Biology subjects

Bressan, D.

Publications and source records attributed to Bressan, D..

14 recordsLinked to original sources

bioRxiv2026

A three-dimensional imaging pipeline for the detection of vasculogenic mimicry in mouse tumor models

Vasculogenic mimicry (VM) describes the ability for tumor cells to mimic endothelial cells and form tumor-lined blood vessels. Although VM is associated with poor prognosis, resistance to therapeutics and metastasis, its presence, relevance and functionality have been debated, largely due to the techniques employed to determine its presence. Dual CD31 and periodic acid-Schiff (PAS) histological staining, the method widely used to detect VM within tumor tissue, is hampered by issues with artifacts of 2D sections and does not assess active blood flow through vessels and hence cannot confirm vessel functionality. Here, we present a 3D imaging pipeline to detect functionally perfused VM and host vessels within mouse tumor models. Mice tumor models are intravenously injected with fluorescently-labelled tomato lectin which binds to the lumen of functional blood vessels. These tumors are thickly sliced, optically-cleared, stained with endothelial markers and imaged using light-sheet microscopy. We apply this imaging modality to image tumors from six breast cancer patient-derived tissue xenograft models, an orthotopic mammary cancer model and two small cell lung cancer circulating-tumor cell explant models, where VM vessels, mosaic vessels and host-VM vessel junctions can be detected. To our knowledge, this is the largest collection of 3D VM vessel images to date, providing convincing evidence of the presence and functionality of VM within tumors and defining the level of evidence necessary to detect VM in vivo.

cancer biology↗

bioRxiv2026

4D spatial transcriptomics reveals nodule identity emerges through stacked parallel developmental programs

Legume root nodules enable symbiotic nitrogen fixation through the development of specialized cells that accommodate nitrogen-fixing bacteria intracellularly and support bacterial nitrogenase activity. Here, we present a 4D (3D space and time) spatial transcriptomic atlas of Medicago truncatula nodules and lateral roots, revealing specialized symbiotic cell types that develop alongside a conserved lateral-root-derived program that underpins vascularization. Spatial profiling of both plant and bacterial transcripts resolves distinct transcriptional states and previously unrecognized cell states. Spatial analysis of developmental regulator mutants uncovers a cascading series of cell-type-specific programs during nodule maturation. LSH1/LSH2 are central regulators of these programs, and lsh1/lsh2 mutants exhibit collapse of hormonal gradients and nodule identity. Strikingly, loss of nodule identity collapses to a primary-root identity rather than lateral-root fate. This work reveals how tissue complexity emerges through stacked developmental programs sustained in distinct cellular compartments, allowing the emergence of cell types specialized for harboring nitrogen-fixing bacteria. HIGHLIGHTSO_LI>136,000 cells define a 4D spatial atlas of nodules and lateral roots C_LIO_LI3D spatial and dual-species analysis resolves dynamic host and rhizobial cell states C_LIO_LIA shared meristem generates 3 spatially coordinated symbiotic, non-symbiotic, and vascular cell programs C_LIO_LILSH1/LSH2 are critical for regulatory programs underlying nodule development and identity C_LIO_LINodule identity loss collapses toward a primary root-associated state, not a lateral root fate C_LI

plant biology↗

bioRxiv2026

Spatially resolved transcriptomic and proteomic profiling reveals cell interaction programs that predict Barrett's esophagus progression

