertility. Despite its prevalence, the pathogenesis of endometriosis remains poorly understood. Here, we present a comprehensive single-cell transcriptomic atlas comprising 228,000 cells derived from 43 eutopic endometrial biopsies from patients with endometriosis, fibroid controls and healthy controls, sampled across the menstrual cycle. This analysis reveals previously uncharacterized subpopulations of endometrial fibroblasts and epithelial cells undergoing epithelial-mesenchymal transition, alongside disrupted immune cell communication networks. Comparative gene expression profiling implicates oxidative stress, aberrant cell migration, and dysregulated apoptosis as central features of the disease state. These findings suggest that endometriosis alters eutopic endometrial homeostasis, with potential consequences for fertility, regeneration, and disease progression. Our dataset provides a valuable resource for biomarker discovery and identifies candidate therapeutic targets aimed at restoring endometrial function and alleviating symptoms in affected individuals.

bioinformatics↗

bioRxiv2025

Anticlustering for Sample Allocation To Minimize Batch Effects

High throughput sequencing is a powerful tool for processing large amounts of DNA and RNA samples in batches. Proper experimental design and statistical methods are required to mitigate systematic technical factors due to differences in batches ("batch effects"), as data variation due to these non-biological factors can mask actual biological differences. We propose using anticlustering as an automated method to assign samples to balanced batches. Anticlustering effectively negates differences in (numeric and/or categorical) covariates among batches, and implements user-defined restrictions on the number of batches, the number of samples per batch, and whether to assign certain samples to the same batch ("must-link constraints"). A simulation study shows that anticlustering is better at achieving balance among batches than previous approaches. An application from the UCSF-Stanford Endometriosis Center for Discovery, Innovation, Training and Community Engagement ("ENACT", https://enactcenter.org/) is presented as a real-life example. In the application, multiple samples provided by an individual had to be processed on the same batch, so that comparisons among different samples of the same patient were not diluted by batch effects. The novel Two Phase Must Link (2PML) anticlustering algorithm realized the must-link restrictions while simultaneously obtaining balance among batches regarding disease stage, menstrual cycle phase, case versus control sample, and clinical site. All methods presented here are accessible via the free and open source R package anticlust (https://cran.r-project.org/package=anticlust). An interactive visualization and web-based batch assignment tool are made available in the Rshiny app "anticlust" (https://anticlust.org/).

bioinformatics↗

bioRxiv2024

Single-cell spatial transcriptomics of fixed, paraffin-embedded biopsies reveals colitis-associated cell networks

Background & AimsImaging-based, single-cell spatial transcriptomics (iSCST) using formalin-fixed, paraffin-embedded (FFPE) tissue could transform translational research by retaining all tissue cell subsets and spatial locations while enabling the analysis of archived specimens. We aimed to develop a robust framework for applying iSCST to archived clinical FFPE mucosal biopsies from patients with inflammatory bowel disease (IBD). MethodsWe performed a comprehensive benchmarking comparison of three iSCST platforms capable of analyzing FFPE specimens. We analyzed FFPE mucosal biopsies (n=57) up to 5 years old from non-IBD controls (HC; n=9) and patients with ulcerative colitis (UC;n=11). After platform-specific cell segmentation, we applied a uniform data processing pipeline to all datasets, including transcript detection, cell annotation, differential gene expression, and neighborhood enrichment. Transcriptomic signatures identified with iSCST were validated using external, publicly available bulk transcriptomic datasets. ResultsA custom 290-plex Xenium gene panel exhibited the highest sensitivity and specificity for transcript detection, enabling precise identification and quantification of diverse cell subsets and differentially expressed genes across cell types and disease states. We mapped transcriptionally distinct fibroblast subsets to discrete spatial locations and identified inflammation-associated fibroblasts (IAFs) and monocytes as a colitis-associated cellular neighborhood. We also identified signatures associated with Vedolizumab (VDZ) responsiveness. VDZ non-responders were characterized by an IAF-monocyte transcriptional signature, while responders exhibited enrichment of epithelial gene sets. ConclusionsOur optimized iSCST framework for archived FFPE biopsies provides unique advantages for assessing the role of colitis-associated cellular networks in routinely collected clinical samples. FFPE-based biomarkers could integrate with existing clinical workflows and potentially aid in risk-stratifying patients.

immunology↗

bioRxiv2024

Single-Nuclei Analysis of the Unfolded Protein Response (SNUPR): A Novel Method revealing bortezomib resistance mechanisms in Multiple Myeloma

