Biology subjects

Barbosa, C.

Publications and source records attributed to Barbosa, C..

13 recordsLinked to original sources

bioRxiv2026

Rapid vaccine induction of macaque HIV-1 V2 Apex broadly neutralizing antibodies with immunogenetic signatures that are potentially translatable to humans

Due to the complex biology of HIV-1 broadly neutralizing antibodies (bnAbs), HIV-1 vaccines must target unmutated germline precursor antibodies with B cell receptors that have the appropriate specificity and genetic features to develop neutralization breadth. Previous work has shown that immunization or infection in macaques primes unmutated precursor antibodies that target the broadly neutralizing epitope composed of the second variable region and proximal glycans (termed V2-apex site) of HIV-1 envelope (Env). Macaque V2-apex bnAb precursors elicited thus far have homogeneous usage of the second reading frame of a diversity (D) gene found only in macaques, calling into question whether HIV-1 Env immunogens can elicit only this canonical, macaque-specific V2-apex antibody response, limiting human vaccination success. Here, we show that vaccination of rhesus macaques with Env conjugated to a ferritin nanoparticle (OPT4-scNP) rapidly elicited V2-apex bnAbs with distinct D gene segment usage and motifs that are not restricted only to macaques. After two priming immunizations, V2-apex antibodies with non-canonical HCDR3s exhibited greater neutralization potency and breadth than V2-apex antibodies with previously observed HCDR3 motifs. Following sequential boosting immunizations, a V2-apex bnAb lineage with a novel HCDR3-encoded EDGED motif increased its neutralization breadth, including neutralization of viral isolates bearing the N130 glycan, which shields the V2-apex from recognition. High-resolution structures of two members of this V2-apex bnAb lineage, called DH2050, defined a novel binding mode in which it used its EDGED motif to contact the C-strand peptide and the N160 glycan within the V2-apex site. Altogether, we define a novel bnAb binding mode to the V2 Apex and demonstrate that HIV-1 Env sequential vaccination elicits V2-apex bnAbs with immunogenetic signatures that are potentially translatable to the human immune system.

immunology↗

bioRxiv2025

Opposite patterns of association of TWIST1 expression with patient survival in SHH and Group 4 medulloblastoma

PurposeTwist1 is a transcription factor that regulates embryonic development, stemness, and differentiation, and can also stimulate initiation of tumorigenesis in peripheral solid cancers. However, its role in central nervous system tumors, including medulloblastoma (MB), the main type of malignant brain cancer that afflicts children, remains poorly understood. Here, we examined expression of Twist1, and its potential significance in prognosis, in different histological variants and molecular subgroups of MB. MethodsGene expression data for TWIST1 and corresponding overall survival (OS) of patients was analyzed in 612 MB samples using a previously described dataset. A cross-sectional analysis of Twist1 protein content in 24 MB tumor samples from patients was carried out by immunohistochemistry. ResultsTWIST1 transcript levels were higher in classic MB compared to desmoplastic tumors. Within samples with classic histology, higher TWIST1 expression was associated with a longer OS. Tumors in the SHH subgroup had lower TWIST1 expression compared to all other subgroups, and Group 4 showed lower expression than WNT tumors. In Group 4 MB, higher TWIST1 levels were associated with shorter OS, whereas patients with SHH tumors and higher TWIST1 levels showed longer OS. Twist1 protein was detectable in part of classic and LCA MB tumors belonging to the SHH, WNT or Group 3/4 subgroups. ConclusionWe found opposite patterns of association between TWST1 and patient survival in Group 4 and SHH MB subgroups. Our results highlight the importance of stratifying tumors by molecular subgroup and histological classification when exploring novel potential biomarkers and therapeutic targets in MB.

cancer biology↗

bioRxiv2024

Hotspot of Exotic Benthic Marine Invertebrates Discovered in the Tropical East Atlantic: DNA Barcoding Insights from the Bijagos Archipelago, Guinea-Bissau

