Biology subjects

Maracaja-Coutinho, V.

Publications and source records attributed to Maracaja-Coutinho, V..

9 recordsLinked to original sources

bioRxiv2026

RNA-binding proteins and regulatory networks involved in life-stage, stress temperature, and drug resistance in Leishmania parasites

Trypanosomatid parasites of the genus Leishmania rely on post-transcriptional regulation of gene expression because gene transcription is not canonically regulated at the single-gene level. RNA-binding proteins (RBPs) are central to this regulatory architecture, yet their genome-wide diversity, conservation, and condition-specific associations remain incompletely defined across the genus. Here, we combined comparative genomics and systems-level transcriptomic analyses to map the RBP repertoire in 33 strains spanning 19 Leishmania species. We also connect RBPs to developmental, stress, and drug-resistance contexts, using Leishmania braziliensis as an example. Using probabilistic domain detection and homology-based annotation, we identified 38,662 putative RBPs across all genomes, with 1,114 to 1,491 RBPs per genome. Comparative genomics analysis revealed a conserved core of 404 RBP clusters shared across all examined species, alongside lineage-restricted clusters in major Leishmania groups. We notably detected widespread conservation of enzymes linked to messenger RNA modification (for example, NAT10, TRMT6/61A, and NSUN2), but failed to identify canonical N6-methyladenosine writer orthologs, suggesting divergence of this machinery across Leishmania genomes. In L. braziliensis, expression profiling in different life-cycle stages and stress conditions highlighted stage-biased RBPs, including elevated ZC3H20 in amastigotes and increased RBP6 in metacyclic promastigotes. Finally, co-expression network analysis of trivalent antimony (SbIII) resistant genotypes identified RBPs co-expressed with genes previously associated with antimony resistance. In contrast, motif-based analysis supported a putative DRBD3-centered post-transcriptional module that includes 10 candidate stabilized transcripts in SbIII-resistant promastigotes. Together, these results provide a comparative framework to prioritize RBPs and associated regulatory programs implicated in parasite adaptation and antimony resistance. AUTHOR SUMMARYLeishmaniasis results from infection by Leishmania parasites and remains challenging to control due to limited treatments and the continual emergence of drug resistance, especially to antimonials. These parasites exhibit an unusual gene regulation method; instead of activating or deactivating transcription for individual genes, they depend heavily on proteins that bind RNA to determine which messages are retained, translated, or degraded. In this study, we created a comprehensive atlas of RNA-binding proteins across the Leishmania genus by analyzing 33 parasite strains from 19 species. We identified a large core set of conserved RNA-binding proteins shared by all species, along with lineage-specific proteins that may help different parasite groups adapt to various hosts and environments. Additionally, we mapped enzymes responsible for RNA chemical modifications and found that the typical machinery for m6A marks in many organisms appears to be divergent in Leishmania. Finally, by associating RNA-binding proteins with specific life-cycle stages, stress responses, and antimony resistance in L. braziliensis, we pinpointed candidate regulators and gene modules for further experimental validation. This resource helps prioritize regulatory factors that could drive parasite adaptation and resistance.

genomics↗

bioRxiv2025

SiteCELL enables on-site PBMCs purification and cryopreservation for immune single cell profiling of diverse ancestries

Single cell genomics has improved our knowledge of immune function and heterogeneity. In recent years, the steady increase in the number of cells and individuals profiled as part of large multinational projects has enabled the characterization of cellular differences across human populations and ancestries. However, methods for collecting and processing peripheral blood mononuclear cells (PBMCs) for downstream single cell sequencing are difficult to implement in remote and rural settings. This has resulted in a lack of representation of underserved communities across the Global South in current initiatives. Hence, we developed SiteCELL, a method that enables purification and cryopreservation of PBMCs from whole blood at the site of collection using minimal laboratory equipment and without electricity. By comparing matched samples of purified PBMCs, we showed that SiteCELL performs as well as ficoll density gradient (FDG), both in laboratory and rural settings. This method ensures accurate recovery of cell type proportions and excels in reducing stress and minimizing variability across sampling batches. These advantages make it particularly well suited for implementation in challenging settings across countries, thereby enabling the inclusion of underrepresented ancestries in cellular atlases.

immunology↗

bioRxiv2025

Effects of Willow and Pine tree growth in bacterial abundance, interactions and metabolic profile in a copper mine tailing

