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Roman, C.

Publications and source records attributed to Roman, C..

4 recordsLinked to original sources

Longitudinal proteomic analysis of T cell differentiation in vivo reveals dynamic changes of the interactome

CD8 T cell exhaustion impedes immune responses to cancer and chronic infections, and a biochemical understanding of exhaustion is essential to improving immunotherapy. Here, we present the first longitudinal protein abundance and phosphoproteomic analysis of antigen-specific CD8 T cells undergoing differentiation in vivo during acute (LCMV-Armstrong) and chronic (LCMV-Clone 13) infection. Comparing protein abundance across the two infection conditions identified over 180 known and novel exhaustion-associated proteins, including proteins missed by transcriptional analyses. Phosphoproteomic analysis identified >900 differentially regulated phosphosites on >400 proteins, including known inhibitory phosphosites on PD1, PAG1, SHP-1/PTPN6, SLAMF1/CD150. We also calculated phosphosite conservation across mammals, to direct follow-up studies towards sites with likely essential function. Lastly, our analysis uncovers exhaustion-associated kinases with clinical-stage inhibitors, underscoring the translational utility of our dataset to guide immunotherapy development. Together, our datasets define a biochemical atlas of T cell exhaustion in vivo, shedding light on the molecular mechanisms of T cell dysfunction.

immunology↗

CD4+ T Cell Depletion Before Primary Dengue and/or Secondary Zika Infection Reveals Mechanistic Correlates of Antibody Functionality in Rhesus Macaques.

Dengue (DENV) virus and Zika virus (ZIKV) are two flaviviruses of major public health concern. One drawback designing effective vaccines is our limited understanding of the mechanisms ruling protection or harm among DENV serotypes, or between DENV and ZIKV. Here, we depleted rhesus macaques of CD4+ T cells in vivo before primary DENV infection and/or secondary ZIKV challenge to recreate a sub-optimal priming of the humoral immune response. Our results support that CD4+ T cells are needed to induce a quantitative and type-specific effective humoral immune response against primary DENV, but also against secondary ZIKV in DENV-experimented subjects. Our results also indicate a limited contribution of the DENV-Memory B cells to anti-ZIKV response. Furthermore, our results suggest that a suboptimal B cell priming during a primary DENV infection does differentially impact different antibody (Abs) properties. While binding or neutralization of ZIKV or DENV during a subsequent exposure to ZIKV is not affected by the lack of CD4+ T - B cells interaction during a primary DENV infection, that interaction is critical to guarantee the Abs specificity. Also, we found that depleting CD4+ T cells before DENV primary infection but not before ZIKV challenge significantly increases Abs cross-reactivity against DENV-EDIII domain and DENV-NS1 protein but not against ZIKV-EDIII domain or NS1 protein. Furthermore, there was more cross-reactivity among the DENV-NS1 proteins than against DENV-EDIII domains, suggesting that during a primary DENV infection CD4+ T cells have a different weight in the responses against EDIII domain and NS1 protein. The proper Abs binding and neutralization with increased cross-reactivity profile was associated with limited frequency of circulating peripheral T helper cells (pTfh) with T helper 1 phenotype (CD4+/CXCR5+/CXCR3+) and expressing markers related to B cell activation (CXCR5+/CXCR3+/PD-1+/ICOS+) in the group depleted of CD4+ T cells only before primary DENV infection. However, memory B cells - but not Antibody Secreting Cells (ASC) activation 7 days after the infection - positively correlate with those two populations of pTfh. Finally, when Abs cross-reactivity values were incorporated in a Principal Component Analysis (PCA), the DENV-CD4+ T depleted group separates from the other two groups with similar Abs binding and neutralization profiles. Our result strongly suggests that during a heterologous sequential DENV/ZIKV infections Abs binding, and neutralization, may be regulated by different factors than their specificity. Before, the induction of cross-neutralizing Abs has been described in the context of secondary DENV infection. Here, for the first time, we are reproducing the experimental conditions leading to the generation of such Abs population in vivo. In summary, we show that suboptimal immune priming during a primary flavivirus infection has functional consequences during a secondary heterologous infection. Finally, we shown that CD8+ T cells are essential to guarantee an optimal Abs neutralization activity. These results have huge implications understanding the immune response to DENV vaccines (and maybe ZIKV), including why an optimal vaccine or natural-induced neutralizing response not necessarily protects or enhances pathogenesis during a subsequent natural heterologous exposure.

