Biology subjects

Rosa, R.

Publications and source records attributed to Rosa, R..

14 recordsLinked to original sources

bioRxiv2026

Focal radiotherapy improves CAR T cell therapy targeting prostate cancer

Chimeric antigen receptor (CAR) T cell therapy has limited efficacy against solid tumors such as prostate cancer due to the immunosuppressive tumor microenvironment (TME). Combining CAR T cells with existing therapies that remodel the TME and promote endogenous immune responses, such as radiation therapy and chemotherapies, may strengthen antitumor responses. Here, we assessed the potency of combining focal radiotherapy (RT), cyclophosphamide (Cy) preconditioning, and prostate stem cell antigen (PSCA)-CAR T cells against syngeneic prostate cancer models. Focal RT alone increased T cell and dendritic cell infiltration and activation in the irradiated tumor. Furthermore, the combination of all three therapies was critical for enhanced antitumor responses and survival across multiple subcutaneous, bone-metastatic, and multifocal disease models. This combination, in the irradiated TME and tumor-draining lymph nodes (tdLN), led to greater antigen presentation by myeloid cells and endogenous T cell activation and cytotoxicity. Our study demonstrates the potency of combining focal RT with PSCA-CAR T cells, significantly improving therapeutic responses in the irradiated tumor and contributing to a more robust systemic immune response against metastatic burden in prostate cancer.

Cancer Biology↗

bioRxiv2026

Beyond competence: a mechanistic model of avian demographic drivers in West Nile virus dynamics

BackgroundWest Nile virus (WNV) is a vector-borne zoonotic pathogen maintained in an enzootic cycle between birds and mosquitoes which is considered a significant public health concern in Europe, particularly in relation to its recent increase in reported human cases and range expansion. While a comprehensive understanding of the viruss epidemiological dynamics is essential to inform effective prevention and control strategies, to date significant knowledge gaps remain in quantifying interspecific differences within the complex avian communities involved in WNV circulation. Globally, WNV-infection has indeed been documented across more than 300 bird species, however, whether and how inter-specific differences in avian hosts traits affect the spread of WNV is still largely unknown. A substantial body of research has investigated how epidemiological traits, such as the duration of infection and competence, influence WNV dynamics. However, much less is known about the role of avian demography. Methodology/Principal findingsWe therefore investigated through mathematical modelling the role of avian demographic traits in shaping patterns of mosquito WNV infection dynamics in northern Italy (Lombardy Region, 2016-2018). We focused on the effects of annual offspring production, timing and synchrony of breeding which ultimately affect seasonal abundance of competent avian hosts. We highlighted that timing of breeding has the greatest effect on the number of infected mosquitoes, while annual offspring production influences the timing of the infection peak. Our simulations provide evidence that non-corvid species can have a key impact on WNV transmission. Conclusion/SignificanceThese results can support future research by providing priority bird species to direct further studies and by suggesting that the acknowledgment of spatio-temporal variation in the abundance of competent avian hosts plays a key role in the development of effective surveillance strategies and mosquito control actions. Author summaryWest Nile virus (WNV) is endemic in Italy and represents a significant public health threat in Europe, with increasing cases of severe neuroinvasive disease in humans in recent years. Surveillance data reveal marked spatial and temporal variability in infection dynamics, suggesting that key drivers of WNV transmission remain poorly understood. The contribution of different bird species (over 300 are implicated in the WNV cycle) is often overlooked despite evidence that species-specific traits are critical determinants of WNV infection dynamics. Few studies have examined birds demographic traits, despite their well-established importance in shaping infection dynamics across diseases. Given the challenges in collecting detailed wildlife data, we employed mechanistic models to explore transmission scenarios and test whether avian demographic traits influence bird species roles in WNV transmission and maintenance in Lombardy. Our findings demonstrate that brood size, hatching synchrony, and hatching time significantly affect estimated WNV prevalence in mosquitoes.

ecology↗

bioRxiv2026

Evidence of thermal selection from experimental evolution in the arboviral vector Aedes albopictus

