Biology subjects

Souza, T. M.

Publications and source records attributed to Souza, T. M..

4 recordsLinked to original sources

bioRxiv2026

A Cross-Study Multi-Organ Cell Atlas ofMacaca fascicularis Informed by Human Foundation Model Annotation: A Resource for Translational Target Assessment

Non-human primates (NHPs), particularly Macaca fascicularis (cynomolgus macaque), represent an essential model for preclinical assessment of biologics due to their high genetic and physiological similarity to humans. However, mounting regulatory pressure to reduce NHP use and the lack of a unified, well-annotated single-cell atlas currently limits both target qualification and mechanistic interpretation of toxicity in this species. To address this gap, we assembled and harmonized the largest single-cell transcriptomic atlas of M. fascicularis to date, integrating 30 publicly available studies spanning 57 anatomical regions, 43 organs and 14 physiological systems. We implemented a scalable framework for cross-species cell type annotation by embedding both cynomolgus monkeys and human (Tabula Sapiens V2) datasets into a shared reference space using Universal Cell Embeddings (UCE), enabling consistent harmonization of cell identities. In total, 27 organs were annotated using human reference labels, while the remaining sets retained author-provided annotations or labels transferred from other cynomolgus studies with available annotations. The resulting atlas comprises over 2.5 million cells and demonstrates concordance in cell-type-specific expression patterns between cynomolgus and humans, including tissue-specific markers and targets relevant for biologics development. Through translational use cases, we illustrate how this resource can be applied to assess target expression in tissues affected by concordant human-NHP toxicities, investigate ocular adverse events associated with antibody-drug conjugates (ADCs), and identify species-specific features of immune cell subtypes with known safety implications. By enabling scalable, high-resolution, cross-species comparisons of gene expression across organs, tissues, and cell states, this atlas supports improved target qualification, more mechanistic interpretation of toxicities, and evidence-based decisions on the relevance and design of NHP studies. Collectively, this work provides a unified cross-species single-cell resource for cynomolgus monkey and a modular computational framework that advances new approach methodologies and contributes to the refinement and reduction of NHP use in preclinical research.

bioinformatics↗

bioRxiv2025

Cyclodextrin-Based Delivery of the Annexin A1 Mimetic Peptide Ac2-26 Enhances Anti-Inflammatory Effects and PreventsDengue-Induced Lethality in Combination with AntiviralTherapy

Severe dengue is characterized by systemic inflammation, cytokine storm, vascular leakage, and hemorrhagic manifestations, largely driven by the host immune response to dengue virus (DENV) infection. Despite its burden, no licensed antivirals or host-directed therapies are currently available. Our group has previously identified Annexin A1 (AnxA1) as an endogenous regulator of inflammation in dengue. Treatment with the AnxA1 peptidomimetic, Ac2-26, improved clinical outcomes in murine models of severe dengue by promoting resolution of inflammation without affecting viral control. To explore new delivery strategies, we developed a novel formulation of Ac2-26 complexed with hydroxypropyl-{beta}-cyclodextrin (CDX-Ac2-26). In DENV-2-infected A129 mice, both intraperitoneal and oral CDX-Ac2-26 improved clinical scores and reversed thrombocytopenia. Notably, CDX-Ac2-26 reduced mast cell degranulation, MCPT-1 plasma levels, and CCL2 expression in spleen, with no effect on viral titers, indicating a host-targeted mechanism and overcoming the anti-inflammatory effects of the free peptide. Intraperitoneal administration achieved the same efficacy as oral dosing with only one-third of the dose. Importantly, the combination of CDX-Ac2-26 with the antiviral nucleotide analog sofosbuvir fully prevented disease and mortality in infected mice, highlighting a combinatorial effect between host-directed and antiviral therapies. These findings underscore the therapeutic potential of anti-inflammatory/pro-resolving strategies in severe dengue and support the development of CDX-Ac2-26 as a novel adjunctive treatment. Combining anti-inflammatory and antiviral approaches may enhance efficacy and reduce treatment-associated toxicity, offering a promising path for clinical translation. What is already known on this topic?O_LIPlasma levels of Annexin A1 are inversely correlated with the severity of clinical outcomes in dengue virus infection. C_LIO_LIThe Annexin A1 peptidomimetic Ac2-26 exhibits anti-inflammatory and pro-resolving effects against severe dengue in a murine model. C_LI What does this study add?O_LIThe Ac2-26-cyclodextrin complex enhances the anti-inflammatory effects of the peptide against dengue virus infection, allowing for lower dosing and oral administration. C_LIO_LIThe administration of the CDX-Ac2-26 with a nucleoside analog antiviral exhibits a combinatorial effectt, providing complete protection against the lethal outcome of severe dengue. C_LI What is the clinical significance?O_LICurrent dengue treatment relies on symptomatic management, as no directed anti-inflammatory agents or antivirals are currently available. We have identified a novel host-targeted strategy to resolve the disease. C_LIO_LIOur findings strongly support CDX-Ac2-26 as a promising adjunctive treatment strategy in combination with antiviral therapy for severe dengue, highlighting the potential of combinatorial approaches. C_LI