Barretts esophagus (BE) is the precursor lesion of esophageal adenocarcinoma (EAC). It affects approximately 5% of adults in the United States and significantly increases the risk of developing EAC. However, current surveillance strategies cannot reliably distinguish patients who will progress from those who will remain stable. Direct studies of progressor BE are extremely limited due to availability of tissue with known progression outcomes, and have largely been restricted to genomic profiling approaches. The premalignant cellular landscape of progressor BE remains poorly understood. Here, we used complementary spatial transcriptomic and proteomic imaging to profile 34 non-dysplastic BE patients under endoscopic surveillance, including those who subsequently progressed to dysplasia or EAC, termed "Progressors" and those who remained stable, termed "Non-progressors". Transcriptomics based Xenium analysis captured 974,604 cells across 70 whole-biopsy regions, while protein based imaging mass cytometry profiled 372,242 cells across 119 selected regions. FUME-TCRseq further quantified T cell clonotypes from matched tissues scrolls. Cellular composition was generally similar between Progressors and Non-progressors. However, Progressors showed increased intestinal Barretts columnar cells, B cells and gastric progenitor-like cells, together with enhanced immune-epithelial interactions, whereas Non-progressors retained coordinated stromal organization. Spatial interaction features strongly outperformed cell composition and density for progression prediction. Combined spatial interaction model achieved an area under the curve (AUC) of 0.97, compared with 0.62 and 0.68 for comparison and density alone. Complementary imaging mass cytometry further resolved the underlying immune programs, identifying cytotoxic and antigen presenting myeloid features enriched in progressors, and CD56 associated memory T cell interactions enriched in non progressors. Together, these findings support a model that BE progression is driven by progressive remodeling of epithelial-immune-stromal architecture rather than emergence of distinct dysplasia-like cell subsets. Increased T cell clonal diversity and recruitment of cytotoxic and antigen-presenting immune niches may also reflect an evolving response to genomic alteration prior to dysplasia. These results establish spatial tissue architecture, rather than specific cell types, captures progression associated microenvironmental states in BE and provides a framework for spatially informed patient stratification and early cancer risk assessment.

systems biology↗

bioRxiv2025

Non-neuronal, TGF-β- extracellular matrix restructuring promotes neurodegeneration in a PSP-Richardson syndrome model

Progressive supranuclear palsy-Richardson syndrome (PSP-RS) is a rapidly progressive tauopathy lacking effective therapies. Although tau aggregation is a defining feature, the initiating mechanisms remain elusive. Here we used patient-derived induced pluripotent stem cell midbrain organoids, integrating single-cell transcriptomics, bulk RNA profiling, and quantitative proteomics, to dissect early pathogenic events. We identified vascular leptomeningeal-like cells (VLMCs) as the first altered population, exhibiting TGF-{beta}-driven extracellular matrix (ECM) remodeling enriched in collagens, integrins, and TGFBI. The resulting pathological ECM increased stiffness, induced integrin clustering, and activated RhoA-ROCK-mediated cytoskeletal disorganization. These changes sustained PI3K-AKT and MAPK-ERK signaling, suppressed PP2A, hyperactivated mTOR, and impaired autophagy, culminating in tau hyperphosphorylation and mislocalization. Pharmacological inhibition of TGF-{beta}, AKT, ERK, or mTORC1 restored autophagic flux, reduced tau burden, and rescued neuronal architecture. Our findings establish non-neuronal, matrix-producing niche cells as upstream drivers of tauopathy and reveal TGF-{beta}-mediated ECM restructuring as a mechanochemical trigger of neurodegeneration, opening multiple therapeutic avenues for PSP-RS and related tauopathies.

neuroscience↗

bioRxiv2025

Robust Consensus Nuclear and Cell Segmentation

Cell segmentation is a crucial step in numerous biomedical imaging endeavors; so much so that the community is flooded with publicly available, state-of-the-art segmentation techniques ready for out of the box use. Assessing the virtues and limitations of each method on a tissue sample set and then selecting the optimum method for each research objective and input image is a time consuming and exacting task that often monopolizes the resources of biologists, biochemists, immunologists and pathologists; despite not being their project primary research goal. In this work, we present a segmentation software wrapper, coined CellSampler, which runs a selection of established segmentation methods and then combines their individual segmentation masks into a single optimized mask. This, so called uber mask, selects the best of the established masks across local neighborhoods within the image, where the neighborhood size and the statistical measure which determines the qualitative term best are both chosen by the user.

bioinformatics↗

bioRxiv2024

Spatially tuneable multi-omics sequencing using light-driven combinatorial barcoding of molecules in tissues

Mapping the molecular identities and functions of cells within their spatial context is key to understanding the complex interplay within and between tissue neighbourhoods. A wide range of methods have recently enabled spatial profiling of cellular anatomical contexts, some offering single-cell resolution. These use different barcoding schemes to encode either the location or the identity of target molecules. However, all these technologies face a trade-off between spatial resolution, depth of profiling, and scalability. Here, we present Barcoding by Activated Linkage of Indexes (BALI), a method that uses light to write combinatorial spatial molecular barcodes directly onto target molecules in situ, enabling multi-omic profiling by next generation sequencing. A unique feature of BALI is that the user can define the number, size, and shape, and resolution of the spatial locations to be interrogated, with the potential to profile millions of distinct regions with subcellular precision. As a proof of concept, we used BALI to capture the transcriptome, chromatin accessibility, or both simultaneously, from distinct areas of the mouse brain in single tissue sections, demonstrating strong concordance with publicly available datasets. BALI therefore combines high spatial resolution, high throughput, histological compatibility, and workflow accessibility to enable powerful spatial multi-omic profiling.