The extent to which phenotypic plasticity and adaptation are coupled during ectotherm thermal evolution is poorly understood. We carried out thermal experimental evolution for 20 generations in the arboviral vector Aedes albopictus, an efficient invasive species that has newly conquered climatically diverse regions in the past few decades. During acclimation (one generation of evolution) we saw accelerated development and increased reproduction that traded off against survival. After only another 10 generations, we saw adaptation in the form of major changes in mosquito fitness, metabolism and gene expression, revealing the consolidation of a temperature-dependent trade-off between reproduction and longevity. These shifts demonstrate that Ae. albopictuscan adapt at the pace of warming. When selection was relaxed, most of the thermally shifted phenotypes reverted to control levels, revealing the importance of plasticity after prolonged evolution. Furthermore, 250 warm evolution-altered genes did not return to control levels. These genes exhibited significant negative correlation between mean and variance in warm-evolved mosquitoes, but a two-fold variance reduction without mean change in relaxed-selection mosquitoes. Both signals are consistent with the action of selection operating on a polygenic trait architecture. Ecological modelling identified egg-to-adult viability as the primary driver of thermal reproductive success, highlighting juvenile stages as a crucial control target under continued warming.

evolutionary biology↗

bioRxiv2025

Reference-based variant detection with varseek

Variant detection from sequencing data is fundamental for genomics and is the first step in a wide range of applications, ranging from genome-wide association studies to disease diagnosis. Widely used tools for variant detection utilize a de novo approach that is based on a combination of read mapping algorithms and statistical methods for identifying genetic variation from error-prone sequencing data. This approach has been successful, although the detection of insertion and deletion variants, as well as the detection of variants from low-coverage data, remain challenging problems. We introduce varseek, a reference-based approach to variant detection that provides large improvements in performance in these challenging cases. The varseek approach utilizes a k-mer pseudoalignment approach, which provides the ability to identify variants at single-cell resolution in single-cell transcriptomics data. We showcase the versatility and performance of varseek for detecting tumor-specific COSMIC variants in glioblastoma single-cell sequencing.

bioinformatics↗

bioRxiv2025

Solid tumor CAR T cells engineered with fusion proteins targeting PDL1 for localized IL-12 delivery

CAR T cell efficacy in solid tumors is limited due in part to the immunosuppressive TME. To improve anti-tumor responses, we hypothesized that enabling CAR T cells to secrete bifunctional fusion proteins consisting of a cytokine modifier (e.g., TGF{beta}trap, IL15, or IL12) combined with an immune checkpoint inhibitor (e.g., PDL1) will provide tumor localized immunomodulation to improve CAR T cell functionality. To that end, we engineered CAR T cells to secrete TGF{beta}trap, IL15, or IL12 molecules fused to PDL1 scFv, and assessed in vitro functionality and in vivo safety and efficacy in prostate and ovarian cancer models. CAR T cells engineered with PDL1-IL12 were superior in safety and efficacy compared to CAR T cells alone and to those engineered with PDL1 fused with TGF{beta}trap or IL15. Further, PDL1-IL12 engineered CAR T cells improved T cell trafficking and tumor infiltration, localized IFN{gamma} production, TME modulation, and anti-tumor responses, with reduced systemic inflammation-associated toxicities. We believe our PDL1-IL12 engineering strategy presents an opportunity to improve CAR T cell clinical efficacy and safety across multiple solid tumor types.

bioengineering↗

bioRxiv2025

Climate-driven warming disrupts the symbiosis of bobtail squid Euprymna scolopes and the luminous bacterium Vibrio fischeri

