Biology subjects

Bravo, I.

Publications and source records attributed to Bravo, I..

4 recordsLinked to original sources

bioRxiv2025

Active Liposomal Targeting for Head and Neck Squamous Cell Carcinoma Treatment

Head and neck squamous cell carcinoma (HNSCC) is a major oncological challenge due to its high recurrence rates, biological heterogeneity, and poor long-term survival outcomes. Despite advances in surgery and radiotherapy, chemotherapeutic options are limited. Cisplatin (CDDP) remains the mainstay, while small molecule inhibitors, such as the selective PI3K inhibitor Alpelisib, are still under clinical evaluation. However, systemic side effects and suboptimal tumor specificity hamper the clinical utility of both standard and novel specific therapies. In this study, we developed passive- and active-targeting liposomes encapsulating Cisplatin (CDDP) and Alpelisib. To achieve active targeting, the anti-epidermal growth factor receptor (EGFR) antibody Cetuximab was conjugated to the liposome surface. All formulations were characterized based on size, morphology, encapsulation efficiency, and drug release profiles. In vitro assays demonstrated that liposomal encapsulation preserved the cytotoxic effects of both CDDP and Alpelisib in HNSCC cell lines, with CDDP showing adequate encapsulation efficiency for in vivo evaluation. In vivo near-infrared fluorescence imaging demonstrated that active-targeting liposomes achieved greater tumor accumulation and a better tumor-to-spleen ratio compared to passive formulations. Tumor growth by CDDP-loaded activetargeting liposomes was comparable to that of the free drug, likely due to the hydrophilic nature and rapid release of CDDP from liposomes in physiological conditions. Importantly, blood chemistry analysis indicated a favorable toxicity profile for the targeted liposomal formulation. These findings highlight the potential of liposome-based targeted strategies to improve therapeutic outcomes in HNSCC and underscore the value of nanotechnology in the development of next-generation oncological therapies.

cancer biology↗

bioRxiv2022

GliaMorph: A modular image analysis toolkit to quantify Müller glial cell morphology

Cell morphology is critical for all cell functions. This is particularly true for glial cells as they rely on their complex shape to contact and support neurons. However, methods to quantify complex glial cell shape accurately and reproducibly are lacking. To address this gap in quantification approaches, we developed an analysis pipeline called "GliaMorph". GliaMorph is a modular image analysis toolkit developed to perform (i) image pre-processing, (ii) semi-automatic region-of-interest (ROI) selection, (iii) apicobasal texture analysis, (iv) glia segmentation, and (v) cell feature quantification. Muller Glia (MG) are the principal retinal glial cell type with a stereotypic shape linked to their maturation and physiological status. We here characterized MG on three levels, including (a) global image-level, (b) apicobasal texture, and (c) apicobasal vertical-to-horizontal alignment. Using GliaMorph, we show structural changes occurring in the developing retina. Additionally, we study the loss of cadherin2 in the zebrafish retina, as well as a glaucoma mouse disease model. The GliaMorph toolkit enables an in-depth understanding of MG morphology in the developing and diseased retina. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=144 HEIGHT=200 SRC="FIGDIR/small/490765v1_ufig1.gif" ALT="Figure 1"> View larger version (73K): org.highwire.dtl.DTLVardef@198fca6org.highwire.dtl.DTLVardef@f319fcorg.highwire.dtl.DTLVardef@2f0fadorg.highwire.dtl.DTLVardef@1ae4ce7_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIGlial morphology is complex, making it challenging to accurately quantify 3D cell shape. C_LIO_LIWe developed the GliaMorph toolkit for image pre-processing, glial segmentation, and quantification of Muller glial cells. C_LIO_LIMuller glia elaborate their morphology and rearrange subcellular features during embryonic development. C_LIO_LIGliaMorph accurately identifies subcellular changes in models with disrupted glia cells, including zebrafish cadherin2 loss of function and a mouse glaucoma model. C_LI

developmental biology↗

bioRxiv2020

Evolution of differential codon usage preferences and subfunctionalisation in paralogous genes: the showcase of polypyrimidine tract binding proteins.

