Biology subjects

Rossi, F.

Publications and source records attributed to Rossi, F..

At least 19 recordsLinked to original sources

bioRxiv2026

GABAergic Circuit Activation Induces a Therapeutically Responsive State for anti-PD-L1 Immunotherapy in Glioblastoma

Glioblastoma (GBM) disrupts cortical excitatory-inhibitory balance and establishes an immunosuppressive microenvironment that limits therapeutic efficacy. Whether restoring inhibitory signaling can restrain glioma progression and improve responsiveness to immune checkpoint blockade remains unknown. Peritumoral parvalbumin-positive (PV+) interneurons were bidirectionally manipulated by chemogenetics in orthotopic GL261 gliomas to assess tumor growth and neurological function. GABAB signaling was pharmacologically activated with baclofen in GL261 and CT-2A models and combined with anti-PD-L1 blockade in GL261. Therapeutic response, survival, tumor rechallenge, and early myeloid remodeling were evaluated. Human GBM single-cell transcriptomic data were analyzed to examine the relationship between GABAergic and PD-L1 intercellular signaling. PV activation transiently restrained glioma growth, reduced tumor proliferation and preserved cortical function, whereas PV+ silencing increased seizure susceptibility and neurological impairment without accelerating tumor growth. Baclofen monotherapy did not affect survival, whereas its combination with anti-PD-L1 immunotherapy induced complete tumor eradication in 66% of GL261-bearing mice, prolonged survival, and conferred durable protection against tumor rechallenge. Combination therapy also altered the proportions of Arg1+ and CD11c+ cells within the intratumoral F4/80+ compartment. Human single-cell analysis revealed a shared myeloid-centered communication axis linking GABAB and PD-L1 signaling. These findings identify GABAergic signaling as a modulator of GBM progression and demonstrate that combining baclofen with anti-PD-L1 induces durable tumor regression, and prolongs survival in the GL261 model, supporting a neuro-immune framework for combining GABAergic modulation with immunotherapy.

cancer biology↗

bioRxiv2026

Pathology-Targeted EP4 Agonism Reverses Fibrosis in a Rat Model of DMD

Duchenne muscular dystrophy (DMD) presents a critical therapeutic gap in adolescent patients, where extensive fibro-fatty muscle replacement and depletion of the regenerative niche render existing interventions insufficient. Prostaglandin E2 signaling through the EP4 receptor stimulates bone and muscle regeneration and repair, but systemic off-target effects have limited the clinical translation of EP4 agonism in diseases such as DMD. We therefore evaluated irodanoprost (IROD), a bone-targeted prodrug of an EP4-selective agonist, in a DMD rat model, comparing early- and late-intervention cohorts. In adolescent rats, 8 weeks of treatment reduced body weight deficit by 41.4% and restored hindlimb muscle mass and maximum tetanic force to wild-type levels. IROD dose-dependently inhibited fibro-adipogenic progenitor differentiation into -SMA myofibroblasts, facilitating active resolution of established fibrosis below pre-treatment baseline. This was accompanied by re-activation of a synchronized regenerative program marked by clustered eMHC fibers, restoring the total myofiber pool to wild-type levels. A strong linear correlation between intramuscular fat reduction and fibrosis resolution suggests that MRI-based fat imaging may serve as a non-invasive surrogate for monitoring anti-fibrotic efficacy. The efficacy of IROD is likely aided by the fact that while it selectively distributes to bone in healthy animals, we observed markedly enhanced accumulation of the drug in dystrophic muscle. These findings establish IROD as a pathology-targeted approach capable of resolving the fibro-fatty niche and restoring regenerative capacity in advanced DMD. SummaryPathology-targeted EP4 agonism resolves established fibrosis and restores myofiber regeneration in a rat model of adolescent Duchenne dystrophy. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/728674v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@20447dorg.highwire.dtl.DTLVardef@70929dorg.highwire.dtl.DTLVardef@a99628org.highwire.dtl.DTLVardef@1c158f4_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2026

