Biology subjects

Sala, E.

Publications and source records attributed to Sala, E..

14 recordsLinked to original sources

bioRxiv2026

Linking Host Covariates to COVID-19 Vaccine-Induced Antibody Dynamics in a Large Healthcare Worker Cohort

Antibody responses to COVID-19 vaccination vary widely across individuals, but the factors shaping these differences and their relation to underlying host-response processes are still not fully understood. Here, we combined longitudinal serological data from 4,553 healthcare workers with a nonlinear mixed-effects model to quantify determinants of vaccine-induced antibody dynamics. This framework captured both population-level trends and inter-individual variability in anti-spike antibody trajectories after vaccination. We found that age, sex, and pre-vaccine infection significantly influenced response dynamics. Male sex and increasing age were associated with weaker initial antibody production but slower waning, while individuals with a pre-vaccine infection had pre-existing anti-spike antibodies and slower initial antibody production and faster waning. These effects translated into substantial long-term differences in predicted antibody levels, reaching up to a 27% decrease in antibody levels one year after the third vaccination. Our results provide a dynamic view of the determinants of vaccine-induced humoral immunity and establish a framework for analyzing heterogeneous immune responses in large longitudinal cohorts.

Systems Biology↗

bioRxiv2025

Aerobic scope is sustained through a heatwave in juvenile Atlantic salmon

Aquatic ectotherms are vulnerable to heatwave-induced physiological stress, which arises from increased energy demands and reduced dissolved oxygen content in warmer waters. Understanding thermal physiology is critical for predicting how commercially and ecologically important populations could be affected by the increasing risk of rising temperatures. Heatwave risk assessments often examine extremities of time scales: immediate impacts or long-term consequences. However, little is known about how consistently increasing mid-term thermal stress shapes aerobic performance in commercially important species such as Atlantic salmon (Salmo salar), which may face heat stress in rivers, especially at the juvenile life stage. By measuring how salmon juveniles manage their aerobic capacity at 16, 19 and 22{degrees}C using intermittent respirometry, we test if their thermal performance curve shows a decline at temperatures commonly occurring during heatwaves. Whole-animal metabolism was measured from control individuals kept at 16 {degrees}C before and after the heatwave, and after 4-5 days exposure at 19 and 22{degrees}C during the heatwave. We show that standard metabolic rate increases with temperature, but maximum metabolic rate and aerobic scope do not change between these temperatures. These findings suggest that juvenile Atlantic salmon may have limited capacity to increase aerobic performance during moderate heatwaves, leaving them vulnerable to cumulative effects of oxygen limitation to vital functions such as growth and stress responses. As climate change intensifies, incorporating thermal performance curves into conservation strategies can be utilized for predicting population resilience and informing effective management. Lay SummaryIn juvenile Atlantic salmon, standard metabolic rate increases but there is no difference in maximum metabolic rate and aerobic scope with increasing temperatures. Considering the increased metabolic costs of activities at higher temperatures, our results show that juvenile salmon are vulnerable to deteriorating performance at temperatures commonly experienced in present-day heatwaves.

physiology↗

bioRxiv2025

T cell-derived IFN-γ Suppresses T Follicular Helper Cell Differentiation and Antibody Responses during Viral Infections

CD4+ T cells play a critical role in antiviral humoral and cellular immune responses. We have previously reported that subcutaneous lymphocytic choriomeningitis virus (s.c. LCMV) infection is characterized by a stark compartmentalization of CD4+ T cells, leading to strong TH1 polarization but virtually absent T follicular helper (TFH) cells, a key driver of humoral immunity. Here, we investigated the mechanisms responsible for this impaired TFH differentiation. We found that T-bet+ cells induced by s.c. LCMV infection encompass a TH1 subset expressing Granzyme-B (GzmB) and a Tcf-1+ subset that retains the potential for TFH differentiation without expressing mature TFH markers. Interestingly, IFN-{gamma} blockade enables full differentiation of Tcf-1+ cells into TFH, formation of germinal centers and increased antibody production. Of note, the suppression of TFH cells by IFN-{gamma} is not directly mediated through CD4+ T cells but rather involves another cell type, likely dendritic cells (DCs). Our study provides novel insights into the mechanisms directing early CD4+ T cell polarization and affecting humoral responses to viruses, laying a foundation for the development of effective vaccine strategies.

immunology↗

bioRxiv2023

LSD1 inhibition improves efficacy of adoptive T cell therapy by enhancing CD8+ T cell responsiveness.

