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Delgado, J.

Publications and source records attributed to Delgado, J..

9 recordsLinked to original sources

Context-dependent tonic signaling shapes the performance and manufacturability of a 4-1BB- based HER2 CAR-T cell therapy

The development of clinically effective CAR-T cell therapies for solid tumors requires careful optimization of receptor design, functional fitness, and manufacturability. While advancing low-affinity HER2-targeting CAR-T cells toward clinical application, we found that the candidate with the strongest in vivo antitumor activity--comprising a CD8 hinge and transmembrane region and a 4-1BB co-stimulatory domain--exhibited measurable tonic signaling. This basal antigen-independent signaling, likely driven by high CAR surface expression, was associated with increased apoptosis and reduced ex vivo expansion under research-grade manufacturing conditions. Modification of the transmembrane domain reduced CAR surface expression but did not alleviate tonic signaling and instead impaired antitumor activity. By contrast, transient pharmacologic inhibition of CAR signaling with dasatinib rescued expansion and reduced apoptosis in small-scale research cultures. Notably, these tonic-signaling-associated defects were largely absent during large-scale, GMP-compliant manufacturing, which enabled robust CAR-T cell expansion without additional benefit from dasatinib supplementation. Together, these findings show that tonic signaling is not inherently detrimental to CAR-T cell performance and that its functional consequences are highly dependent on manufacturing context. Our study underscores the importance of evaluating CAR candidates within clinically relevant production platforms and supports the advancement of this 4-1BB-based HER2-specific CAR-T cell product toward clinical testing.

immunology↗

Artificial Intelligence And First Principle Methods In Protein Redesign: A Marriage Of Convenience?

Since AlphaFold2s rise, many deep learning methods for protein design have emerged. Here, we validate widely used and recognized tools, compare them with first-principle methods, and explore their combinations, focusing on their effectiveness in protein redesign and potential for therapeutic repurposing. We address two challenges: evaluating tools and combinations ability to detect the effects of multiple concurrent mutations in protein variants, and leveraging large-scale datasets to compare modeling-free methods, namely force fields, which handle point mutations well with limited backbone rearrangement, and inverse folding tools, which excel at native sequence recovery but may struggle with non-natural proteins. Debuting TriCombine, a tool that identifies residue triangles in input structures, matches them to a structural database, and scores mutants based on substitution frequencies, we shortlisted candidates, modeled them with FoldX, and generated 16 SH3 mutants carrying up to 9 concurrent substitutions. The dataset was expanded to include 36 mutants and 11 crystal structures (7 newly solved), along with a parallel set of multiple non-concurrent mutants from three additional proteins. For broader validation, we analyzed 160,000 four-site GB1 mutants and 163,555 (single and double) variants across 179 natural and de novo domains. We show that combining AI-based modeling tools with force field scoring functions yields the most reliable results. Inverse folding tools perform very well but lose accuracy on less-represented proteins. First-principle force fields like FoldX remain the most accurate for point mutations. All methods perform worse when applied to unsolved de novo models, underscoring the need for hybrid strategies in robust protein design.

bioinformatics↗

Integrative single-cell multi-omics of CD19CARpos and CARneg T cells suggest drivers of immunotherapy response in B-cell neoplasias

How phenotypic, clonal, and functional heterogeneity of CAR-T-cells impact clinical outcomes remain understudied. Here, we integrated clonal kinetics with transcriptomic heterogeneity resolved by single-cell omics to explore cellular dynamics response of both non-transduced (CARneg) and transduced (CARpos)T-cells. CARneg and CARposT-cells were longitudinally interrogated in the manufactured infusion product (IP) and in-vivo at CAR-T cell expansion peak in five B-ALL patients treated with CD19CAR-T-cells (varni-cel). Significant differences were found in the cellular dynamics between CARpos and CARnegT-cells in response to therapy. CARposT-cells in the IP exhibited a significant higher CD4:CD8 ratio than CARnegT-cells, and the CD4:CD8 CARposT-cell composition impacted therapy outcome as confirmed in a larger cohort of 24 varni-cel-treated B-ALL patients. Conversely, an inverted trend in the CD4:CD8 CARposT-cell ratio was consistently observed at the expansion peak, with clonally expanding CD8+ effector memory and cytotoxic T-cells being the most abundant populations. Expanded cytotoxic CARpos{gamma}{delta}T cells emerged at the expansion peak, and the extent of their in-vivo expansion positively correlated with treatment efficacy, which was validated in a large cohort of B-ALL patients (n=18) treated with varni-cell and B-cell lymphoma patients (n=58) treated with either lisa-cel or axi-cel. Our data provide insights into the complexity and diversity of T-cell responses following CAR-T cell therapy and suggest drivers of immunotherapy response.