Under the current climate crisis, marine heatwaves (MHW) are expected to intensify and become more frequent in the future, leading to adverse effects on marine life. Here, we aimed to investigate the impact of environmental warming on the symbiotic relationship between the Hawaiian bobtail squid (Euprymna scolopes) and the bioluminescent bacterium Vibrio fischeri. We exposed eggs of E. scolopes to three different temperatures during the embryogenesis, namely: i) 25 {degrees}C (yearly average), ii) 27 {degrees}C (average summer), or iii) 30 {degrees}C (category IV MHW), followed by a colonisation assay under the same conditions. Decreased hatching success and reduced developmental time were observed across warmer conditions compared to 25 {degrees}C. Moreover, exposure to the category IV MHW led to a significant decrease in survival after 48 hours. With increasing temperature, bobtail squids required more bacteria in the surrounding seawater for successful colonisation. When colonised, the regression of the light organs appendages was not dependent on temperature, but the opposite was found in non-colonised bobtail squids. Furthermore, the capacity to maintain the symbiosis diminished significantly with temperature. Finally, the capacity for crypt 3 formation in the squids light organ, which is crucial for enhancing resilience under stress, also declined with warming conditions. This study emphasises the critical need to study the dynamics of microbial symbiosis under the projected conditions for the ocean of tomorrow.

ecology↗

bioRxiv2024

Effect of MisMatch Repair Deficiency on metastasis occurrence modelized in a syngeneic mouse model

Mismatch repair deficiency leads to high mutation rates and microsatellite instability (MSI-H), associated with immune infiltration and responsiveness to immunotherapies. In early stages, MSI-H tumors generally have a better prognosis and lower metastatic potential than microsatellite-stable (MSS) tumors, especially in colorectal cancer. However, in advanced stages, MSI-H tumors lose this survival advantage for reasons that remain unclear. We developed a syngeneic mouse model of MSI cancer by knocking out the MMR gene Msh2 in the metastatic 4T1 breast cancer cell line. This model mirrored genomic features of MSI-H cancers and showed reduction in metastatic incidence compared to their MSS counterparts. In MSI-H tumors, we observed an enrichment of immune gene-signatures that negatively correlated with metastasis incidence. Importantly, a hybrid epithelial-mesenchymal signature, related to aggressiveness was detected only in metastatic MSI-H tumors which may explain the worse outcomes after recurrence of MSI tumors compared to MSS. Interestingly, we identified immature myeloid cells at primary and metastatic sites in MSI-H tumor-bearing mice, suggesting that MMR deficiency elicits specific immune responses beyond T-cell activation. SignificanceA novel syngeneic mouse model of MSI cancer demonstrates that the immune system regulates MSI cancer cell dissemination, offering an important tool to model advanced stages of human MSI-driven disease.

cancer biology↗

bioRxiv2024

Developmental and transcriptomic responses of Hawaiian bobtail squid early stages to ocean warming and acidification

1Cephalopods play a central ecological role across all oceans and realms. However, under the current climate crisis, their physiology and behaviour are impacted, and we are beginning to comprehend the effects of environmental stressors at a molecular level. Here, we study the Hawaiian bobtail squid (Euprymna scolopes), known for its specific binary symbiosis with the bioluminescent bacterium Vibrio fischeri acquired post-hatching. We aim to understand the response (i.e., developmental and molecular) of E. scolopes after the embryogenetic exposure to different conditions: i) standard conditions (control), ii) increased CO2 ({Delta}pH 0.4 units), iii) warming (+3{o}C), or iv) a combination of the two treatments. We observed a decrease in hatching success across all treatments relative to the control. Using transcriptomics, we identified a potential trade-off in favour of metabolism and energy production, at the expense of development under increased CO2. In contrast, elevated temperature shortened the developmental time and, at a molecular level, showed signs of alternative splicing and the potential for RNA editing. The data also suggest that the initiation of the symbiosis may be negatively affected by these environmental drivers of change in the biosphere, although coping mechanisms by the animal may occur.

ecology↗

bioRxiv2023

Neuromolecular responses in disrupted mutualistic cleaning interactions under future environmental conditions