The lysine-specific histone demethylase 1A (LSD1) has been described to play a role in antitumor immunity; however, the role of LSD1 in shaping CD8+ T cell (CTL) differentiation and function is not understood. Here, we showed that pharmacological inhibition of LSD1 (LSD1i) in CTL elicited phenotypic and functional alterations of the CTL that led to robust antitumor immunity in the context of adoptive T cell therapy (ACT). In addition, the combination of anti-PDL1 therapy with LSD1i-based ACT resulted in a complete tumor eradication and long-lasting tumor-free survival. This study demonstrated that LSD1i together with anti-PDL1 therapy complement each others deficiencies and produce a better tumor response in a melanoma model, in which both immune and epigenetic therapy alone have shown limited efficacy. Collectively, these results set the translational potential of modulating LSD1 to improve antitumoral responses generated by ACT and anti-PDL1 therapy, which provide a strong rationale for a combination trial of LSD1i and immunotherapy.

immunology↗

bioRxiv2023

A fluorescent reporter model for the visualization and characterization of TDC

TDC are hematopoietic cells that combine dendritic cell (DC) and conventional T cell markers and functional properties. They were identified in secondary lymphoid organs (SLOs) of naive mice as cells expressing CD11c, major histocompatibility molecule (MHC)-II, and the T cell receptor (TCR) {beta} chain. Despite thorough characterization as to their potential functional properties, a physiological role for TDC remains to be determined. Unfortunately, using CD11c as a marker for TDC has the caveat of its upregulation on different cells, including T cells, upon activation. Therefore, a more specific marker is needed to further investigate TDC functions in peripheral organs in different pathological settings. Here we took advantage of Zbtb46-GFP reporter mice to explore the frequency and localization of TDC in peripheral tissues at steady state and upon viral infection. RNA sequencing analysis confirmed that TDC identified with this reporter model have a gene signature that is distinct from conventional T cells and DC. In addition, frequency and total numbers of TDC in the SLOs recapitulated those found using CD11c as a marker. This reporter model allowed for identification of TDC in situ not only in SLOs but also in the liver and lung of naive mice. Interestingly, we found that TDC numbers in the SLOs increased upon viral infection, suggesting that TDC might play a role during viral infections. In conclusion, we propose a visualization strategy that might shed light on the physiological role of TDC in several pathological contexts, including infection and cancer.

immunology↗

bioRxiv2022

The guanine nucleotide exchange factor Rin-like acts as a gatekeeper for T follicular helper cell differentiation via regulating CD28 signaling

T follicular helper (Tfh) cells are essential for the development of germinal center B cells and high-affinity antibody producing B-cells in human and mice. Here, we identify the guanine nucleotide exchange factor (GEF) Rin-like (Rinl) as a negative regulator of Tfh generation. Loss of Rinl leads to an increase of Tfh in aging, upon in vivo immunization and acute LCMV Armstrong infection in mice, and in human CD4+ T cell in vitro cultures. Further, adoptive transfer experiments using WT and Rinl-KO naive CD4+ T cells unraveled T cell-intrinsic functions of Rinl. Mechanistically, Rinl regulates CD28 internalization and signaling, thereby shaping CD4+ T cell activation and differentiation. Thus, our results identify the GEF Rinl as a negative regulator of global Tfh differentiation in an immunological context and species-independent manner, and furthermore connect Rinl with CD28 internalization and signaling pathways in CD4+ T cells, demonstrating for the first-time the importance of endocytic processes for Tfh differentiation. HighlightsO_LIRinl-KO CD4+ T cells show increased Tfh differentiation in a context independent manner C_LIO_LIThe regulation of Tfh differentiation is T cell-intrinsic C_LIO_LIRinl controls CD28 endocytosis and shapes Tfh-specific CD28 signal transduction C_LIO_LIHuman Tfh differentiation is regulated by Rinl C_LI