immunology↗

Reduced Monocyte Proportions and Responsiveness in Convalescent COVID-19 Patients

The clinical manifestations of acute severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection and COVID-19 suggest a dysregulation of the host immune response that leads to inflammation, thrombosis, and organ dysfunction. It is less clear whether these dysregulated processes persist during the convalescent phase of disease or during long COVID. We investigated the effects of SARS-CoV-2 infection on the proportions of classical, intermediate, and non-classical monocytes, their activation status, and their functional properties in convalescent COVID-19 patients and uninfected control subjects. We found that the percentage of total monocytes was decreased in convalescent COVID-19 patients compared to uninfected controls. This was due to decreased intermediate and non-classical monocytes. Classical monocytes from convalescent COVID-19 patients demonstrated a decrease in activation markers, such as CD56, in response to stimulation with bacterial lipopolysaccharide (LPS). In addition, classical monocytes from convalescent COVID-19 patients showed decreased expression of CD142 (tissue factor), which can initiate the extrinsic coagulation cascade, in response to LPS stimulation. Finally, we found that monocytes from convalescent COVID-19 patients produced less TNF- and IL-6 in response to LPS stimulation, than those from uninfected controls. In conclusion, SARS-CoV-2 infection exhibits a clear effect on the relative proportions of monocyte subsets, the activation status of classical monocytes, and proinflammatory cytokine production that persists during the convalescent phase of disease.

immunology↗

The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome

We report a systematic analysis of the biological and clinical implications of DNA methylation variability in five categories of B-cell tumors derived from B cells spanning the entire maturation spectrum. We used 2056 primary samples including training and validation series and show that 88% of the human DNA methylome is dynamically modulated under normal and neoplastic conditions. B-cell tumors display both epigenetic imprints of their cellular origin and de novo, disease-specific epigenetic alterations that in part are related to differential transcription factor binding. These differential methylation patterns were used by a machine-learning approach to create a diagnostic algorithm that accurately classifies 14 B-cell tumor entities and subtypes with different clinical management. Beyond this, we identified extensive patient-specific epigenetic variability targeting constitutively silenced chromatin regions, a phenomenon we could relate to the proliferative history of normal and neoplastic B cells. We observed that, depending on the maturation stage of the tumor cell of origin, mitotic activity leaves different imprints into the DNA methylome. Subsequently, we constructed a novel DNA methylation-based mitotic clock called epiCMIT (epigenetically-determined Cumulative MIToses), whose lapse magnitude represents a strong independent prognostic variable within specific B-cell tumor subtypes and is associated with particular driver genetic alterations. Our findings reveal DNA methylation as a holistic tracker of B-cell tumor developmental history, with implications in the differential diagnosis and prediction of the outcome of the patients.

cancer biology↗

Frequency but not phase specific modulation of binocular rivalry with transcranial alternating current stimulation

Recent transcranial alternating current stimulation (tACS) literature suggests that tACS effects can in principle be both frequency and phase specific. In a series of three experiments using 69 participants used binocular rivalry percepts as a read-out for the effects of phase-synchronized tACS stimulation. To test for phase specificity, with frequency the same in each eye, we visually stimulated each eye with 3Hz, with stimuli in each eye presented in temporal in antiphase. The frequency-specific paradigm visually stimulated the right eye with 3Hz, and the left eye with 5Hz. Each experiment was accompanied by 3Hz tACS, whose phase with respect to the visual stimulus was varied by 0{degrees}, 90{degrees}, 180{degrees}, or 270{degrees} in relation to the right eyes stimulus. A baseline no-tACS block preceded the stimulation blocks and two more followed, immediately and ten minutes after. Individual blocks lasted 4 minutes. Additionally, a no-tACS control experiment identical to the 3 Hz anti-phase visual stimuli setup was conducted, keeping all parameters the same but eliminating tACS. During stimulation, the 3 Hz anti-phase visual stimuli setup slowed the rate of rivalry in both eyes. Conversely, the 3Hz-right, 5Hz-left setup slowed the right (targeted) eye significantly while leaving the left (unstimulated) eye unchanged. In both experiments, durations returned to baseline after 10 minutes. Our results are consistent with the frequency-specific model of tACS, and with the Leveltian hypothesis that stimulation weakens the stimulated eye, as the right eye got weaker when it was directly targeted, and both eyes got weaker when targeted in antiphase. tACS does not appear to preferentially modulating percept durations in one phase more than in another.