Mutualistic interactions, which constitute some of the most advantageous interactions among fish species, are highly vulnerable to environmental changes. A key mutualistic interaction is the cleaning service rendered by the cleaner wrasse, Labroides dimidiatus, which involves intricate processes of social behaviour to remove ectoparasites from client fish and can be altered in near-future environmental conditions. Here, we evaluated the neuromolecular mechanisms behind the behavioural disruption of cleaning interactions in response to future environments. We subjected cleaner wrasses and surgeonfish (Acanthurus leucosternon, serving as clients) to elevated temperature (Warming, 32{degrees}C), increased levels of CO2 (High CO2, 1000 ppm), and a combined condition of elevated CO2 and temperature (Warming & High CO2, 32{degrees}C & 1000 ppm) for 28 days. Each of these conditions resulted in behavioural disruptions concerning the motivation to interact and the quality of interaction (High CO2 -80.7%, Warming - 92.6%, Warming & High CO2 -79.5%, p<0.001). Using transcriptomic of the fore-, mid-, and hindbrain, we discovered that most transcriptional reprogramming in both species under warming conditions occurred primarily in the hind- and forebrain. The associated functions under warming were linked to stress, heat shock proteins, hypoxia, and behaviour. In contrast, elevated CO2 exposure affected a range of functions associated with GABA, behaviour, visual perception, and circadian rhythm. Interestingly, in the combined Warming & High CO2 condition, we did not observe any expression changes of behaviour. However, we did find signs of endoplasmic reticulum stress and apoptosis, suggesting not only an additive effect of the environmental conditions but also a trade-off between physiological performance and behaviour in the cleaner wrasse. We suggest that impending environmental shifts can affect the behaviour and molecular processes that sustain mutualistic interactions between L. dimidiatus and its clients, which could have a cascading effect on their adaptation potential and possibly cause large-scale impacts on coral reef ecosystems.

animal behavior and cognition↗

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

Transgenerational exposure to deoxygenation and warming disrupts mate-detection in Gammarus locusta

Ocean deoxygenation and warming have been shown to pose a growing threat to the health of marine organisms and ecosystems. Yet, the potential for acclimation and adaptation to these threats remains poorly understood. The aim of this study was to evaluate the effects of transgenerational exposure to reduced oxygen availability and elevated seawater temperature on the chemosensory-dependent mating mechanisms of male amphipods Gammarus locusta. After exposure, the number of individuals that reached adulthood (in F0 and F2) was gauged, and adult males from F0 and F1 were subjected to behavioral trials to assess their capacity of long-distance female cue detection through quantification of (i) response time; (ii) first direction of movement; (iii) activity rate and (iv) proportion of time spent in female scent cues. Ocean warming induced mortality (especially in F2), and reduced oxygen availability had adverse effects on each of the investigated behavioral traits, which were amplified when combined with elevated temperature. Still, when compared to F0, the F1 generation demonstrated more adaptability (i.e., higher activity rate and preference for female odors) to the combination of the two stressors, suggesting positive carry-over effects. Nevertheless, full recovery to control levels was not observed. Altogether, this study indicates that future scenarios of ocean deoxygenation and warming have the potential to disrupt chemosensory-dependent mate-detection in amphipods, but also suggests possible behavioral adaptations. We call for greater research efforts on long-term impacts of ocean change on the behavioral and physiological processes of benthic coastal communities.

ecology↗

bioRxiv2022

Understanding West Nile virus spread: Mathematical modelling to determine the mechanisms with the most influence on infection dynamics.