The Cauquenes tailings is one of the largest mine tailings in Chile and represents a significant environmental hazard due to its high copper levels and acidic pH. However, there is evidence of willow and pine tree growth in these terrains, which is unexpected given the extreme conditions of this environment. Considering the importance of plants in restoration strategies, the objective of this study was to analyze the effect that willow and pine growth have on the heavy metal contents of their surrounding soil, and the abundance, interaction, metabolic profile and assembly of the bacterial community. In the Cauquenes tailing, we collected samples from willow and pine vegetated soils as well as the surrounding non-vegetated soils. We analyzed characteristics such as heavy metal concentrations and pH levels in all sampled soils, and in tree leaves and roots. Vegetated sites exhibited lower copper levels and a neutral pH, while both tree species accumulated heavy metals in their tissues. We also determined bacterial abundance in all soil samples, and co-occurrence networks were constructed to assess bacterial interactions. Both trees promoted a higher abundance of Proteobacteria and had networks with higher modularity compared to non-vegetated soils. Finally, we estimated the metabolic profile of the bacterial community using PICRUSt 2 analysis and determined carbon source utilization with BioLog Ecoplates. PICRUSt 2 predicted higher metabolic activity in vegetated soils, and BioLog Ecoplate analysis revealed the utilization of a greater number of carbon sources. The microbial communities from vegetated soils were assembled in a deterministic manner, while the community from non-vegetated soils were stochastically assembled. In conclusion, tree growth mitigated the extreme conditions of the tailing and promoted a more active and healthier bacterial community. HighlightsO_LIWillow and pine tree can grow and mitigate toxic metal conditions in the tailings C_LIO_LIBoth trees provoked a shift in bacterial abundance and interaction network C_LIO_LIThe provoked shift was tree-dependent C_LIO_LIMicrobial activity was higher in vegetated soils C_LI

microbiology↗

bioRxiv2025

The Single-Cell Landscape of Peripheral and Tumor-infiltrating Immune Cells in HPV- HNSCC

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. HPV-negative HNSCC, which arises in the upper airway mucosa, is particularly aggressive, with nearly half of patients succumbing to the disease within five years and limited response to immune checkpoint inhibitors compared to other cancers. There is a need to further explore the complex immune landscape in HPV-negative HNSCC to identify potential therapeutic targets. Here, we integrated two single-cell RNA sequencing datasets from 29 samples and nearly 300,000 immune cells to investigate immune cell dynamics across tumor progression and lymph node metastasis. Notable shifts toward adaptative immune cell populations were observed in the 14 distinct HNSCC-associated peripheral blood mononuclear (PBMCs) and 21 tumor-infiltrating immune cells (TICs) considering disease stages. All PBMCs and TICs revealed unique molecular signatures correlating with lymph node involvement; however, broadly, TICs increased ligand expression among effector cytokines, growth factors, and interferon-related genes. Pathway analysis comparing PBMCs and TICs further confirmed active cell signaling among Monocyte-Macrophage, Dendritic cell, Natural Killer (NK), and T cell populations. Receptor-ligand analysis revealed significant communication patterns shifts among TICs, between CD8+ T cells and NK cells, showing heightened immunosuppressive signaling that correlated with disease progression. In locally invasive HPV-negative HNSCC samples, highly multiplexed immunofluorescence assays highlighted peri-tumoral clustering of exhausted CD8+ T and NK cells, alongside their exclusion from intra-tumoral niches. These findings emphasize cytotoxic immune cells as valuable biomarkers and therapeutic targets, shedding light on the mechanisms by which the HNSCC sustainably evades immune responses.

cancer biology↗

bioRxiv2024

Profiling extremophile bacterial communities recovered from a mining tailing against soil ecosystems through comparative genome-resolved metagenomics and evolutionary analysis

Microbial communities inhabiting mining environments harbor a diverse array of bacteria with specialized metabolic capacities adapted to extreme conditions. Here, we utilized comparative genome-resolved metagenomics of a high-quality Illumina-sequenced sample from the Cauquenes copper tailing in central Chile. We investigate the metabolic roles and evolutionary behaviors of the resident microorganisms, focusing on capacities related to copper, iron, and sulfur metabolism. We recovered 44 medium and high-quality metagenome-assembled genomes (MAGs), primarily classified belonging to phylum Actinobacteriota (21), Proteobacteria (10), and Acidobacteriota (6). These MAGs were compared to the Global Soil MAGs project (SMAG catalog), which includes bacteria from conventional or natural ecosystems, to uncover specialized properties of mining bacteria. Notably, we discovered a new phylum, Nitrospirota_A, and provided insights into the unexplored taxonomic classifications at the lowest ranks such as genus and species. Functional potential analysis revealed that the mining community has enhanced molecular capabilities associated with sulfur and copper metabolism. Evolutionary analysis revealed that mining genes involved in targeted metabolism are under strong negative selection, indicating conservative evolutionary pressure within the mining environment. In particular, it was possible to identify a MAG from the genus Acidithrix with a global dN/dS ratio greater than 1, suggesting positive selection. Additionally, core proteins essential for bacterial survival, such as flagellar motors, cell cycle regulators, and biogenesis proteins, were also under positive selection. The latter points to the need for enhanced mobility in these microorganisms to locate resources efficiently. We demonstrate that copper mining communities are diverse and possess a significant metabolic repertoire under extreme conditions in sulfur and copper proteins. Those specialized genes appear to be in a conservative state rather than undergoing adaptive evolution. This study enhances our understanding of extremophile mining microbiomes, highlighting their high variability in classification, metabolic functions, evolution, and adaptation, which can be leveraged for further biotechnological applications.