AimThis study aimed to explore and document putative exotic marine benthic invertebrate species in the Bijagos Archipelago, Guinea-Bissau, to enhance understanding of marine biodiversity and address the extent of marine species introductions. LocationThe research was conducted in the Bijagos Archipelago, a UNESCO Biosphere Reserve located in Guinea-Bissau. MethodsThe study involved the regions first scuba-diving survey of marine biodiversity. DNA barcoding was employed to assist in the identification of benthic invertebrate species. Molecular phylogenetic analyses were conducted with the available DNA barcodes to ensure accurate taxonomic assignments, detect cryptic species, and investigate the phylogeography of the taxa. ResultsThe survey resulted in the discovery of 28 new species records for the Bijagos Archipelago, including octocorals, scleractinians, hydroids, bryozoans, barnacles, and ascidians. Among these, seven species were documented for the first time in the East Atlantic: Stragulum bicolor, Tubastraea tagusensis, Nemalecium lighti, Diphasia sp., Amathia alternata, A. distans, and Symplegma rubra. Molecular analyses revealed pervasive cryptic diversity within species previously listed as exotic, suggesting that some, such as the hydroids Plumularia setacea, Obelia geniculata, and Dynamena disticha, are not exotic due to their restricted biogeographic distributions. Many other species reported as introduced present only a few genetic lineages capable of long-distance dispersal due to human activities. Main ConclusionsThe study highlights considerable gaps in the knowledge of West African marine biodiversity and suggests a substantial underestimation of the anthropogenic trade in exotic marine species between the Tropical East Atlantic and the Americas, and between the Indo-Pacific and West Africa. Detailed taxonomic and genomic analyses are necessary for understanding marine exotic species biogeography and adaptive traits. Our findings challenge current classifications of exotic species and underscore the need for improved monitoring and management to prevent the spread of non-native marine species.

zoology↗

bioRxiv2023

Broadly neutralizing antibody induction by non-stabilized SARS-CoV-2 Spike mRNA vaccination in nonhuman primates

Immunization with mRNA or viral vectors encoding spike with diproline substitutions (S-2P) has provided protective immunity against severe COVID-19 disease. How immunization with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spike elicits neutralizing antibodies (nAbs) against difficult-to-neutralize variants of concern (VOCs) remains an area of great interest. Here, we compare immunization of macaques with mRNA vaccines expressing ancestral spike either including or lacking diproline substitutions, and show the diproline substitutions were not required for protection against SARS-CoV-2 challenge or induction of broadly neutralizing B cell lineages. One group of nAbs elicited by the ancestral spike lacking diproline substitutions targeted the outer face of the receptor binding domain (RBD), neutralized all tested SARS-CoV-2 VOCs including Omicron XBB.1.5, but lacked cross-Sarbecovirus neutralization. Structural analysis showed that the macaque broad SARS-CoV-2 VOC nAbs bound to the same epitope as a human broad SARS-CoV-2 VOC nAb, DH1193. Vaccine-induced antibodies that targeted the RBD inner face neutralized multiple Sarbecoviruses, protected mice from bat CoV RsSHC014 challenge, but lacked Omicron variant neutralization. Thus, ancestral SARS-CoV-2 spike lacking proline substitutions encoded by nucleoside-modified mRNA can induce B cell lineages binding to distinct RBD sites that either broadly neutralize animal and human Sarbecoviruses or recent Omicron VOCs. One Sentence SummaryNon-stabilized SARS-CoV-2 Spike mRNA vaccination activated B cells that target either conserved epitopes on SARS-CoV-2 Omicron variants of concern, or cross-neutralizing epitopes on pre-emergent Sarbecoviruses.

immunology↗

bioRxiv2023

Vaccine induction of CD4-mimicking broadly neutralizing antibody precursors in macaques

The CD4 binding site (CD4bs) is a conserved epitope on HIV-1 envelope (Env) that can be targeted by protective broadly neutralizing antibodies (bnAbs). HIV-1 vaccines have not elicited CD4bs bnAbs for many reasons, including the CD4bs is occluded by glycans, immunogen expansion of appropriate naive B cells, and selection of functional antibody mutations. Here, we demonstrate immunization of macaques with a CD4bs-targeting immunogen elicits neutralizing bnAb precursors with structural and genetic features of CD4-mimicking bnAbs. Structures of the CD4bs nAbs bound to HIV-1 Env demonstrated binding angles similar to human bnAbs and heavy chain second complementarity determining region-dependent binding characteristic of all known human CD4-mimicking bnAbs. Macaque nAbs were derived from variable and joining gene segments orthologous to the genes of human VH1-46-class bnAbs. This vaccine study initiated the B cells from which derive CD4bs bnAbs in primates, accomplishing the key first step in development of an effective HIV-1 vaccine.