AO_SCPLOWBSTRACTC_SCPLOWGene paralogs are copies of an ancestral gene that appear after gene or full genome duplication. When two sister gene copies are maintained in the genome, redundancy may release certain evolutionary pressures, allowing one of them to access novel functions. Here, we focused our study on gene paralogs on the evolutionary history of the three polypyrimidine tract binding protein genes (PTBP) and their concurrent evolution of differential codon usage preferences (CUPrefs) in vertebrate species. PTBP1-3 show high identity at the amino acid level (up to 80%), but display strongly different nucleotide composition, divergent CUPrefs and, in humans, distinct tissue-specific expression levels. Our phylogenetic inference results show that the duplication events leading to the three extant PTBP1-3 lineages predate the basal diversification within vertebrates, and genomic context analysis illustrates that synteny has been well preserved over time for the three paralogs. We identify a distinct evolutionary pattern towards GC3-enriching substitutions in PTBP1, concurrent with an enrichment in frequently used codons and with a tissue-wide expression. In contrast, PTBP2s are enriched in AT-ending, rare codons, and display tissue-restricted expression. As a result of this substitution trend, CUPrefs are sharply different between mammalian PTBP1s and the rest of PTBPs. Genomic context analysis shows that GC3-rich nucleotide composition in PTBP1s is driven by local substitution processes, while the evidence in this direction is thinner for PTBP2-3. An actual lack of co-variation between the observed GC composition of PTBP2-3 and that of the surrounding non-coding genomic environment would raise an interrogation on the origin of CUPrefs, warrantying further research on a putative tissue-specific translational selection. Finally, we communicate an intriguing trend for the use of the UUG-Leu codon, which matches the trends of AT-ending codons. We interpret that our results are compatible with an scenario in which a combination of directional mutation-selection processes would have differentially shaped CUPrefs of PTBPs in Vertebrates: the observed GC-enrichment of PTBP1 in Mammals may be linked to genomic location and to the strong and broad tissue-expression, while AT-enrichment of PTBP2 and PTBP3 would be associated with rare CUPrefs and thus, possibly to specialized spatio-temporal expression. Our interpretation is coherent with a gene subfunctionalisation process by differential expression regulation associated to the evolution of specific CUPrefs. 1 Significance StatementIn vertebrates, PTBP paralogs display strong differences in gene composition, gene expression regulation, and their expression in cell culture depends on their codon usage preferences. We show that placental mammals PTBP1 have become GC-rich because of local substitution pressures, resulting in an enrichment of frequently used codons and in a strong, tissue-wide expression. On the contrary, PTBP2 in vertebrates are AT-rich, with a lower contribution of local substitution processes to their specific nucleotide composition, show high frequency of rare codons and in placental mammals display a restricted expression pattern contrasting to that of PTBP1. The systematic study of composition and expression patterns of gene paralogs can help understand the complex mutation-selection interplay that shape codon usage bias in multicellular organisms.

evolutionary biology↗

bioRxiv2018

Genome plasticity in Papillomaviruses and de novo emergence of E5 oncogenes

The clinical presentations of papillomavirus (PV) infections come in many different flavors. While most PVs are part of a healthy skin microbiota and are not associated to physical lesions, other PVs cause benign lesions, and only a handful of PVs are associated to malignant transformations linked to the specific activities of the E5, E6 and E7 oncogenes. The functions and origin of E5 remain to be elucidated. These E5 ORFs are present in the genomes of a few polyphyletic PV lineages, located between the early and the late viral gene cassettes. We have computationally assessed whether these E5 ORFs have a common origin and whether they display the properties of a genuine gene. Our results suggest that during the evolution of Papillomaviridae, at least four events lead to the presence of a long non-coding DNA stretch between the E2 and the L2 genes. In three of these events, the novel regions evolved coding capacity, becoming the extant E5 ORFs. We then focused on the evolution of the E5 genes in AlphaPVs infecting humans. The sharp match between the type of E5 protein encoded in AlphaPVs and the infection phenotype (cutaneous warts, genital warts or anogenital cancers) supports the role of E5 in the differential oncogenic potential of these PVs. In our analyses, the best-supported scenario is that the five types of extant E5 proteins within the AlphaPV genomes may not have a common ancestor. However, the chemical similarities between E5s regarding amino acid composition prevent us from confidently rejecting the model of a common origin. Our evolutionary interpretation is that an originally non-coding region entered the genome of the ancestral AlphaPVs. This genetic novelty allowed to explore novel transcription potential, triggering an adaptive radiation that yielded three main viral lineages encoding for different E5 proteins, and that display distinct infection phenotypes. Overall, our results provide an evolutionary scenario for the de novo emergence of viral genes and illustrate the impact of such genotypic novelty in the phenotypic diversity of the viral infections.

evolutionary biology↗