Differential impact of FLASH and conventional radiotherapy on a pivotal metabolic organ: White Adipose Tissue

BACKGROUNDSubcutaneous white adipose tissue (scWAT), a key metabolic and endocrine organ, is inevitably exposed during radiotherapy (RT). While RT is a cornerstone of cancer treatment, its efficacy is limited by toxicity to surrounding healthy tissues. Ultra-high dose rate (FLASH) RT has emerged as a promising modality capable of preserving tumor control while reducing normal tissue damage - the so-called FLASH effect. Clinical evidence indicates that childhood exposure to conventional (CONV) RT is associated with long-term dysmetabolism and WAT dysfunction. However, the impact of FLASH-RT on WAT has not been investigated. AIMTo compare the effects of FLASH- and CONV-RT on adipocyte function and scWAT homeostasis, and to identify molecular and structural changes associated with each modality. METHODSWe evaluated the effects of FLASH- and CONV-RT on adipocytes and scWAT using a dedicated linear accelerator capable of delivering both modalities. Experiments were performed in the human SGBS preadipocyte/adipocyte cell line and in a mouse model subjected to proximal hind limb irradiation, with analyses conducted 70 days post-exposure. RESULTSRT impaired adipogenic differentiation in a dose-dependent manner, with a relative sparing effect of FLASH at 4-8 Gy. Mature adipocytes exhibited radioresistance, with protection by FLASH at 8 Gy. In vivo, both regimens reduced fat mass without affecting body weight, with greater loss following CONV-RT. Transcriptomic profiling of scWAT revealed inflammatory and neurodegenerative signatures after CONV-RT, whereas FLASH-RT induced minimal transcriptional changes. Histological and ultrastructural analyses confirmed increased cellular damage, vacuolization, lipid spill-over, and reduced PLIN1 expression, predominantly in CONV-treated mice. CONCLUSIONSWAT homeostasis is sensitive to conventional RT, whereas FLASH-RT better preserves tissue structure and function, with implications for long-term metabolic health in cancer survivors.

physiology↗

bioRxiv2026

Co-expression-based models improve eQTL predictions and highlightnovel transcriptome-wide genes associated with schizophrenia

Non-coding genetic variants statistically associated with complex heritability phenotypes are thought to act primarily through transcriptome regulatory mechanisms. Predictions of gene expression in tissue like the human brain traditionally rely primarily on cis-eQTLs. Here, we introduce INGENE and MODULE, trans-eQTLs models designed to enhance the prediction of gene expression by capturing the collective impact of candidate trans-eQTLs acting within co-expression networks. Exploiting RNA-seq data in six post-mortem brain regions (amygdala, caudate nucleus, dorsal/subgenual anterior cingulate cortex, dorsolateral prefrontal cortex, and hippocampus), we validate our models on two testing datasets, demonstrating increased gene predictability compared to both an original cis-based model and to EpiXcan, the leading benchmark in cis-model performance. Integration of cis- and trans-predictions significantly improves gene-level expression imputation (MLE = 0.05) for 18,744 genes across the six brain regions considered. Applying cis and trans models to PGC wave 3 genotypes identifies 766 SCZ-associated genes across brain regions (pFDR < .01), emphasizing the complementary nature of cis and trans predictions in trait association discovery. Of these genes, 641 represent novel transcriptome-wide associations with schizophrenia, highlighting the role of trans-heritability and genetic interactions underlying risk for this disorder, in addition to further supporting 125 previous candidates.

genomics↗

bioRxiv2025

Localized FLASH Radiotherapy Reduces Long-Term Skin and Muscle Damage While Preserving Systemic Homeostasis