immunology↗

bioRxiv2022

Mutation-Guided Vaccine Design: A Strategy for Developing Boosting Immunogens for HIV Broadly Neutralizing Antibody Induction

A major goal of HIV-1 vaccine development is induction of broadly neutralizing antibodies (bnAbs). While success has been achieved in initiating bnAb B cell lineages, design of boosting immunogens that select for bnAb B cell receptors with improbable mutations required for bnAb affinity maturation remains difficult. Here we demonstrate a process for designing boosting immunogens for a V3-glycan bnAb B cell lineage. The immunogens induced affinity-matured antibodies by selecting for functional improbable mutations in bnAb precursor knock-in mice. Moreover, we show similar success in prime and boosting with nucleoside-modified mRNA-encoded HIV-1 envelope trimer immunogens, with improved selection by mRNA immunogens of improbable mutations required for bnAb binding to key envelope glycans. These results demonstrate the ability of both protein and mRNA prime-boost immunogens for selection of rare B cell lineage intermediates with neutralizing breadth after bnAb precursor expansion, a key proof-of concept and milestone towards development of an HIV vaccine. One-Sentence SummaryA vaccine strategy for selecting key rare antibody mutations is shown to induce HIV broadly neutralizing antibodies in mice.

immunology↗

bioRxiv2021

Genetic determinants of antibiotic resistance and the evolution of trade-offs during adaptation in a single patient

The processes by which pathogens evolve within single hosts dictate the efficacy of treatment strategies designed to slow antibiotic resistance evolution and influence the population-wide resistance levels. The aim of this study is to describe the underlying genetic and phenotypic changes leading to antibiotic resistance within a single patient who died as resistance evolved to available antibiotics. We assess whether robust patterns of collateral sensitivity and response to combinations exist that might have been leveraged to improve therapy. Whole-genome sequencing was completed for nine isolates taken from this patient over 279 days of chronic infection with Enterobacter hormaechei, along with systematic measurements of changes in resistance against five of the most relevant drugs considered for treatment. The entirety of the genetic change is consistent with de novo mutations and plasmid loss events, without the acquisition of foreign genetic material via horizontal gene transfer. The isolates formed three genetically distinct lineages, with early evolutionary trajectories being supplanted by previously unobserved multi-step evolutionary trajectories. Importantly, no single isolate evolved resistance to all of the antibiotics considered for treatment against E. hormaechei (i.e., none was pan-resistant). Patterns of collateral sensitivity and response to combination therapy revealed contrasting patterns across this diversifying population. Translating antibiotic resistance management strategies from theoretical and laboratory data to clinical situations, such as this, may require managing diverse populations with unpredictable resistance trajectories.

evolutionary biology↗

bioRxiv2021

Aspirin-triggered resolvin D1 reduces parasitic cardiac load by decreasing inflammation through N-formyl peptide receptor 2 in a chronic murine model of Chagas disease