immunology↗

bioRxiv2021

Controlled administration of aerosolized SARS-CoV-2 to K18-hACE2 transgenic mice uncouples respiratory infection and anosmia from fatal neuroinvasion

The development of a tractable small animal model faithfully reproducing human COVID-19 pathogenesis would arguably meet a pressing need in biomedical research. Thus far, most investigators have used transgenic mice expressing the human ACE2 in epithelial cells (K18-hACE2 transgenic mice) that are intranasally instilled with a liquid SARS-CoV-2 suspension under deep anesthesia. Unfortunately, this experimental approach results in disproportionate high CNS infection leading to fatal encephalitis, which is rarely observed in humans and severely limits this models usefulness. Here, we describe the use of an inhalation tower system that allows exposure of unanesthetized mice to aerosolized virus under controlled conditions. Aerosol exposure of K18-hACE2 transgenic mice to SARS-CoV-2 resulted in robust viral replication in the respiratory tract, anosmia, and airway obstruction, but did not lead to fatal viral neuroinvasion. When compared to intranasal inoculation, aerosol infection resulted in a more pronounced lung pathology including increased immune infiltration, fibrin deposition and a transcriptional signature comparable to that observed in SARS-CoV-2- infected patients. This model may prove useful for studies of viral transmission, disease pathogenesis (including long-term consequences of SARS-CoV-2 infection) and therapeutic interventions.

immunology↗

bioRxiv2021

Immunogenicity and pre-clinical efficacy of an OMV-based SARS-CoV-2 vaccine

The vaccination campaign against SARS-CoV-2 relies on the world-wide availability of effective vaccines, with a potential need of 20 billion vaccine doses to fully vaccinate the world population. To reach this goal, the manufacturing and logistic processes should be affordable to all countries, irrespectively of economical and climatic conditions. Outer membrane vesicles (OMVs) are bacterial-derived vesicles that can be engineered to incorporate heterologous antigens. Given the inherent adjuvanticity, such modified OMVs can be used as vaccine to induce potent immune responses against the associated protein. Here we show that OMVs engineered to incorporate peptides derived from the receptor binding motif (RBM) of the spike protein from SARS-CoV-2 elicit an effective immune response in immunized mice, resulting in the production of neutralizing antibodies. The immunity induced by the vaccine is sufficient to protect K18-hACE2 transgenic mice from intranasal challenge with SARS-CoV-2, preventing both virus replication in the lungs and the pathology associated with virus infection. Furthermore, we show that OMVs can be effectively decorated with RBM peptides derived from a different genetic variant of SARS-CoV-2, inducing a similarly potent neutralization activity in vaccinated mice. Altogether, given the convenience associated with ease of engineering, production and distribution, our results demonstrate that OMV-based SARS-CoV-2 vaccines can be a crucial addition to the vaccines currently available.

immunology↗

bioRxiv2021

COVID-eVax, an electroporated plasmid DNA vaccine candidate encoding the SARS-CoV-2 Receptor Binding Domain, elicits protective immune responses in animal models of COVID-19