Radiotherapy (RT) is a cornerstone treatment for nearly 50% of cancer patients, but its curative potential and safe dosing are constrained by cumulative toxicity to surrounding healthy tissues. Delivering RT at ultra-high dose rates (FLASH-RT) represents a transformative strategy, as it appears to maintain tumor control, while sparing normal tissue. Melanoma is among the most radioresistant tumors, and skin and muscle are invariably exposed during RT, also in case of deep seated tumors. Here, we compared electron FLASH-RT and conventional RT (CONV-RT) in melanoma-bearing and naive mice assessing tumor control, tissue integrity, and systemic homeostasis over the medium to long term. Both modalities achieved comparable tumor suppression. However, CONV-RT induced persistent skin damage, dermal fibrosis, muscle dysfunction and systemic inflammatory-metabolic alterations, while FLASH-RT largely spared normal tissue and systemic balance. Bulk RNA sequencing revealed striking differences: FLASH induced minimal transcriptional disruption in skin and muscle, whereas CONV-RT triggered thousands of differentially expressed genes, including massive activation of fibrosis, inflammation, cell death-related pathways in skin, and broad dysregulation of genes linked to muscle function, remodeling and the unfolded protein response. Histological and ultrastructural analyses corroborated the findings, showing reduced immune infiltration in the skin and preserved tissue architecture both in skin and muscle following FLASH. In conclusion our study not only confirms the protective nature of FLASH but also provides novel mechanistic insights into the cascade linking local injury to systemic dysfunction under CONV-RT, reinforcing the translational potential of FLASH to expand the therapeutic window of radiotherapy. One Sentence SummaryComparative analysis of FLASH and conventional radiotherapy in a murine model of melanoma and naive mice - Therapeutical efficacy, local and systemic effects.

physiology↗

bioRxiv2025

Form Follows Function: A New Paradigm of Pancreatic Cancer Progression

Pancreatic ductal adenocarcinoma (PDAC) exhibits a distinctive propensity to invade nearby organs and infiltrate large blood vessels, even in the absence of distant metastasis. While the genetic and transcriptomic drivers of PDAC progression have been well studied, the mechanisms by which these molecular changes translate into functional, invasive behavior remain largely unknown. Here, we uncover a striking level of tissue organization, characterized by previously unrecognized spatial and geometric properties within and among tumor structures. Leveraging the first large-scale, AI-assisted, human-curated PDAC atlas from hematoxylin and eosin (H&E) images, we annotated, classified, and characterized 144,474 malignant and normal structures from treatment-naive (n=118) and neoadjuvant-treated PDAC patients (n=50). Additionally, we developed a new computational tool, SHAPE, to investigate PDAC aggressiveness through a comprehensive "geometrization" of cancer progression. Using traditional H&E-stained slides and three-dimensional (3D) tissue reconstruction experiments, we observed that invading tumor structures display an eccentric morphology with pronounced local angular coherence. These geometric and spatial properties revealed coherent architectural patterns, with invasive structures closely tracking vessels and nerves as they infiltrate surrounding tissue. Mechanistically, integration of morphological features from 39,045 annotated tumor structures with whole-genome and RNA sequencing data revealed that PDACs with numerous eccentric structures exhibit increased copy number alterations (CNAs), loss of heterozygosity (LoH) on the p-arm of chromosome 17, and a quasi-mesenchymal/basal-like molecular subtype. Spatial transcriptomic analysis of 1,650 tumor structures from six additional PDAC patients further confirmed upregulation of invasive cellular programs within highly eccentric structures, such as epithelial-to-mesenchymal transition (EMT), angiogenesis, coagulation, and complement pathways, underscoring their infiltrative nature. Finally, cross-validation of our AI-based method enabled a fully automated, highly interpretable computational approach to assist pathologists and clinicians in evaluating neoadjuvant chemotherapy response, predicting patient survival, and guiding chemotherapy in adjuvant settings. Collectively, these findings deepen our understanding of PDAC progression, identify a new hallmark of tumor architecture, and pave the way for full integration of AI-driven morphology-based approaches into clinical workflows to improve the management of PDAC patients.