AbstractThe unfolded protein response (UPR) is a key stress resistance pathway that has become a key potential target for improving the efficacy of cancer chemotherapy. The UPR involves the activation of three ER-resident stress sensors: PERK, IRE-1 and ATF6 with different signalling outcomes leading to cell death or survival. These cell-fate decisions are difficult to predict and are the result of the complex interaction of PERK, IRE-1 and ATF6 downstream events that have differences in their dynamics and their interplay. These characteristics of the UPR are still poorly defined due to lack of methods to monitor their activation simultaneously at single-cell level. We developed SNUPR (Single Nuclei analysis of the Unfolded Protein Response), an accessible technique that allows the profiling of the three UPR branches in nuclear suspensions by flow cytometry, and applied it to study UPR dynamics in a cancer-specific context. By performing transcriptomic analysis, we found that ER-stress sensor specific gene signatures correlate with patient survival in several blood malignancies, and by using SNUPR, we detected high heterogeneity during UPR activation in vitro in different human cancer cell lines, which could not be have been predicted by the level of expression of the sensors. Our SNUPR analyses further indicate that this heterogeneity is explained by variations in the intensity and duration of ER stress-induced protein synthesis inhibition via PERK, acting as upstream regulator of both the IRE-1/XBP1 and ATF6 dependent transcriptional programs. We extend the relevance of these observations by demonstrating that IRE-1/XBP1s pathway plays a critical role in bortezomib resistance of multiple myeloma cells and patients. We present here SNUPR, that can be used to monitor UPR dynamics with single-cell resolution and identified clinical contexts in which targeting a specific UPR branch could be detrimental or help circumventing chemotherapy resistance. One Sentence SummarySNUPR method enable single-cell UPR profiling and reveals the role of IRE-1 axis in predicting bortezomib resistance in multiple myeloma. HighlightsO_LISNUPR allows simultaneous profiling of PERK, IRE-1 and ATF6 activation with single- cell resolution. C_LIO_LIInhibition of protein synthesis via PERK control the activation levels of the IRE-1/XBP1s and ATF6 pathway. C_LIO_LIIRE-1 activation and associated transcriptional signatures predict the outcome of patients with multiple myeloma treated with Bortezomib. C_LIO_LIIRE-1 activity, but not PERK or ATF6, is essential to acquire bortezomib resistance in multiple myeloma cell lines. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=190 HEIGHT=200 SRC="FIGDIR/small/617161v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@297668org.highwire.dtl.DTLVardef@1cab0eorg.highwire.dtl.DTLVardef@2238b4org.highwire.dtl.DTLVardef@b8ebf6_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Body size interacts with the structure of the central nervous system: A multi-center in vivo neuroimaging study

Clinical research emphasizes the implementation of rigorous and reproducible study designs that rely on between-group matching or controlling for sources of biological variation such as subjects sex and age. However, corrections for body size (i.e. height and weight) are mostly lacking in clinical neuroimaging designs. This study investigates the importance of body size parameters in their relationship with spinal cord (SC) and brain magnetic resonance imaging (MRI) metrics. Data were derived from a cosmopolitan population of 267 healthy human adults (age 30.1{+/-}6.6 years old, 125 females). We show that body height correlated strongly or moderately with brain gray matter (GM) volume, cortical GM volume, total cerebellar volume, brainstem volume, and cross-sectional area (CSA) of cervical SC white matter (CSA-WM; 0.44[≤]r[≤]0.62). In comparison, age correlated weakly with cortical GM volume, precentral GM volume, and cortical thickness (-0.21[≥]r[≥]-0.27). Body weight correlated weakly with magnetization transfer ratio in the SC WM, dorsal columns, and lateral corticospinal tracts (-0.20[≥]r[≥]-0.23). Body weight further correlated weakly with the mean diffusivity derived from diffusion tensor imaging (DTI) in SC WM (r=-0.20) and dorsal columns (-0.21), but only in males. CSA-WM correlated strongly or moderately with brain volumes (0.39[≤]r[≤]0.64), and weakly with precentral gyrus thickness and DTI-based fractional anisotropy in SC dorsal columns and SC lateral corticospinal tracts (-0.22[≥]r[≥]-0.25). Linear mixture of sex and age explained 26{+/-}10% of data variance in brain volumetry and SC CSA. The amount of explained variance increased at 33{+/-}11% when body height was added into the mixture model. Age itself explained only 2{+/-}2% of such variance. In conclusion, body size is a significant biological variable. Along with sex and age, body size should therefore be included as a mandatory variable in the design of clinical neuroimaging studies examining SC and brain structure.