The COVID-19 pandemic caused by the {beta}-coronavirus SARS-CoV-2 has made the development of safe and effective vaccines a critical global priority. To date, four vaccines have already been approved by European and American authorities for preventing COVID-19 but the development of additional vaccine platforms with improved supply and logistics profiles remains a pressing need. Here we report the preclinical evaluation of a novel COVID-19 vaccine candidate based on the electroporation of engineered, synthetic cDNA encoding a viral antigen in the skeletal muscle, a technology previously utilized for cancer vaccines. We constructed a set of prototype DNA vaccines expressing various forms of the SARS-CoV-2 Spike (S) protein and assessed their immunogenicity in animal models. Among them, COVID-eVax - a DNA plasmid encoding a secreted monomeric form of SARS-CoV-2 S protein RBD - induced the most potent anti-SARS-CoV-2 neutralizing antibody responses (including against the current most common variants of concern) and a robust T cell response. Upon challenge with SARS-CoV-2, immunized K18-hACE2 transgenic mice showed reduced weight loss, improved pulmonary function and significantly lower viral replication in the lungs and brain. COVID-eVax conferred significant protection to ferrets upon SARS-CoV-2 challenge. In summary, this study identifies COVID-eVax as an ideal COVID-19 vaccine candidate suitable for clinical development. Accordingly, a combined phase I-II trial has recently started in Italy.

immunology↗

bioRxiv2019

Comprehensive characterisation of cell-free tumour DNA in plasma and urine of patients with renal tumours

Cell-free tumour-derived DNA (ctDNA) allows non-invasive monitoring of cancers but its utility in renal cell cancer (RCC) has not been established. Here, untargeted and targeted sequencing methods, applied to two independent cohorts of renal tumour patients (n=90), were used to determine ctDNA content in plasma and urine. Our data revealed lower plasma ctDNA levels in RCC relative to other cancers, with untargeted detection of [~]33%. A sensitive personalised approach, applied to plasma and urine from select patients improved detection to [~]50%, including in patients with early-stage and even benign lesions.\n\nA machine-learning based model predicted detection, potentially offering a means of triaging samples for personalised analysis. In addition, with limited data we observed that plasma, and for the first time, urine ctDNA may better represent tumour heterogeneity than tissue biopsy. Furthermore, longitudinal sampling of >200 plasma samples revealed that ctDNA can track disease course. Additional datasets will be required to validate these findings.\n\nOverall, our data highlight RCC as a ctDNA-low malignancy, but indicate potential clinical utility provided improvement in detection approaches.\n\nOne sentence summaryComplementary sequencing methods show that cell-free tumour DNA levels are low in renal cancer though, via various strategies, may still be informative.

cancer biology↗

bioRxiv2019

3D-printed moulds of renal tumours for image-guided tissue sampling in the clinical setting

PURPOSESpatial heterogeneity of tumours is a major challenge in precision oncology. The relationship between molecular and imaging heterogeneity is still poorly understood, as it relies on the accurate co-registration of medical images and tissue biopsies. tumour moulds can guide the localization of biopsies, but their creation is time consuming, technologically challenging, and difficult to interface with routine clinical practice. These hurdles have so far hindered the progress in the area of multiscale integration of tumour heterogeneity data. METHODSWe have developed an open source computational framework to automatically produce patient-specific 3D-printed moulds that can be used in the clinical setting. Our approach achieves accurate co-registration of sampling location between tissue and imaging, and integrates seamlessly with clinical, imaging and pathology workflows. RESULTSWe applied our framework to patients with renal cancer undergoing radical nephrectomy. We created personalised moulds for five patients, obtaining Dice similarity coefficients between imaging and tissue sections ranging from 0.86 to 0.93 for tumour regions, and between 0.70 and 0.76 for healthy kidney. The framework required minimal manual intervention, producing the final mould design in just minutes, while automatically taking into account clinical considerations such as a preference for specific cutting planes. CONCLUSIONOur work provides a robust and automated interface between imaging and tissue samples, enabling the development of clinical studies to probe tumour heterogeneity on multiple spatial scales.

bioengineering↗

bioRxiv2019

4q-D4Z4 chromatin architecture regulates the transcription of muscle atrophic genes in FSHD