cancer biology↗

bioRxiv2025

Circuit-Based Understanding of Fine Spatial Scale Clustering of Orientation Tuning in Mouse Visual Cortex

In sensory cortex of brain it is often the case that neurons are spatially organized by their functional properties. A hallmark of primary visual cortex (V1) in higher mammals is a columnar functional map, where neurons tuned to different stimuli features are regularly organized in space. However, rodent visual cortex is at odds with this rule and lacks any spatially ordered functional architecture, and rather neuron feature preference is haphazardly organized in patterns termed salt-and-pepper. This sharp contrast in feature organization between the visual cortices of rodents and higher mammals has been a persistent mystery, fueled in part by abundant evidence of conserved cortical physiology between species. In this work, we applied a novel GCaMP indicator that are localized in the nucleus of neurons during two-photon imaging in mouse V1, which enabled us to overcome most spurious spatially correlated activity due to fluorescence contamination, and to ensure a faithful observation of functional organization over space. We found that the orientation tuning properties of distant neuron pairs (> 20 {micro}m) are irregularly and randomly organized, while neuron pairs that are extremely close (< 20 {micro}m) have strongly correlated orientation tuning, indicating a narrow yet strong spatially clustered organization of orientation preference, which we term micro-clustered organization. Exploring a circuit-based model of recurrently coupled mouse V1 we derived two key predictions for the micro-cluster: spatially localized recurrent connections over a comparable narrow spatial scale, and common relative spatial spreads of balanced excitation and inhibition in the network over broad spatial scales. These predictions are validated by both anatomical and optogenetic-based physiological circuit mapping experiments. Altogether, our work takes an important step in building a circuit-based theory of visual processing in mouse V1 over spatial scales that are often ignored, yet contain powerful synaptic interactions.

neuroscience↗

bioRxiv2024

Single-cell resolution spatial analysis of antigen-presenting cancer-associated fibroblast niches

Recent studies have identified a unique subtype of cancer-associated fibroblasts (CAFs) termed antigen-presenting CAFs (apCAFs), which remain the least understood CAF subtype. To gain a comprehensive understanding of the origin and function apCAFs, we construct a fibroblast molecular atlas across 14 types of solid tumors. Our integration study unexpectedly reveals two distinct apCAF lineages present in most cancer types: one associated with mesothelial-like cells and the other with fibrocytes. Using a high-resolution single-cell spatial imaging platform, we characterize the spatial niches of these apCAF lineages. We find that mesothelial-like apCAFs are located near cancer cells, while fibrocyte-like apCAFs are associated with tertiary lymphoid structures. Additionally, we discover that both apCAF lineages can up-regulate the secreted protein SPP1, which facilitates primary tumor formation and peritoneal metastasis. Taken together, this study offers an unprecedented resolution in analyzing apCAF lineages and their spatial niches.

cancer biology↗

bioRxiv2024

DnaB and DciA: Mechanisms of Helicase Loading and Translocation on ssDNA

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/622779v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@b0641dorg.highwire.dtl.DTLVardef@7caf59org.highwire.dtl.DTLVardef@1dc0fccorg.highwire.dtl.DTLVardef@913ce2_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO The Vibrio cholerae (Vc) DnaB replicative helicase structure bound to single-stranded (ss) DNA is depicted in the ribbon (top left) and sphere-cylinder representation (top right). In the bottom center is a native mass spectrum showing Vc DnaB helicase loading onto single-stranded DNA (ssDNA). C_FIG Replicative helicases are assembled on chromosomes by helicase loaders before initiation of DNA replication. Here, we investigate mechanisms used by the bacterial Vibrio cholerae (Vc) DnaB replicative helicase and the DciA helicase loader. Structural analysis of the ATP{gamma}S form of the VcDnaB-ssDNA complex reveals a configuration distinct from that seen with GDP*AlF4. With ATP{gamma}S, the amino-terminal (NTD) tier, previously found as an open spiral in the GDP*AlF4 complex, adopts a closed planar arrangement. Further, the DnaB subunit at the top of the carboxy-terminal spiral (CTD) tier is displaced by [~]25 [A] between the two forms. We suggest that remodeling the NTD layer between closed planar and open spiral configurations and migration of two distinct CTDs to the top of the DnaB spiral, repeated three times, mediates hand-over-hand translocation. Biochemical analysis suggests that VcDciA leverages its Lasso domain to contact DnaB near its Docking-Linker-Helix interface. Up to three copies of VcDciA bind to VcDnaB and suppress its ATPase activity during loading onto physiological DNA substrates. Our data suggest that DciA loads DnaB onto DNA using the ring-opening mechanism.

