Biology subjects

Vendrame, E.

Publications and source records attributed to Vendrame, E..

5 recordsLinked to original sources

bioRxiv2024

Distinct immune profiles in children living with HIV based on timing and duration of suppressive antiretroviral treatment

Timely initiation of antiretroviral therapy (ART) remains a major challenge in the effort to treat children living with HIV ("CLH") and little is known regarding the dynamics of immune normalization following ART in CLH with varying times to and durations of ART. Here, we leveraged two cohorts of virally-suppressed CLH from Nairobi, Kenya to examine differences in the peripheral immune systems between two cohorts of age-matched children (to control for immune changes with age): one group which initiated ART during early HIV infection and had been on ART for 5-6 years at evaluation (early, long-term treated; "ELT" cohort), and one group which initiated ART later and had been on ART for approximately 9 months at evaluation (delayed, short-term treated; "DST" cohort). We profiled PBMC and purified NK cells from these two cohorts by mass cytometry time-of-flight (CyTOF). Although both groups of CLH had undetectable viral RNA load at evaluation, there were marked differences in both immune composition and immune phenotype between the ELT cohort and the DST cohort. DST donors had reduced CD4 T cell percentages, decreased naive to effector memory T cell ratios, and markedly higher expression of stress-induced markers. Conversely, ELT donors had higher naive to effector memory T cell ratios, low expression of stress-induced markers, and increased expression of markers associated with an effective antiviral response and resolution of inflammation. Collectively, our results demonstrate key differences in the immune systems of virally-suppressed CLH with different ages at ART initiation and durations of treatment and provide further rationale for emphasizing early onset of ART. AUTHOR SUMMARYMany children living with HIV lack access to both antiviral treatments and testing for HIV infection and are therefore unable to initiate treatment in a timely manner. When children do begin treatment, their immune systems take time to recover from the uncontrolled HIV infection. In this study, we examine how the immune systems of children living with HIV normalize after treatment onset by looking at two groups of children whose HIV is well-controlled by treatment and who therefore dont have virus replicating in their blood. One group started treatment within the first year of life and has been on treatment for 5-6 years, while the other began treatment after the first year and has been treated for around 9 months. Although both of these groups are virally-suppressed, we found significant differences in their immune profiles, with the children who had delayed and short-term treatment showing signs of inflammation and immune dysfunction. Collectively, our study helps us understand how variation in the timing and duration of ART treatment impacts the immune system in children with viral suppression and therefore provides clinicians with additional knowledge that can inform the care of children living with HIV, improving their health and quality of life.

immunology↗

bioRxiv2020

CytoGLMM: Conditional Differential Analysis for Flow and Mass Cytometry Experiments

BackgroundFlow and mass cytometry are important modern immunology tools for measuring expression levels of multiple proteins on single cells. The goal is to better understand the mechanisms of responses on a single cell basis by studying differential expression of proteins. We focus on cell-specific differential analysis and one fixed cell type. In contrast, most current methods learn cell types and perform differential analysis jointly. Our narrower field of application allows us to define a more specific statistical model with easier to control statistical guarantees. ResultsDifferential analysis of marker expressions can be difficult due to marker correlations and inter-individual heterogeneity, particularly for studies of human immunology. We address these challenges with two multiple regression strategies: A bootstrapped generalized linear model and a generalized linear mixed model. On simulated datasets, we compare the robustness towards marker correlations and heterogeneity of both strategies. For paired experiments, we find that both strategies maintain the target false discovery rate under medium correlations and that mixed models are statistically more powerful under the correct model specification. For unpaired experiments, our results indicate that much larger patient sample sizes are required to detect differences. We illustrate the CytoGLMM R package and workflow for both strategies on a pregnancy dataset. ConclusionsOur approach to find differential proteins in flow and mass cytometry data reduces biases arising from maker correlations and safeguards against false discoveries induced by patient heterogeneity.

bioinformatics↗

bioRxiv2020

CyTOF analysis identifies unusual immune cells in urine of BCG-treated bladder cancer patients