Despite increasing insights in genome structure organization, the role of DNA repetitive elements, accounting for more than two thirds of the human genome, remains elusive. Facioscapulohumeral Dystrophy (FSHD) is associated with deletion of D4Z4 repeat array below 11 units at 4q35.2. It is known that the deletion alters chromatin structure in cis, leading to genes upregulation. Here we show a genome-wide role of 4q-D4Z4 array in modulating gene expression via 3D nuclear contacts. We have developed an integrated strategy of 4q-D4Z4 specific 4C-seq and chromatin segmentation analyses, showing that 4q-D4Z4 3D interactome and chromatin states of interacting genes are impaired in FSHD1 condition; in particular, genes which have lost the 4q-D4Z4 interaction and with a more active chromatin state are enriched for muscle atrophy transcriptional signature. Expression level of these genes is restored by the interaction with an ectopic 4q-D4Z4 array, suggesting that the repeat directly modulates the transcription of contacted targets.\n\nOf note, the upregulation of atrophic genes is a common feature of several FSHD1 and FSHD2 patients, indicating that we have identified a core set of deregulated genes involved in FSHD pathophysiology.

genomics↗

bioRxiv2019

Computed Tomography Measures of Inter-site tumor Heterogeneity for Classifying Outcomes in High-Grade Serous Ovarian Carcinoma: a Retrospective Study

AbstractO_ST_ABSBackgroundC_ST_ABSHigh grade serous ovarian carcinoma shows marked intra-tumoral heterogeneity which is associated with decreased survival and resistance to platinum-based chemotherapy. Pre-treatment quantification of spatial tumor heterogeneity by multiple tissue sampling is not clinically feasible. Using standard-of-care CT imaging to non-invasively quantify heterogeneity could have high clinical utility and would be highly cost-effective. Texture analysis measures local variations in computed tomography (CT) image intensity. Haralick texture methods are typically used to capture the heterogeneity of entire lesions; however, this neglects the possible presence of texture habitats within the lesion, and the differences between metastatic sites. The primary aim of this study was to develop texture analysis of intra-site and inter-site spatial heterogeneity from standard-of-care CT images and to correlate these measures with clinical and genomic features in patients with HGSOC. Methods and findingsWe analyzed the data from a retrospective cohort of 84 patients with HGSOC consisting of 46 patients from Memorial Sloan Kettering Cancer Center (MSKCC) and 38 non-MSKCC cases selected from The Cancer Imaging Archive (TCIA). Inclusion criteria consisted of FIGO stage II-IV HGSOC, attempted primary cytoreductive surgery, intravenous contrast-enhanced CT of abdomen and pelvis performed prior to surgery and availability of molecular tumor data analysed as per the Cancer Genome Atlas (TCGA) Research Network ovarian cancer project. Manual segmentation and image analysis was performed on 463 metastatic tumor sites from 84 patients. In the MSKCC cohort the median number of tumor sites was 7 (interquartile range 5-9) and 4 (interquartile range 3-4) in the TCIA patients. Sub-regions were produced within each tumor site by grouping voxels with similar Haralick texture using the Kernel K-means method. We derived statistical measures of intra- and inter-site tumor heterogeneity (IISTH) including cluster sites entropy (cSE), cluster sites standard deviation (cluDev) and cluster sites dissimilarity (cluDiss) from sub-regions identified within and between individual tumor sites. Unsupervised clustering was used to group patient IISTH measures into low, medium, high, and ultra-high heterogeneity clusters from each cohort. The IISTH measure cluDiss was an independent predictor of progression-free survival (PFS) in multivariable analysis in both datasets (MSKCC hazard ratio [HR] 1.04, 95% CI 1.01-1.06, P = 0.002; TCIA HR 1.05, 95% CI 1.00-1.10, P = 0.049). Low and medium IISTH clusters were associated with longer PFS in multivariable analysis (MSKCC HR 2.94, 90% CI 1.29-6.70, P = 0.009, TCIA HR 5.94, 95% CI 1.05-33.6, P = 0.044). IISTH measures were robust to differences in the CT imaging systems. Average Haralick textures contrast (TCIA HR 1.08, 95% CI 1.01-1.10, P = 0.019) and homogeneity (TCIA HR 1.09, 95% CI 1.02-1.16, P = 0.008) were associated with PFS in mutivariate analysis only in the TCIA dataset. All other average Haralick textures and total tumor volume were not associated with PFS in either dataset. ConclusionsTexture measures of intra- and inter-site tumor heterogeneity from standard of care CT images are correlated with shorter PFS in HGSOC patients. These quantitative methods are independent of the CT imaging system and can thus be applied in clinical practice. The methodology proposed here enables the non-invasive quantification of intra-tumoral heterogeneity and disease stratification for future experimental medicine studies and clinical trials, particularly in cases where total tumour volume and averaged textures have low predictive power. Author summaryO_ST_ABSWhy was this study done?C_ST_ABSO_LITumor heterogeneity is a feature of many solid malignancies including ovarian cancer. C_LIO_LIRecent genomic research suggests that intra-site tumor heterogeneity (heterogeneity within a single tumor site) and inter-site tumor heterogeneity (heterogeneity between different metastatic sites in the same patient) correlate with clinical outcome in HGSOC. C_LI What did the researchers do and find?O_LIWe developed quantitative and non-invasive image-analysis based measures for predicting outcome in HGSOC patients by combining image-based information from within and between multiple tumor sites. C_LIO_LIUsing datasets from two sources, we demonstrate that these image-based tumor heterogeneity measures predict progression free survival in patients with HGSOC. C_LI What do these findings mean?O_LINon-invasive measures of CT image heterogeneity may predict outcomes in HGSOC patients. C_LIO_LIWider application of these CT image heterogeneity measures could prove useful for stratifying patients to different therapies given that total tumour volume and averaged textures have low predictive power. C_LI