genomics↗

bioRxiv2024

Rarγ-Foxa1 signaling promotes luminal identity in prostate progenitors and is disrupted in prostate cancer

Retinoic acid (RA) signaling is a master regulator of vertebrate development with crucial roles in directing body axis orientation and tissue differentiation, including in the reproductive system. However, a mechanistic understanding of how RA signaling promotes cell lineage identity in different tissues is often missing. Here, leveraging prostate organoid technology, we demonstrated that RA signaling orchestrates the commitment of adult mouse prostate progenitors to glandular identity, epithelial barrier integrity, and ultimately, proper specification of the prostatic lumen. Mechanistically, RA-dependent RAR{gamma} activation promotes the expression of the pioneer factor Foxa1, which synergizes with the androgen pathway for proper luminal expansion, cytoarchitecture and function. FOXA1 nucleotide variants are common in human prostate and breast cancers and considered driver mutations, though their pathogenic mechanism is incompletely understood. Combining functional genetics experiments with structural modeling of FOXA1 folding and chromatin binding analyses, we discovered that FOXA1F254E255 is a loss-of-function mutation leading to compromised transcriptional function and lack of luminal fate commitment of prostate progenitors. Overall, we define RA as a crucial instructive signal for glandular identity in adult prostate progenitors. We propose deregulation of vitamin A metabolism as a risk factor for benign and malignant prostate disease, and identified cancer associated FOXA1 indels affecting residue F254 as loss-of-function mutations promoting dedifferentiation of adult prostate progenitors. Summary: Retinoic acid signaling orchestrates luminal differentiation of adult prostate progenitors

cancer biology↗

bioRxiv2023

Gene editing in the Chagas disease vector Rhodnius prolixus by Cas9-mediated ReMOT Control

Rhodnius prolixus is currently the model vector of choice for studying Chagas disease transmission, a debilitating disease caused by Trypanosoma cruzi parasites. Despite the broad use of double-stranded RNA interference for the knockdown of gene function in R. prolixus, transgenesis and gene editing protocols are still lacking. Here we tested Receptor-Mediated Ovary Transduction of Cargo (ReMOT Control) and direct parental injection of CRISPR (DIPA-CRISPR) for the maternal delivery of CRISPR/Cas9 elements to developing R. prolixus oocytes, and strategies for the identification of insertions/deletions (indels) in target loci of resulting gene-edited G0 nymphs. We demonstrate successful ReMOT Control-mediated gene editing of the eye color markers Rp-scarlet and Rp-white, and the cuticle color marker Rp-yellow, with highest effectiveness obtained using the ovary-targeting BtKV ligand. These results provide proof-of-concepts for generating somatic mutations in R. prolixus and potentially for generating germline edited lines in triatomines. Our studies also suggest that optimal strategies for recovery of mutations include performing multiple gRNA injections and the use of visible phenotypes such as those displayed in the Rp-scarlet, Rp-white and Rp-yellow loci for future Co-CRISPR experiments. These results will lay the foundation for gene editing protocols for triatomines and could lead to the development of novel control strategies for vectors of Chagas disease. Author SummaryRhodnius prolixus is an insect vector of the protozoan Trypanossoma cruzi, causative agent of debilitating Chagas disease. To fight the spread of the disease, it has been suggested that biological control of the insect should be attempted. Gene editing by the novel CRISPR methodology holds great promise in this sense, as it enables to target almost any gene in the genome for mutagenesis, thus allowing the control of insect physiology and reproduction. Here we have tested protocols for the delivery of CRISPR reagents as an attempt to enable genome editing of the vector. Our results show that maternal delivery of CRISPR by the ReMOT Control method is efficient for mutating eye and cuticle color genes in the resulting nymphs, generating edited animals with red eyes, white eyes or a yellow cuticle. This is the first report of gene editing in a vector of Chagas disease and should lay the basis to produce modified animals either unable to carry the T. cruzi parasite or to reproduce.