neuroscience↗

Brain functional connectivity dynamics in the aftermaths of affective and cognitive events.

Neuroimaging studies have shown carry-over effects on brain activity and connectivity following both emotional and cognitive events, persisting even during subsequent rest. Here, we investigate the functional dynamics of such effects by identifying recurring co-activation patterns (CAPs). Using the precuneus as seed region, we compare carrying-over effects on brain-wide CAPs and their modulation after both affective and cognitive challenges. Female volunteers (n=19) underwent fMRI scanning during emotional induction with sad movie clips, and executive control tasks, each followed by resting periods. Several CAPs, overlapping the default mode, salience, attention, and social cognition networks were impacted by both the preceding events (movie or task) and their valence (neutral or negative), with differential fluctuations over time. Specifically, a modulation of CAPs in posterior cingulate and ventromedial prefrontal cortex was observed after exposure to negatively valenced emotional content and predicted changes in subjective affect. Additionally, CAPs in anterior cingulate cortex and dorsal fronto-parietal areas were induced by cognitive control in a negative, but not neutral context, and amplified by the task difficulty. These findings provide new insights on the anatomical organization and temporal inertia of intrinsic functional brain networks, engaged by transient emotions and presumably involved in subsequent adaptive homeostatic processes.

neuroscience↗

An introduction to MPEG-G, the new ISO standard for genomic information representation

The MPEG-G standardization initiative is a coordinated international effort to specify a compressed data format that enables large scale genomic data to be processed, transported and shared. The standard consists of a set of specifications (i.e., a book) describing: i) a nor-mative format syntax, and ii) a normative decoding process to retrieve the information coded in a compliant file or bitstream. Such decoding process enables the use of leading-edge com-pression technologies that have exhibited significant compression gains over currently used formats for storage of unaligned and aligned sequencing reads. Additionally, the standard provides a wealth of much needed functionality, such as selective access, data aggregation, ap-plication programming interfaces to the compressed data, standard interfaces to support data protection mechanisms, support for streaming and a procedure to assess the conformance of implementations. ISO/IEC is engaged in supporting the maintenance and availability of the standard specification, which guarantees the perenniality of applications using MPEG-G. Fi-nally, the standard ensures interoperability and integration with existing genomic information processing pipelines by providing support for conversion from the FASTQ/SAM/BAM file formats.\n\nIn this paper we provide an overview of the MPEG-G specification, with particular focus on the main advantages and novel functionality it offers. As the standard only specifies the decoding process, encoding performance, both in terms of speed and compression ratio, can vary depending on specific encoder implementations, and will likely improve during the lifetime of MPEG-G. Hence, the performance statistics provided here are only indicative baseline examples of the technologies included in the standard.

bioinformatics↗

VarQ: a tool for the structural analysis of Human Protein Variants

Understanding the functional effect of Single Amino acid Substitutions (SAS), derived from the occurrence of single nucleotide variants (SNVs), and their relation to disease development is a major issue in clinical genomics. Even though there are several bioinformatic algorithms and servers that predict if a SAS can be pathogenic or not they give little or non-information on the actual effect on the protein function. Moreover, many of these algorithms are able to predict an effect that no necessarily translates directly into pathogenicity. VarQ Web Server is an online tool that given an UniProt id automatically analyzes known and user provided SAS for their effect on protein activity, folding, aggregation and protein interactions among others. VarQ assessment was performed over a set of previously manually curated variants, showing its ability to correctly predict the phenotypic outcome and its underlying cause. This resource is available online at http://varq.qb.fcen.uba.ar/.\n\nContact: lradusky@qb.fcen.uba.ar\n\nSupporting Information & Tutorials may be found in the webpage of the tool.

bioinformatics↗