High grade non-muscle-invasive bladder tumours are treated with transurethral resection followed by recurrent intravesical instillations of Bacillus Calmette Guerin (BCG). Although bladder cancer patients respond well to BCG, important questions remain unanswered, including how to identify at early stages non-responder patients and patients at risk to abandon the treatment. Here, we analysed the cells released into the urine of bladder cancer patients longitudinally 3-7 days after BCG instillations. Mass cytometry (CyTOF) analyses revealed that most cells were granulocytes and monocytes rather than effector lymphocytes, and most expressed activation markers. A novel population of CD15+CD66b+CD14+ CD16+ cells was very abundant in several samples and expression of these markers was confirmed using flow cytometry and qPCR. Samples of patients with a stronger inflammatory response contained more cells in urine; however, this was not due to haematuria, as the proportions of the cell populations observed were different from blood. We provide the proof-of-concept for a new approach to analyse samples that may help classify patients and identify those at risk of BCG infection and other unwanted BCG-related events.

immunology↗

bioRxiv2019

Characterization of the impact of daclizumab beta on circulating natural killer cells by mass cytometry

Daclizumab beta is a humanized monoclonal antibody that binds to CD25 and selectively inhibits high-affinity IL-2 receptor signaling. As a former treatment for relapsing forms of multiple sclerosis (RMS), daclizumab beta induces robust expansion of the CD56bright subpopulation of NK cells that is correlated with the drugs therapeutic effects. As NK cells represent a heterogeneous population of lymphocytes with a range of phenotypes and functions, the goal of this study was to better understand how daclizumab beta altered the NK cell repertoire to provide further insight into the possible mechanism(s) of action in RMS. We used mass cytometry to evaluate expression patterns of NK cell markers and provide a comprehensive assessment of the NK cell repertoire in individuals with RMS treated with daclizumab beta or placebo over the course of one year. Treatment with daclizumab beta significantly altered the NK cell repertoire compared to placebo treatment. As previously reported, daclizumab beta significantly increased expression of CD56 on total NK cells. Within the CD56bright NK cells, treatment was associated with multiple phenotypic changes, including increased expression of NKG2A and NKp44, and diminished expression of CD244, CD57, and NKp46. While the changes were less dramatic, CD56dim NK cells responded distinctly to daclizumab beta treatment, with higher expression of CD2 and NKG2A, and lower expression of FAS-L, HLA-DR, NTB-A, NKp30, and Perforin. Together, these data indicate that the expanded NK cells share features of both immature and mature NK cells. These findings show that daclizumab beta treatment is associated with unique changes in NK cells that may enhance their ability to kill autoreactive T cells or to exert immunomodulatory functions.

immunology↗

bioRxiv2019

TIGIT is upregulated by HIV-1 infection and marks a highly functional adaptive and mature subset of natural killer cells

ObjectiveOur objective was to investigate the mechanisms that govern natural killer (NK) cell responses to HIV, with a focus on specific receptor-ligand interactions involved in HIV recognition by NK cells.\n\nDesign and MethodsWe first performed a mass cytometry-based screen of NK cell receptor expression patterns in healthy controls and HIV+ individuals. We then focused mechanistic studies on the expression and function of T cell immunoreceptor with Ig and ITIM domains (TIGIT).\n\nResultsThe mass cytometry screen revealed that TIGIT is upregulated on NK cells of untreated HIV+ women, but not in antiretroviral-treated women. TIGIT is an inhibitory receptor that is thought to mark exhausted NK cells; however, blocking TIGIT did not improve anti-HIV NK cell responses. In fact, the TIGIT ligands CD112 and CD155 were not upregulated on CD4+ T cells in vitro or in vivo, providing an explanation for the lack of benefit from TIGIT blockade. TIGIT expression marked a unique subset of NK cells that express significantly higher levels of NK cell activating receptors (DNAM-1, NTB-A, 2B4, CD2) and exhibit a mature/adaptive phenotype (CD57hi, NKG2Chi, LILRB1hi, FcR{gamma}lo, Syklo). Furthermore, TIGIT+ NK cells had increased responses to mock-infected and HIV-infected autologous CD4+ T cells, and to PMA/ionomycin, cytokine stimulation and the K562 cancer cell line.\n\nConclusionsTIGIT expression is increased on NK cells from untreated HIV+ individuals. Although TIGIT does not participate directly in NK cell recognition of HIV, it marks a population of mature/adaptive NK cells with increased functional responses.

immunology↗