neuroscience↗

bioRxiv2023

Multimodal identification of rare potent effector CD8 T cells in solid tumors

The anti-tumor function of CD8 T cells is limited through well-established pathways of T cell exhaustion (TEX). Strategies to capture emergent functional states amongst this dominant trajectory of dysfunction are necessary to find pathways to durable anti-tumor immunity. By leveraging transcriptional reporting (by the fluorescent protein TFP) of the T cell activation marker Cd69, related to upstream AP-1 transcription factors, we define a classifier for potent versus sub-optimal CD69+ activation states arising from T cell stimulation. In tumors, this delineation acts an additional functional readout along the TEX differentiation trajectory, within and across TEX subsets, marked by enhanced effector cytokine and granzyme B production. The more potent state remains differentially prominent in a T cell-mediated tumor clearance model, where they also show increased engagement in the microenvironment and are superior in tumor cell killing. Employing multimodal CITE-Seq in human head and neck tumors enables a similar strategy to identify Cd69RNAhiCD69+ cells that also have enhanced functional features in comparison to Cd69RNAloCD69+ cells, again within and across intratumoral CD8 T cell subsets. Refining the contours of the T cell functional landscape in tumors in this way paves the way for the identification of rare exceptional effectors, with imminent relevance to cancer treatment. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/559470v2_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@4a9429org.highwire.dtl.DTLVardef@4535d9org.highwire.dtl.DTLVardef@1d26e03org.highwire.dtl.DTLVardef@34acd2_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

Influence of preprocessing, distortion correction and cardiac triggering on the quality of diffusion MR images of spinal cord

Diffusion MRI of the spinal cord (SC) is susceptible to geometric distortion caused by field inhomogeneities, and prone to misalignment across time series and signal dropout caused by biological motion. Several modifications of image acquisition and image processing techniques have been introduced to overcome these artifacts, but their specific benefits are largely unproven and warrant further investigations. We aim to evaluate two specific aspects of image acquisition and processing that address image quality in diffusion studies of the spinal cord: susceptibility corrections to reduce geometric distortions, and cardiac triggering to minimize motion artifacts. First, we evaluate 4 distortion preprocessing strategies on 7 datasets of the cervical and lumbar SC and find that while distortion correction techniques increase geometric similarity to structural images, they are largely driven by the high-contrast cerebrospinal fluid, and do not consistently improve the geometry within the cord nor improve white-to-gray matter contrast. We recommend at a minimum to perform bulk-motion correction in preprocessing and posit that improvements/adaptations are needed for spinal cord distortion preprocessing algorithms, which are currently optimized and designed for brain imaging. Second, we design experiments to evaluate the impact of removing cardiac triggering. We show that when triggering is foregone, images are qualitatively similar to triggered sequences, do not have increased prevalence of artifacts, and result in similar diffusion tensor indices with similar reproducibility to triggered acquisitions. When triggering is removed, much shorter acquisitions are possible, which are also qualitatively and quantitatively similar to triggered sequences. We suggest that removing cardiac triggering for cervical SC diffusion can be a reasonable option to save time with minimal sacrifice to image quality.

neuroscience↗

bioRxiv2023

Single-cell and spatial multi-omics identify innate and stromal modules targeted by anti-integrin therapy in ulcerative colitis.

Ulcerative colitis (UC) is driven by immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin antibody that is effective for treating UC. VDZ is known to inhibit lymphocyte trafficking to the intestine, but its broader effects on other cell subsets are less defined. To identify the inflammatory cells that contribute to colitis and are affected by VDZ, we performed single-cell transcriptomic and proteomic analyses of peripheral blood and colonic biopsies in healthy controls and patients with UC on VDZ or other therapies. Here we show that VDZ treatment is associated with alterations in circulating and tissue mononuclear phagocyte (MNP) subsets, along with modest shifts in lymphocytes. Spatial multi-omics of formalin-fixed biopsies demonstrates trends towards increased abundance and proximity of MNP and fibroblast subsets in active colitis. Spatial transcriptomics of archived specimens pre-treatment identifies epithelial-, MNP-, and fibroblast-enriched genes related to VDZ responsiveness, highlighting important roles for these subsets in UC.