genomics↗

bioRxiv2022

Single cell transcriptional landscape of long non-coding RNAs orchestrating mouse heart development

Long non-coding RNAs (lncRNAs) comprise the most representative transcriptional units of the mammalian genome, and theyre associated with organ development that can be associated with the emergence of diseases, such as cardiovascular diseases. Thus, we used bioinformatic approaches, machine learning algorithms and statistical techniques to define lncRNAs involved in mammalian cardiac development. We used a single-cell transcriptome dataset generated from 4 embryonic and 4 postnatal stages. Our study identified 8 distinct cell types, novel marker transcripts (coding/lncRNAs) and also, differential expression and functional enrichment analysis reveal cardiomyocyte subpopulations associated with cardiac function; meanwhile modular co-expression analysis reveals cell-specific functional insights for lncRNAs during myocardial development, including a potential association with key genes related to disease and the "fetal gene program". Our results evidence the role of particular lncRNAs in heart development, and highlights the usage of co-expression modular approaches in the cell-type functional definition.

bioinformatics↗

bioRxiv2021

Comparative and systems analyses of Leishmania spp. non-coding RNAs through developmental stages

Leishmania spp. is the etiological agent of leishmaniases, neglected diseases that seek to be eradicated in the coming years. The life cycle of these parasites involve different host and stress environments. In recent years, many studies have shown that several protein coding genes are directly involved with the development and host interactions, however, little is still known about the role of ncRNAs in life cycle progression. In this study, we aimed to identify the genomic structure and function of ncRNAs from Leishmania spp. and to get insights into the RNAome of this protozoan genus. We studied 26 strains corresponding to 16 different species of Leishmania. Our RNAome analysis revealed the presence of several ncRNAs that are shared through different species, allowing us to differentiate between subgenus as well as species that are canonically related to visceral leishmaniasis. We also studied co-expression relationships between coding genes and ncRNAs which in the amastigote developmental stage for Leishmania braziliensis and L. donovani revealed the presence of miRNA-like co-expressed with several coding genes involved in starvation, survival and histone modification. This work constitutes the first effort to characterize the Leishmania RNAome, supporting further approaches to better understand the role of ncRNAs in the gene regulation, infective process and host-parasite interaction.

genomics↗

bioRxiv2020

RNAmining: A machine learning stand-alone and web server tool for RNA coding potential prediction

Non-coding RNAs (ncRNAs) are important players in the cellular regulation of organisms from different kingdoms. One of the key steps in ncRNAs research is the ability to distinguish coding/non-coding sequences. We applied 7 machine learning algorithms (Naive Bayes, SVM, KNN, Random Forest, XGBoost, ANN and DL) through 15 model organisms from different evolutionary branches. Then, we created a stand-alone and web server tool (RNAmining) to distinguish coding and noncoding sequences, selecting the algorithm with the best performance (XGBoost). Firstly, we used coding/non-coding sequences downloaded from Ensembl (April 14th, 2020). Then, coding/non-coding sequences were balanced, had their tri-nucleotides counts analysed and we performed a normalization by the sequence length. Thus, in total we built 180 models. All the machine learning algorithms tests were performed using 10-folds cross-validation and we selected the algorithm with the best results (XGBoost) to implement at RNAmining. Best F1-scores ranged from 97.56% to 99.57% depending on the organism. Moreover, we produced a benchmarking with other tools already in literature (CPAT, CPC2, RNAcon and Transdecoder) and our results outperformed them, opening opportunities for the development of RNAmining, which is freely available at https://rnamining.integrativebioinformatics.me/.

bioinformatics↗

bioRxiv2020

Genome-wide analysis of in vivo CcpA binding with and without its key co-factor HPr in the major human pathogen group A Streptococcus.

Catabolite control protein A (CcpA) is a master regulator of carbon source utilization and contributes to the virulence of numerous medically important Gram-positive bacteria. Most functional assessments of CcpA, including interaction with its key co-factor HPr, have been performed in non-pathogenic bacteria. In this study we aimed to identify the in vivo DNA binding profile of CcpA and assess the extent to which HPr is required for CcpA-mediated regulation and DNA binding in the major human pathogen group A Streptococcus (GAS). Using a combination RNAseq/ChIPseq approach, we found that CcpA affects transcript levels of 514 of 1667 GAS genes (31%) whereas direct DNA binding was identified for 105 GAS genes. Three of the directly regulated genes encode the key GAS virulence factors Streptolysin S, PrtS (IL-8 degrading proteinase), and SpeB (cysteine protease). Mutating CcpA Val301 to Ala (strain 2221-CcpA-V301A) abolished interaction between CcpA and HPr and impacted the transcript levels of 205 genes (40%) in the total CcpA regulon. By ChIPseq analysis, CcpAV301A bound to DNA from 74% of genes bound by wild-type CcpA, but generally with lower affinity. These data delineate the direct CcpA regulon and clarify the HPr-dependent and independent activities of CcpA in a key pathogenic bacterium. Data sharing and data availabilityThe data that support the findings of this study are available from the corresponding author upon reasonable request.

microbiology↗