immunology↗

bioRxiv2020

Repurposing the Ebola and Marburg Virus Inhibitors Tilorone, Quinacrine and Pyronaridine: In vitro Activity Against SARS-CoV-2 and Potential Mechanisms

SARS-CoV-2 is a newly identified virus that has resulted in over 1.3 M deaths globally and over 59 M cases globally to date. Small molecule inhibitors that reverse disease severity have proven difficult to discover. One of the key approaches that has been widely applied in an effort to speed up the translation of drugs is drug repurposing. A few drugs have shown in vitro activity against Ebola virus and demonstrated activity against SARS-CoV-2 in vivo. Most notably the RNA polymerase targeting remdesivir demonstrated activity in vitro and efficacy in the early stage of the disease in humans. Testing other small molecule drugs that are active against Ebola virus would seem a reasonable strategy to evaluate their potential for SARS-CoV-2. We have previously repurposed pyronaridine, tilorone and quinacrine (from malaria, influenza, and antiprotozoal uses, respectively) as inhibitors of Ebola and Marburg virus in vitro in HeLa cells and of mouse adapted Ebola virus in mouse in vivo. We have now tested these three drugs in various cell lines (VeroE6, Vero76, Caco-2, Calu-3, A549-ACE2, HUH-7 and monocytes) infected with SARS-CoV-2 as well as other viruses (including MHV and HCoV 229E). The compilation of these results indicated considerable variability in antiviral activity observed across cell lines. We found that tilorone and pyronaridine inhibited the virus replication in A549-ACE2 cells with IC50 values of 180 nM and IC50 198 nM, respectively. We have also tested them in a pseudovirus assay and used microscale thermophoresis to test the binding of these molecules to the spike protein. They bind to spike RBD protein with Kd values of 339 nM and 647 nM, respectively. Human Cmax for pyronaridine and quinacrine is greater than the IC50 hence justifying in vivo evaluation. We also provide novel insights into their mechanism which is likely lysosomotropic.

pharmacology and toxicology↗

bioRxiv2018

Capturing diverse microbial sequence with comprehensive and scalable probe design

Metagenomic sequencing has the potential to transform microbial detection and characteri zation, but new tools are needed to improve its sensitivity. We developed CATCH (Compact Aggregation of Targets for Comprehensive Hybridization), a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs compact probe sets that achieve full coverage of known sequence diversity and that scale well with this diversity. To illustrate applications of CATCH, we focused on capturing viral genomes. We designed, synthesized, and validated multiple probe sets, including one that targets whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriched unique viral content on average 18x and allowed us to assemble genomes that we could not otherwise recover, while accurately preserving within-sample diversity. We used this approach to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of viral infections in samples with unknown content. Together, this work demonstrates a path toward more sensitive, cost-effective metagenomic sequencing.

genomics↗