Chagas disease, caused by the protozoan Trypanosoma cruzi, is endemic in Latin America and is widely distributed worldwide because of migration. After years of infection and in the absence of treatment, the disease progresses from an acute and asymptomatic phase to a chronic inflammatory cardiomyopathy, leading to heart failure and death. An inadequate balance in the inflammatory response is involved in the progression of chronic Chagas cardiomyopathy. Current therapeutic strategies cannot prevent or reverse the heart damage caused by the parasite. Aspirin-triggered resolvin D1 (AT-RvD1) is a pro-resolving mediator of inflammation that acts through N-formyl peptide receptor 2 (FPR2). AT-RvD1 participates in the modification of cytokine production, inhibition of leukocyte recruitment and efferocytosis, macrophage switching to a nonphlogistic phenotype, and the promotion of healing, thus restoring organ function. In the present study, AT-RvD1 is proposed as a potential therapy aid to regulate the pro-inflammatory state during the chronic phase of Chagas disease. C57BL/6 wild-type and FPR2 knock-out mice chronically infected with T. cruzi were treated for 20 days with 5 g/kg/day AT-RvD1, 30 mg/kg/day benznidazole, or the combination of 5 g/kg/day AT-RvD1 and 5 mg/kg/day benznidazole. At the end of treatment, changes in the immune response, cardiac tissue damage, and parasite load were evaluated. The administration of AT-RvD1 in the chronic phase of T. cruzi infection regulated the inflammatory response both at the systemic level and in the cardiac tissue, and it reduced cellular infiltrates, cardiomyocyte hypertrophy, fibrosis, and the parasite load in the heart tissue. Thus, AT-RvD1 was shown to be an attractive therapeutic due to its regulatory effect on the inflammatory response at the cardiac level and its ability to reduce the parasite load during chronic T. cruzi infection, thereby preventing the chronic cardiac damage induced by the parasite. Author SummaryChagas disease is prevalent in Latin America and is widely distributed worldwide due to migration. If the parasite is left untreated, the disease progresses from an acute symptomless phase to chronic myocardial inflammation, which can cause heart failure and death years after infection. Imbalances in the inflammatory response are related to this progression. Current treatments cannot prevent or reverse the cardiac damage produced by the parasite. Aspirin-triggered resolvin D1, also named AT-RvD1, can modify cellular and humoral inflammatory responses leading to the resolution of inflammation, thus promoting healing and restoring organ function. In this study, AT-RvD1, in an N-formyl peptide receptor 2 (FPR2)-dependent manner, was shown to regulate local and systemic inflammation and decrease cellular infiltration in the heart tissue of mice chronically infected with the parasite and reduce cardiac hypertrophy and fibrosis. Importantly, AT-RvD1 was able to decrease parasite load in the infected hearts. Thus, this research indicates that At-RvD1 treatment is a potential therapeutic strategy that offers an improvement on current drug therapies.

microbiology↗

bioRxiv2021

Ability of nucleoside-modified mRNA to encode HIV-1 envelope trimer nanoparticles

The success of nucleoside-modified mRNAs in lipid nanoparticles (mRNA-LNP) as COVID-19 vaccines heralded a new era of vaccine development. For HIV-1, multivalent envelope (Env) trimer protein nanoparticles are superior immunogens compared to trimers alone for priming of broadly neutralizing antibody (bnAb) B cell lineages. The successful expression of complex multivalent nanoparticle immunogens with mRNAs has not been demonstrated. Here we show that mRNAs can encode antigenic Env trimers on ferritin nanoparticles that initiate bnAb precursor B cell expansion and induce serum autologous tier 2 neutralizing activity in bnAb precursor VH + VL knock-in mice. Next generation sequencing demonstrated acquisition of critical mutations, and monoclonal antibodies that neutralized heterologous HIV-1 isolates were isolated. Thus, mRNA- LNP can encode complex immunogens and are of use in design of germline-targeting and sequential boosting immunogens for HIV-1 vaccine development.

immunology↗

bioRxiv2020

Lipid nanoparticle encapsulated nucleoside-modified mRNA vaccines elicit polyfunctional HIV-1 antibodies comparable to proteins in nonhuman primates

Development of an effective AIDS vaccine remains a challenge. Nucleoside-modified mRNAs formulated in lipid nanoparticles (mRNA-LNP) have proved to be a potent mode of immunization against infectious diseases in preclinical studies, and are being tested for SARS-CoV-2 in humans. A critical question is how mRNA-LNP vaccine immunogenicity compares to that of traditional adjuvanted protein vaccines in primates. Here, we found that mRNA-LNP immunization compared to protein immunization elicited either the same or superior magnitude and breadth of HIV-1 Env-specific polyfunctional antibodies. Immunization with mRNA-LNP encoding Zika premembrane and envelope (prM-E) or HIV-1 Env gp160 induced durable neutralizing antibodies for at least 41 weeks. Doses of mRNA-LNP as low as 5 g were immunogenic in macaques. Thus, mRNA-LNP can be used to rapidly generate single or multi-component vaccines, such as sequential vaccines needed to protect against HIV-1 infection. Such vaccines would be as or more immunogenic than adjuvanted recombinant protein vaccines in primates.

