Human T-lymphotropic virus 1 (HTLV-1) was the first recognized human retrovirus. Infection can lead to two main symptomatologies: adult T-cell lymphoma/leukemia (ATLL) and HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP). Each manifestation is associated with distinct characteristics, as ATLL presents as a leukemia-like disease, while HAM/TSP presents as severe inflammation in the central nervous system, leading to paraparesis. Previous studies have identified molecules associated with disease development, e.g., the downregulation of Foxp3 in Treg cells was associated with increased risk of HAM/TSP. In addition, elevated levels of CXCL10, CXCL9, and Neopterin in cerebrospinal fluid also present increased risk. However, these molecules were only associated with specific patient groups or viral strains. Furthermore, the majority of studies did not jointly compare all clinical manifestations, and robust analysis entails the inclusion of both ATLL and HAM/TSP. The low numbers of samples also pose difficulties in conducting gene expression analysis to identify specific molecular relationships. To address these limitations and increase the power of manifestation-specific gene associations, meta-analysis was performed using publicly available gene expression data. The application of supervised learning techniques identified alterations in two genes observed to act in tandem as potential biomarkers: GBP2 was associated with HAM/TSP, and CD40LG with ATLL. Together, both molecules demonstrated high sample-classification accuracy (AUC values: 0.88 and 1.0, respectively). Next, other genes with expression correlated to these genes were identified, and we attempted to relate the enriched pathways identified with the characteristic of each clinical manifestation. The present findings contribute to knowledge surrounding viral progression and suggest a potentially powerful new tool for the molecular classification of HTLV-associated diseases.

Background: Leishmania spp. are digenetic parasites capable of infecting humans and causing a range of diseases collectively known as leishmaniasis. The main mechanisms involved in the development and permanence of this pathology are linked to evasion of the immune response. Crosstalk between the immune system and particularities of each pathogenic species is associated with diverse disease manifestations. Lipophosphoglycan (LPG), one of the most important molecules present on the surface of Leishmania parasites, is divided into four regions with high molecular variability. Although LPG plays an important role in host-pathogen and vector-parasite interactions, the distribution and phylogenetic relatedness of the genes responsible for its synthesis remain poorly explored. The recent availability of full genomes and transcriptomes of Leishmania parasites offers an opportunity to leverage insight on how LPGrelated genes are distributed and expressed by these pathogens.Results: Using a phylogenomics-based framework, we identified a catalog of genes involved in LPG biosynthesis across 22 species of Leishmania from the subgenera Viannia and Leishmania, as well as 5 non-Leishmania trypanosomatids. The evolutionary relationships of these genes across species were also evaluated. Nine genes related to the production of the glycosylphosphatidylinositol (GPI)-anchor were highly conserved among compared species, whereas 22 genes related to the synthesis of the repeat unit presented variable conservation. Extensive gain/loss events were verified, particularly in genes SCG1-4 and SCA1-2. These genes act, respectively, on the synthesis of the side chain attached to phosphoglycans and in the transfer of arabinose residues. Phylogenetic analyses disclosed evolutionary patterns reflective of differences in host specialization, geographic origin and disease manifestation. Conclusions:The multiple gene gain/loss events identified by genomic data mining help to explain some of the observed intra-and interspecies variation in LPG structure. Collectively, our results provide a comprehensive catalog that details how LPG-related genes evolved in the Leishmania parasite specialization process.

Introduction: Leishmaniasis, a neglected infectious disease affecting humans, domestic, and wild animals, is caused by 20 from 53 Leishmania genus species and transmitted by sandflies. Leishmania genus, belonging to the Trypanosomatidae family and Kinetoplastida order, are grouped into five subgroups according to the biogeographic and evolutive history of parasites and hosts, leading to incongruences and paraphyly. The GH18 Leishmania chitinase, which is encoded by a species-specific single-copy gene, conserved in the basal groups of trypanosomatids, and absent in the genus Trypanosoma, was evaluated as a phylogenetic marker and a diagnostic target. Methods: Primers were designed to detect Leishmania in its host biological samples and obtain the chitinase sequence of species that are unavailable in public databanks. The GH18 chitinase gene and its genomic context were evaluated phylogenetically. A protocol was developed to discriminate Leishmania subgenera by adopting polymerase chain reaction (PCR) and restriction fragment length polymorphism and using in silico tools. The adopted PCR method for detecting a partial 953 bp GH18 chitinase-encoding gene represented high sensibility and specificity on DNA of isolated parasites and was used as negative controls, Trypanosoma cruzi, and DNA from Leishmania hosts. Results: Preservation of the chitinase locus in the aquatic free-living protozoan Bodosaltans disclosed a primitive common origin. Based on the comparative analysis, the amino acid sequence of GH18 trypanosomatidae chitinase demonstrated its high similarity to that of chitinase from marine prokaryotes and protozoans. Phylogenetic reconstruction based on chitinase corroborated the Supercontinent Origins Theory for Leishmania. Conclusion: The chitinase-encoding gene was effectively detected in biological samples and thus could be considered for differential molecular diagnosis among Leishmania clinical important species worldwide.

Leishmaniasis, a neglected infectious disease affecting humans, domestic and wild animals, caused by 20 from 53 Leishmania genus species, is transmitted by sandflies. Leishmania genus, belonging to Trypanosomatide Family and Kinetoplastida Order, are grouped in five subgroups according to biogeographic and evolutive history of parasites and hosts, which has led to incongruences and paraphyly. The GH18 Leishmania chitinase, encoded by a specie-specific single copy gene, conserved in basal groups of trypanosomatids, and absent in the genus Trypanosoma, was evaluated as a phylogenetic marker and a diagnostic target. Primers were designed to detect Leishmania in its host biological samples and to obtain the chitinase sequence of species not available in public databanks. The GH18 chitinase gene and its genomic context was evaluated phylogenetically. A protocol to discriminate among Leishmania subgenera by PCR and restriction fragment length polymorphism (RFLP) was developed using in silico tools. A PCR method to detect a partial 953 bp GH18 quitinase encoding gene presented high sensibility and specificity on isolated parasites DNA and using as negative controls, Trypanosoma cruzi, and DNA from Leishmania hosts. Preservation of the chitinase locus in the aquatic free-living protozoan Bodo saltans, disclose a primitive common origin. GH18 trypanosomatide chitinase amino acid sequence comparative analysis revealed high similarity to chitinase from marine prokaryotes and protozoan. Phylogenetic reconstruction based on chitinase corroborates the Supercontinent Origins theory for Leishmania. The chitinase encoding gene was effectively detected in biological samples and for differential molecular diagnosis among Leishmania clinical important species worldwide.

A, Selective suppression of cellular immunity and increased cytotoxicity in skin lesions of disseminated leishmaniasis uncovered by transcriptome-wide analysis,