biochemistry↗

bioRxiv2023

Clouds, oases for airborne microbes. Differential metagenomics/ metatranscriptomics analyses of cloudy and clear atmospheric situations

Bacteria cells and fungal spores can aerosolize and remain suspended in the atmosphere for several days, exposed to water limitation, oxidation, and lack of nutrients. Using comparative metagenomics/metatranscriptomics, we show that clouds are associated with the activation of numerous metabolic functions in airborne microorganisms, including fungal spore germination. The whole phenomenon mirrors the rapid recovery of microbial activity in soils after rewetting by rain, known as the "Birch effect". Insufficient nutrient resources in cloud droplets cause a famine that recycling cellular structures could alleviate. The recovery of metabolic activity by microorganisms in clouds could favor surface invasion upon deposition, but it may also compromise further survival upon cloud evaporation. In any case, clouds appear as floating biologically active aquatic systems. One-Sentence SummaryClouds activate metabolic processes in airborne microorganisms

ecology↗

bioRxiv2023

Experimental and methodological framework for the assessment of nucleic acids in airborne microorganisms

Studying airborne microorganisms is highly challenging due to ultra-low and spread biomass, and great spatial and temporal variabilities at short scales. Aeromicrobiology is still an emerging discipline of environmental microbiology, and some of the basic practices (replication, control of contaminants, etc) are not yet widely adopted, which potentially limits conclusions. Here we aim at evaluating the benefits of such practices in the study of the aeromicrobiome using molecular-based approaches, and recommend the following: (i) sample at high airflow rate, if possible into a fixative agent, in order to be able to capture specific situations ; (ii) replicate sampling and process samples individually to enable statistical analyses ; (iii) check for contaminants at different steps of the analytical process, and account for their potential stochasticity in sequence decontamination methods ; (iv) include internal references to verify qualitative and quantitative aspects of the data, and (v) eventually investigate multiple analytical procedures to identify potential impacts on the data. In our study, samples were collected at a remote mountain site using high-flow rate impingers collecting airborne material into nucleic acid preservation buffer. As high of [~]75% of the sequences were shared between independent triplicates, gathering 28 to 38% of the richness observed at the ASV level at a given sampling date, which also emphasizes spatial heterogeneity at short scale due to rare taxa. Thanks to replicates, daily variations in the diversity of bacteria could be distinguished statistically, and the inevitable presence of contaminating sequences in controls could be accounted for using established statistical methods. This work opens new perspectives and notably paves the way to untargeted molecular methods in the exploration of aeromicrobiomes composition and functioning. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/561683v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@48bddcorg.highwire.dtl.DTLVardef@1a8c3fforg.highwire.dtl.DTLVardef@dba98forg.highwire.dtl.DTLVardef@159055e_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

GARSA: An integrative pipeline for genome wide association studies and polygenic risk score inference in admixed human populations