molecular biology↗

bioRxiv2023

Dual-modality imaging of immunofluorescence and imaging mass cytometry for whole slide imaging with accurate single-cell segmentation

Imaging mass cytometry (IMC) is a powerful multiplexed tissue imaging technology that allows simultaneous detection of more than 30 makers on a single slide. It has been increasingly used for singlecell-based spatial phenotyping in a wide range of samples. However, it only acquires a small, rectangle field of view (FOV) with a low image resolution that hinders downstream analysis. Here, we reported a highly practical dual-modality imaging method that combines high-resolution immunofluorescence (IF) and high-dimensional IMC on the same tissue slide. Our computational pipeline uses the whole slide image (WSI) of IF as a spatial reference and integrates small FOVs IMC into a WSI of IMC. The high-resolution IF images enable accurate single-cell segmentation to extract robust high-dimensional IMC features for downstream analysis. We applied this method in esophageal adenocarcinoma of different stages, identified the single-cell pathology landscape via reconstruction of WSI IMC images, and demonstrated the advantage of the dual-modality imaging strategy. MotivationHighly multiplexed tissue imaging allows visualization of the spatially resolved expression of multiple proteins at the single-cell level. Although imaging mass cytometry (IMC) using metal isotope-conjugated antibodies has a significant advantage of low background signal and absence of autofluorescence or batch effect, it has a low resolution that hampers accurate cell segmentation and results in inaccurate feature extraction. In addition, IMC only acquires mm2-sized rectangle regions, which limits its application and efficiency when studying larger clinical samples with non-rectangle shapes. To maximize the research output of IMC, we developed the dual-modality imaging method based on a highly practical and technical improvement requiring no extra specialized equipment or agents and proposed a comprehensive computational pipeline that combines IF and IMC. The proposed method greatly improves the accuracy of cell segmentation and downstream analysis and is able to obtain whole slide image IMC to capture the comprehensive cellular landscape of large tissue sections.

bioinformatics↗

bioRxiv2022

Genome wide screen of RNAi molecules against SARS-CoV-2 creates a broadly potent prophylaxis

Expanding the arsenal of prophylactic approaches against SARS-CoV-2 is of utmost importance, specifically those strategies that are resistant to antigenic drift in Spike. Here, we conducted a screen with over 16,000 RNAi triggers against the SARS-CoV-2 genome using a massively parallel assay to identify hyper-potent siRNAs. We selected 10 candidates for in vitro validation and found five siRNAs that exhibited hyper-potent activity with IC50<20pM and strong neutralisation in live virus experiments. We further enhanced the activity by combinatorial pairing of the siRNA candidates to develop siRNA cocktails and found that these cocktails are active against multiple types of variants of concern (VOC). We examined over 2,000 possible mutations to the siRNA target sites using saturation mutagenesis and identified broad protection against future variants. Finally, we demonstrated that intranasal administration of the siRNA cocktail effectively attenuates clinical signs and viral measures of disease in the Syrian hamster model. Our results pave the way to development of an additional layer of antiviral prophylaxis that is orthogonal to vaccines and monoclonal antibodies.

genomics↗

bioRxiv2021

Exploration and analysis of molecularly annotated, 3D models of breast cancer at single-cell resolution using virtual reality

A set of increasingly powerful approaches are enabling spatially resolved measurements of growing numbers of molecular features in biological samples. While important insights can be derived from the two-dimensional data that many of these technologies generate, it is clear that extending these approaches into the third and fourth dimensions will magnify their impact. Realizing biological insights from datasets where thousands to millions of cells are annotated with tens to hundreds of parameters in space will require the development of new computational and visualization strategies. Here, we describe Theia, a virtual reality-based platform, which enables exploration and analysis of either volumetric or segmented, molecularly-annotated, three-dimensional datasets, with the option to extend the analysis to time-series data. We also describe our pipeline for generating annotated 3D models of breast cancer and supply several datasets to enable users to explore the utility of Theia for understanding cancer biology in three dimensions.

cancer biology↗

bioRxiv2021

The Imaging and Molecular Annotation of Xenografts and Tumours (IMAXT) High Throughput Data and Analysis Infrastructure