bioinformatics↗

bioRxiv2018

Unraveling Tumor-Immune Heterogeneity in Advanced Ovarian Cancer Uncovers Immunogenic Effect of Chemotherapy

In metastatic cancer, the role of heterogeneity at the tumor-immune microenvironment, its molecular underpinnings and clinical relevance remain largely unexplored. To understand tumor-immune dynamics at baseline and upon chemotherapy treatment, we performed unbiased pathway and cell type-specific immunogenomics analysis of treatment-naive (38 samples from 8 patients) and paired chemotherapy treated (80 paired samples from 40 patients) high-grade serous ovarian cancer (HGSOC) samples. Whole transcriptome analysis and image-based quantification of T cells from treatment-naive tumors revealed ubiquitous variability in immune signaling and distinct immune microenvironments co-existing within the same individuals and within tumor deposits at diagnosis. To systematically explore cell type composition of the tumor microenvironment using bulk mRNA, we derived consensus immune and stromal cell gene signatures by intersecting state-of-the-art deconvolution methods, providing improved accuracy and sensitivity when compared to HGSOC immunostaining and leukocyte methylation data sets. Cell-type deconvolution and pathway analyses revealed that Myc and Wnt signaling associate with immune cell exclusion in untreated HGSOC. To evaluate the effect of chemotherapy on the intrinsic tumor-immune heterogeneity, we compared site-matched and site-unmatched tumors before and after neoadjuvant chemotherapy. Transcriptomic and T-cell receptor sequencing analyses showed that site-matched samples had increased cytotoxic immune activation and oligoclonal expansion of T cells after chemotherapy, which was not seen in site-unmatched samples where heterogeneity could not be accounted for. These results demonstrate that the tumor-immune interface in advanced HGSOC is intrinsically heterogeneous, and thus requires site-specific analysis to reliably unmask the impact of therapy on the tumor-immune microenvironment.

cancer biology↗