immunology↗

bioRxiv2020

Self-amplifying RNA SARS-CoV-2 lipid nanoparticle vaccine induces equivalent preclinical antibody titers and viral neutralization to recovered COVID-19 patients

The spread of the SARS-CoV-2 into a global pandemic within a few months of onset motivates the development of a rapidly scalable vaccine. Here, we present a self-amplifying RNA encoding the SARS-CoV-2 spike protein encapsulated within a lipid nanoparticle as a vaccine and demonstrate induction of robust neutralization of a pseudo-virus, proportional to quantity of specific IgG and of higher quantities than recovered COVID-19 patients. These data provide insight into the vaccine design and evaluation of immunogenicity to enable rapid translation to the clinic.

immunology↗

bioRxiv2019

Effects of moderate and high intensity isocaloric aerobic training upon microvascular reactivity and myocardial oxidative stress in rats

Systemic and central cardiovascular adaptations may vary in response to chronic exercise performed with different intensities and volumes. This study compared the effects of aerobic training with different intensities but equivalent volume upon microvascular reactivity in cremaster muscle and myocardial biomarkers of oxidative stress in Wistar rats. After peak oxygen uptake (VO2peak) assessment, rats (n=24) were assigned into three groups: moderate-intensity exercise training (MI); high-intensity exercise training (HI); sedentary control (SC). Treadmill training occurred during 4 weeks, with exercise bouts matched by the energy expenditure (3.0-3.5 Kcal). Microvascular reactivity was assessed in vivo by intravital microscopy in cremaster muscle arterioles, while biomarkers of oxidative stress and eNOS expression were quantified at left ventricle and at aorta, respectively. Similar increasing vs. sedentary control group (SC) occurred in moderate intensity training group (MI) and high-intensity training group (HI) for endothelium-dependent vasodilation (10-4M: MI: 168.7%, HI: 164.6% vs. SC: 146.6%, P=0.0004). Superoxide dismutase (SOD) (HI: 0.13 U/mg vs. MI: 0.09 U/mg and SC: 0.06 U/mg; P=0.02), glutathione peroxidase (GPX) (HI: 0.00038 U/mg vs. MI: 0.00034 U/mg and SC: 0.00024 U/mg; P=0.04), and carbonyl protein content (HI: 0.04 U/mg vs. MI: 0.03 U/mg and SC: 0.01 U/mg; P=0.003) increased only in HI. No difference across groups was detected for catalase (CAT) (P=0.12), Thiobarbituric acid reactive substances (TBARS) (P = 0.38) or eNOS expression in aorta (P=0.44). In conclusion, higher exercise intensity induced greater improvements in myocardium antioxidant defenses, while gains in microvascular reactivity appeared to rely more on exercise volume than intensity.

physiology↗

bioRxiv2019

Evolutionary stability of collateral sensitivity to antibiotics in the model pathogen Pseudomonas aeruginosa

Evolution is at the core of the impending antibiotic crisis. Sustainable therapy must thus account for the adaptive potential of pathogens. One option is to exploit evolutionary trade-offs, like collateral sensitivity, where evolved resistance to one antibiotic causes hypersensitivity to another one. To date, the evolutionary stability and thus clinical utility of this trade-off is unclear. We performed a critical experimental test on this key requirement, using evolution experiments with Pseudomonas aeruginosa combined with genomic and genetic analyses, and identified three main outcomes: (i) bacteria commonly failed to counter hypersensitivity and went extinct; (ii) hypersensitivity sometimes converted into multidrug resistance; and (iii) resistance gains occasionally caused re-sensitization to the previous drug, thereby maintaining the trade-off. Drug order affected the evolutionary outcome, most likely due to variation in fitness costs and epistasis among adaptive mutations. Our finding of robust genetic trade-offs and drug-order effects can guide design of evolution-informed antibiotic therapy.

evolutionary biology↗