immunology↗

bioRxiv2022

Myeloid mechano-metabolic programming restricts anti-tumor immunity

Tumor progression is accompanied by fibrosis, which is associated with diminished anti-tumor immune infiltrate. Here, we demonstrate that tumor infiltrating myeloid cells respond to the stiffened fibrotic tumor microenvironment (TME) by initiating a TGF-beta (TGF{beta})-directed, collagen biosynthesis program. A collateral effect of this programming is an untenable metabolic milieu for productive CD8 T cell anti-tumor responses, as collagen-synthesizing macrophages consume environmental arginine, synthesize proline, and secrete ornithine that compromises CD8+ T cell function. Thus, a stiff and fibrotic TME may impede anti-tumor immunity not only by direct physical exclusion of CD8+ T cells, but also via secondary effects of a myeloid mechano-metabolic programming we identified that creates an inhospitable metabolic milieu for CD8+ T cells.

cancer biology↗

bioRxiv2021

Cerebellar stimulations prevent Levodopa-induced dyskinesia in mice and normalize brain activity

Chronic Levodopa therapy, the gold-standard treatment of Parkinsons Disease (PD), leads to the emergence of involuntary movements, called levodopa-induced dyskinesia (LID). Cerebellar stimulations have been shown to decrease LID severity in PD patients. Here, in order to determine how cerebellar stimulations induce LID alleviation, we performed daily short trains of optogenetic stimulations of Purkinje cells (PC) in freely moving mice. We demonstrated that these stimulations are sufficient to suppress LID or even prevent their development. This symptomatic relief is accompanied by the normalization of aberrant neuronal discharge in the cerebellar nuclei, the motor cortex and the parafascicular thalamus. Inhibition of the cerebello-parafascicular pathway counteracted the beneficial effect of cerebellar stimulations. Moreover, cerebellar stimulations reversed plasticity in D1 striatal neurons and normalized the overexpression of FosB, a transcription factor causally linked to LID. These findings demonstrate LID alleviation and prevention by daily PC stimulations, which restore the function of a wide brain motor network, and may be valuable for LID treatment.

neuroscience↗

bioRxiv2019

Direct medical and non-medical costs of a one-year care pathway for early breast cancer: results of a French multicenter prospective study

IntroductionThe organization of health care for breast (BC) constitutes a public health challenge to ensure quality of care, while also controlling expenditure. Few studies have assessed the global care pathway of early BC patients, including a description of direct medical costs and their determinants.\n\nMethodsOPTISOINS01 was a multicenter, prospective, observational study including early BC patients from diagnosis to one-year follow-up. Direct medical costs (in-hospital and out-ofhospital costs, supportive care costs) and direct non-medical costs (transportation and sick leave costs) were calculated by using a cost-of-illness analysis based on a bottom-up approach. Resources consumed were recorded in situ for each patient, using a prospective direct observation method.\n\nResultsData from 604 patients were analyzed. Median direct medical costs of 1 year of management after diagnosis in operable BC patients were {euro}12,250. Factors independently associated with higher direct medical costs were: diagnosis on the basis of clinical signs, invasive cancer, lymph node involvement and conventional hospitalization for surgery. Median sick leave costs were {euro}8,841 per patient and per year. Chemotherapy was an independent determinant of sick leave costs ({euro}3,687/patient/year without chemotherapy versus {euro}10,706 with chemotherapy). Forty percent (n=242) of patients declared additional personal expenditure of {euro}614/patient/year. No drivers of these costs were identified.\n\nConclusionInitial stage of disease and the treatments administered were the main drivers of direct medical costs. Direct non-medical costs essentially consisted of sick leave costs, accounting for one-half of direct medical costs for working patients. Out-of-pocket expenditure had a limited impact on the household.

epidemiology↗

bioRxiv2018

Specific metabolic signatures of fish exposed to cyanobacterial blooms

With the increasing impact of the global warming, occurrences of cyanobacterial blooms in aquatic ecosystems are becoming a main ecological concern around the world. Due to their capacity to produce potential toxic metabolites, interactions between the cyanobacteria/cyanotoxin complex and the other freshwater organisms have been widely studied in the past years. Non-targeted metabolomic analyses have the powerful capacity to study a high number of metabolites at the same time and thus to understand in depth the molecular interactions between various organisms in different environmental scenario and notably during cyanobacterial blooms. In this way during summer 2015, liver metabolomes of two fish species, sampled in peri-urban lakes of the ile-de-France region containing or not high concentrations of cyanobacteria, were studied. The results suggest that similar metabolome changes occur in both fish species exposed to cyanobacterial blooms compared to them not exposed. Metabolites implicated in protein synthesis, protection against ROS, steroid metabolism, cell signaling, energy storage and membrane integrity/stability have shown the most contrasted changes. Furthermore, it seems that metabolomic studies will provide new information and research perspectives in various ecological fields and notably concerning cyanobacteria/fish interactions but also a promising tool for environmental monitoring of water pollutions.

ecology↗