Genome-wide association studies (GWAS) and polygenic risk scores (PRS) are multistep analytical tools to identify genetic variants and to assess their contribution to phenotypes/diseases. These analyses are evolving and becoming instrumental to understand the genetic architecture of complex phenotypes/diseases. Nevertheless, to date, there is no single solution incorporating all major steps related to those analyses combined with robust populational bias correction. Here, we describe a semi-automated pipeline unifying steps involved in GWAS and PRS including widely used software. Our pipeline handles quality control (QC), GWAS, and PRS steps, managing different types of input/output files. Furthermore, it includes robust bias correction steps, such as inference of kinship matrix with correction for population structure, use of principal component analysis (PCA) with detection and removal of outlier variant followed by re-projection of related individuals (if desired), generation of PCA figures that assist in setting the best number of principal components (PCs) for association analysis, availability of mixed models, use of recommended software for GWAS based on population size, and a Markov chain Monte Carlo (MCMC) method to estimate best set of PRS parameters. Finally, we tested GARSA pipeline in a family-based Brazilian admixed population and demonstrated that the corrections implemented indeed mitigate bias in downstream analysis. The pipeline can be implemented on personal or server-side environments. AvailabilityThe development version (open-source) is available in https://github.com/LGCM-OpenSource/GARSA ContactFernando P. N. Rossi - fernando.rossi@hc.fm.usp.br; Jose S. L. Patane - jose.patane@hc.fm.usp.br Supplementary informationSupplementary tutorial.

bioinformatics↗

bioRxiv2023

Leveraging the power of 3D brain-wide imaging and mapping tools for brain injury research in murine models

Despite the fundamental importance of understanding impaired brain activity exhibited in post-traumatic epilepsy and other neurological impairments associated with traumatic brain injury (TBI), knowledge of how brain injury affects neuronal activity remains remarkably incomplete. We describe a whole-brain imaging and analysis approach to identify alterations in neuronal activity after TBI as a complementary method to conventional two-dimensional (2D) histological approaches. Here we report an easy-to-follow experimental pipeline to quantify changes in the whole mouse brain using tissue clearing, light sheet microscopy (LSM) and an optimised open-access atlas registration workflow. We validated the outcome of the pipeline using high throughput image analysis software and a secondary atlas registration method. Using the CHIMERA (Closed-Head Impact Model of Engineered Rotational Acceleration) TBI model, TRAP2 mice were subjected to repeated mild TBI or sham treatment followed by tamoxifen injection to lock c-Fos activity after TBI. Brains were SHIELD fixed and passively cleared for imaging of c-Fos+ cells throughout the rostro-caudal axis of the brain using a light sheet microscope equipped with a specialized whole-brain imaging chamber. Volumetric images were stitched and 3D rendered using Arivis Vision4D image analysis software. For quantitative analysis, 2D image stacks were exported to segment c-Fos+ cells and register them to the Allen Mouse Brain Atlas using the BrainQuant3D python package. As a result, c-Fos+ cell counts were estimated throughout the brain and heatmaps were generated. We identified a brain-wide reduction in c-Fos cell density in the TBI group compared to sham controls, indicative of TBI-induced changes in whole brain neuronal activity. Further studies using multi-dimensional imaging coupled with analysis tools will deepen our understanding of post-TBI brain-wide dynamics.

neuroscience↗

bioRxiv2022

Ocean currents drive the worldwide colonization of the most widespread marine plant, eelgrass (Zostera marina)

Currents are unique drivers of oceanic phylogeography and so determine the distribution of marine coastal species, along with past glaciations and sea level changes. Here, we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Multiple west to east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present since [~]208 Kya (thousand years ago). Mediterranean populations were founded [~]53 Kya while extant distributions along western and eastern Atlantic shores coincide with the end of the Last Glacial Maximum ([~]20 Kya). The recent colonization and 5-to 7-fold lower genomic diversity of Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.