immunology↗

Efficient estimation of time-dependent functional connectivity using Structural Connectivity constraints

Multivariate autoregressive models [MAR] allows estimating effective brain connectivity by considering both power and phase fluctuations of the signals involved. A MAR models brain activity in one region as a linear combination of past activations in all other regions. A Hidden Markov model, HMM, whose states emisions are drawn from state-specific MARs, can then be used to model fast switching of effective brain connectivity over time. However, the large number of MAR parameters, impede the accurate and efficient estimation of such models from neuroimaging timeseries with limited length. We propose a new model for inferring time-dependent effective brain connectivity by using a sparse MAR parameterisation to model the states emisions of a Hidden Semi-Markov Model, HsMM-MAR-AC. The sparse MAR model parameters are restricted by Anatomical Connectivity information in two ways: direct effective connectivity between two regions is only considered if the corresponding structural link/connection exists; and the time-lag associated with each direct connection is computed based on the average fibre length between the two regions, such that only one lag per connection is estimated. We simulated ground truth time-dependent brain connectivity states by generating time-series of 4 to 10 minutes sampled at 5ms, from switching Resting State Networks with a reference structural connectivity, and evaluated the accuracy of the new model in recovering the simulated Brain connectivity States against different levels of connectivity thresholding above and below the reference. We show that even when restricting the MAR to half of the reference connections, the model was able to recover the number of brain states, the associated connectivity features and their dynamics, with as little data as 4 mins. More relaxed structural connectivity thresholds required longer data to estimate the model accurately, and became computationally unfeasible without anatomical restrictions. HsMM-MAR-AC offers an efficient algorithm for estimating time-depend Effective Connectivity (tdEC) from neuroimaging data, that exploits the advantages of MAR without identifiability problems, excessive demand on data collection, or unnecessary computational complexity.

bioinformatics↗

Natural enemies of armored scales (Hemiptera: Diaspididae) and soft scales (Hemiptera: Coccoidae) in Chile: molecular and morphological identification

Scale insects (Hemiptera: Coccoidea) are key pests of agricultural crops and ornamental plants worldwide. Their populations are difficult to control, even with insecticides, due to their cryptic habits. Moreover, there is growing concern over the use of synthetic pesticides for their control, due to deleterious environmental effects and the emergence of resistant populations of target pests. In this context, biological control may be an effective and sustainable approach. Hymenoptera Chalcidoidea includes natural enemies of scale insects that have been successfully used in many biological control programs. However, the correct identification of pest scale species and their natural enemies is particularly challenging because these insects are very small and highly specialized. Integrative taxonomy, coupling DNA barcoding and morphological analysis, has been successfully used to characterize pests and natural enemy species. In this study, we performed a survey of parasitoids and predators of armored and soft scales in Chile, based on 28S and COI barcodes. Fifty-three populations of Diaspididae and 79 populations of Coccidae were sampled over the entire length of the country, from Arica (18{degrees}S) to Frutillar (41{degrees}S), between January 2015 and February 2016. The phylogenetic relationships obtained by Bayesian inference from multilocus haplotypes revealed 40 putative species of Chalcidoidea, five Coccinellidae and three Neuroptera. In Chalcidoidea, 22 species were identified morphologically, resulting in new COI barcodes for 12 species and new 28S barcodes for 14 species. Two predator species (Rhyzobius lophantae and Coccidophilus transandinus) were identified morphologically, and two parasitoid species, Chartocerus niger and Signiphora bifasciata, were recorded for the first time in Chile.

molecular biology↗