With the aim of producing a 3D representation of tumours, IMAXT uses a large variety of modalities in order to acquire tumour samples and produce a map of every cell in the tumour and its host environment. With the large volume and variety of data produced in the project we develop automatic data workflows and analysis pipelines and introduce a research methodology where scientists connect to a cloud environment to perform analysis close to where data are located instead of bringing data to their local computers. Here we present the data and analysis infrastructure, discuss the unique computational challenges and describe the analysis chains developed and deployed to generate molecularly annotated tumour models. Registration is achieved by use of a novel technique involving spherical fiducial marks that are visible in all imaging modalities used within IMAXT.

cancer biology↗

bioRxiv2020

Pigmentation loci as markers for genome editing in the Chagas disease vector Rhodnius prolixus

The kissing bug Rhodnius prolixus is a major vector for Chagas disease in the Americas, and also considered as the primary model for functional studies. Prospective transgenic approaches and genome editing strategies hold great promise for controlling insect populations as well as disease propagation. In this context, identifying visible genetic markers for transgenic methodologies is of paramount importance to advance the field. Here we have identified and analyzed the function of putative cuticle and eye color genes by investigating the effect of gene knockdown on fertility, viability, and the generation of visible phenotypes. Synthesis of the dark, yellow and tan pigments present in the cuticle of most insects depends on the function of key genes encoding enzymes in the tyrosine pathway. Knockdown of the R. prolixus yellow and aaNAT/pro orthologs produces striking alterations in cuticle color. Surprisingly, knockdown of ebony does not generate visible phenotypes. Since loss of ebony function results in a dark cuticle in several insect orders, we conclude that R. prolixus evolved alternative strategies for cuticle coloration, possibly including the loss of a pigmentation function for an entire branch of the tyrosine pathway. Knockdown of the scarlet and brown genes - encoding ABC transporters - alters cuticle and eye pigmentation, implying that the transport of pigment into proper organelles is an important process both for cuticle and eye coloration in this species. Therefore, this analysis identifies for the first time potential visible markers for transgenesis in a hemipteran vector for a debilitating human disease. Author SummaryThe hemipteran Rhodnius prolixus - also known as a kissing bug - is a main vector transmitting the parasite Trypanosoma cruzi, the causative agent of Chagas disease, a debilitating infection estimated to affect more than 6 million people in Central and South America. In order to limit disease spread, an important measure is insect vector control. However, kissing bugs - like other insects - develop resistance to insecticides. Alternative strategies based on transgenesis and the recently developed CRISPR- based genome edition hold great promise to control vector population or generate parasite-resistant insects. For these approaches to be feasible in R. prolixus, it is critical to identify visible phenotypic markers. Here we identify and describe several genes controlling cuticle and eye pigmentation that are well-suited putative landing sites for transformation strategies. Among these, loss-of-function mutations in the ABC transporter encoding scarlet and the tyrosine pathway enzyme encoding aaNAT/pro generate striking and easily visible phenotypes. Importantly, the knockdown of these genes does not affect insect viability and fertility under laboratory conditions. Our results suggest that R. prolixus has developed alternative strategies for cuticle coloration involving the loss of an entire branch of tanning loci, while the other branch producing cuticle patterns by generating non-pigmented areas has gained critical importance.

genetics↗

bioRxiv2017

Using high-throughput barcode sequencing to efficiently map connectomes

The function of a neural circuit is determined by the details of its synaptic connections. At present, the only available method for determining a neural wiring diagram with single synapse precision--a \"connectome\"--is based on imaging methods that are slow, labor-intensive and expensive. Here we present SYNseq, a method for converting the connectome into a form that can exploit the speed and low cost of modern high-throughput DNA sequencing. In SYNseq, each neuron is labeled with a unique random nucleotide sequence--an RNA \"barcode\"--which is targeted to the synapse using engineered proteins. Barcodes in pre- and postsynaptic neurons are then associated through protein-protein crosslinking across the synapse, extracted from the tissue, and then joined into a form suitable for sequencing. Although at present the inefficiency in our hands of barcode joining precludes the widespread application of this approach, we expect that with further development SYNseq will enable tracing of complex circuits at high speed and low cost.

neuroscience↗