evolutionary biology↗

bioRxiv2022

A novel computational approach to identify cancer cells in scRNA-seq data

Single-cell RNA-seq is an invaluable research tool that allows for the investigation of gene expression in heterogeneous cancer cell populations in ways that bulk RNA-seq cannot. However, normal (i.e., non tumor) cells in cancer samples have the potential to confound the downstream analysis of single-cell RNA-seq data. Several existing methods for identifying tumor cells use copy number variation inference. This work aims to extend existing approaches for identifying cancer cells in single-cell RNA-seq samples by incorporating putative driver alterations. We found that putative driver alterations can be detected in single-cell RNA-seq data and that a subset of cells in tumor samples are enriched in putative driver alterations as compared to normal cells. Furthermore, we show that the number of putative driver alterations and inferred copy number variation are not correlated in all samples. Taken together, our findings suggest that combining copy number variation inference with putative driver mutation load can augment the number of tumor cells that can be confidently included in downstream analyses of single-cell RNA-seq datasets.

bioinformatics↗

bioRxiv2022

A SARS-CoV-2 Spike Ferritin Nanoparticle Vaccine is Protective and Promotes a Strong Immunological Response in the Cynomolgus Macaque Coronavirus Disease 2019 (COVID-19) Model

The COVID-19 pandemic has had a staggering impact on social, economic, and public health systems worldwide. Vaccine development and mobilization against SARS-CoV-2 (the etiologic agent of COVID-19) has been rapid. However, novel strategies are still necessary to slow the pandemic, and this includes new approaches to vaccine development and/or delivery, which improve vaccination compliance and demonstrate efficacy against emerging variants. Here we report on the immunogenicity and efficacy of a SARS-CoV-2 vaccine comprised of stabilized, pre-fusion Spike protein trimers displayed on a ferritin nanoparticle (SpFN) adjuvanted with either conventional aluminum hydroxide or the Army Liposomal Formulation QS-21 (ALFQ) in a cynomolgus macaque COVID-19 model. Vaccination resulted in robust cell-mediated and humoral responses and a significant reduction of lung lesions following SARS-CoV-2 infection. The strength of the immune response suggests that dose sparing through reduced or single dosing in primates may be possible with this vaccine. Overall, the data support further evaluation of SpFN as a SARS-CoV-2 protein-based vaccine candidate with attention to fractional dosing and schedule optimization.

microbiology↗

bioRxiv2022

Connecting the Dots: PHF13 and cohesin promote polymer-polymer phase separation of chromatin into chromosomes

How interphase chromatin compacts into mitotic chromosomes has eluded researchers for over a century. Here we show that PHF13, a tightly regulated H3K4me epigenetic reader, and cohesin, a mediator of chromatin architecture, cooperate to drive polymer-polymer-phase-separation (PPPS) and higher order compaction of chromatin into chromosomes. PHF13 interacts with cohesin, shows similar dynamics during mitosis, and their co-depletion dramatically impairs mitotic condensation. Mechanistically, we demonstrate that PHF13 stabilizes cohesin chromatin interactions and that itself oligomerizes, resulting in a polymer with increased chromatin avidity and the ability to bridge neighboring and distant nucleosomes. Consistently, molecular dynamic simulations modelling the ability of PHF13 and cohesin to drive chromatin phase separations recapitulated our in vivo observations and are in line with 2-step condensation models.

cell biology↗

bioRxiv2021

Extraction and high-throughput sequencing of oak heartwood DNA: assessing the feasibility of genome-wide DNA methylation profiling

Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability of oak heartwood and hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies of the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. In this study, we aimed to establish protocols for the extraction of DNA, the high-throughput sequencing of whole-genome DNA libraries (WGS) and the profiling of DNA methylation by whole-genome bisulfite sequencing (WGBS) for oak (Quercus spp.) heartwood drill cores taken from the trunks of living standing trees spanning the AD 1776-2014 time period. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. Whole-genome and DNA methylome library preparation and sequencing consistently failed for oak heartwood samples more than 100 and 50 years of age, respectively. DNA fragmentation increased with sample age and was exacerbated by the additional bisulfite treatment step during methylome library preparation. Relative coverage of the non-repetitive portion of the oak genome was sparse. These results suggest that quantitative methylome studies of oak hardwood will likely be limited to relatively recent samples and will require a high sequencing depth to achieve sufficient genome coverage.

plant biology↗