West Nile disease is a vector-borne disease caused by West Nile virus (WNV), involving mosquitoes as vectors and birds as maintenance hosts. Humans and other mammals can be infected via mosquito bites, developing symptoms ranging from mild fever to severe neurological infection. Due to the worldwide spread of WNV, human infection risk is high in several countries. Nevertheless, there are still several knowledge gaps regarding WNV dynamics. Several aspects of transmission taking place between birds and mosquitoes, such as the length of the infectious period in birds or mosquito biting rates, are still not fully understood, and precise quantitative estimates are still lacking for the European species involved. This lack of knowledge affects the precision of parameter values when modelling the infection, consequently resulting in a potential impairment of the reliability of model simulations and predictions. Further investigations are thus needed to better understand these aspects, but field studies, especially those involving several wild species, such as in the case of WNV, can be challenging. Thus, it becomes crucial to identify which mechanisms most influence the dynamics of WNV transmission. In the present work, we propose a sensitivity analysis to identify the parameters that have the largest impact on the spread of the infection. Based on a mathematical model simulating WNV spread into the Lombardy region (northern Italy), the basic reproduction number of the infection was estimated and used to quantify infection spread into mosquitoes and birds. Then, we quantified how variations in the duration of the infectious period in birds, the mosquito biting rate on birds, and the competence and susceptibility to infection of different bird species might affect WNV transmission. Our study highlights that all considered parameters can affect the spread of WNV, but the duration of the infectious period in birds and mosquito biting rate are the most impactful, highlighting the need for further studies to better estimate these parameters. In addition, our study suggests that a WNV outbreak is very likely to occur in all areas with suitable temperatures, highlighting the wide area where WNV represents a serious risk for public health. Author SummaryInfectious communicable diseases are currently one of the main burdens for human beings and public health. The comprehension of their spread and maintenance is one of the main goals to facilitate their control and eradication, but due to the complexity of their cycles and transmission mechanisms, obtaining this information is often difficult and demanding. The control of vector-borne diseases in particular represents an important and very complex challenge for public health. Mathematical models are suitable tools to investigate disease dynamics and their transmission mechanisms. To build a suitable model that can simulate transmission dynamics, a reliable and precise estimate of parameters for measuring transmission mechanisms is fundamental. We thus propose a sensitivity analysis of four unknown epidemiological parameters (bird recovery rate, mosquito biting rate, avian susceptibility to infection and avian competence to infection) that play a crucial role in driving West Nile virus (WNV) infection to determine which of them have the greatest impact on infection spread. This analysis allows us to identify the investigated parameters that need the most accurate estimate and to further investigate mechanisms that majorly affect WNV spread.

ecology↗

bioRxiv2021

Neuro-molecular characterization of fish cleaning interactions

Coral reef fish exhibit a large variety of behaviours crucial for fitness and survival. The cleaner wrasse Labroides dimidiatus displays cognitive abilities during interspecific interactions by providing services of ectoparasite cleaning, thus serving as a good example to understand the processes of complex social behaviour. However, little is known about the molecular underpinnings of cooperative behaviour between L. dimidiatus and a potential client fish (Acanthurus leucosternon). Therefore, we investigated the molecular mechanisms in three regions of the brain (fore-, mid-, and hindbrain) during the interaction of these fishes. Here we show, using transcriptomics, that most of the transcriptional response in both species was regulated in the hindbrain and forebrain regions and that the interacting behaviour responses of L. dimidiatus involved immediate early gene alteration, dopaminergic and glutamatergic pathways, the expression of neurohormones (such as isotocin) and steroids (e.g. progesterone and estrogen). In contrast, in the client, fewer molecular alterations were found, mostly involving pituitary hormone responses. The particular pathways found suggested learning and memory processes in the cleaner wrasse, while the client indicated stress relief.

animal behavior and cognition↗

bioRxiv2021

Aedes albopictus bionomics in Procida Island, a promising Mediterranean site for the assessment of innovative and community-based integrated pest management methods.

The colonization of Mediterranean Europe and of other temperate regions by Aedes albopictus created in the last decades an unprecedented nuisance problem in highly infested areas, as well as a new public health threat due to the species competence to transmit exotic arboviruses, such as dengue, chikungunya and zika. The Sterile Insect Technique (SIT) and the Incompatible Insect Technique (IIT) are insecticide-free mosquito-control methods relying on mass release of irradiated/manipulated males which are believed to have a potential in complementing existing and only partially effective control tools. Testing and implementing these approaches are challenging and selection of study sites is an instrumental and crucial step. We carried out a 4-year study in Procida Island (Gulf of Naples, Italy) in strict collaboration with local administrators and citizens to estimate: i) the temporal dynamics, spatial distribution, and population size of Ae. albopictus; and ii) the dispersal and survival of irradiated males. Overall, results provide insights on the bionomics of the mosquito in Southern Europe and draw attention to Procida Island as an ideal site to test innovative control programs against Ae. albopictus which may be used in other Mediterranean and temperate areas."

ecology↗