Transcriptomic analysis of N-terminal mutated Trypanosoma cruzi UBP1 knockdown underlines the importance of this RNA-binding protein in parasite development.

BACKGROUND: During its life cycle, the human pathogen Trypanosoma cruzi must quickly adapt to different environments, in which the variation in the gene expression of the regulatory U-rich RNA-binding protein 1 (TcUBP1) plays a crucial role. We have previously demonstrated that the overexpression of TcUBP1 in insect-dwelling epimastigotes orchestrates an RNA regulon to promote differentiation to infective forms. METHODS: In an attempt to generate TcUBP1 knockout parasites by using CRISPR-Cas9 technology, in the present study, we obtained a variant transcript that encodes a protein with 95% overall identity and a modified N-terminal sequence. The expression of this mutant protein, named TcUBP1mut, was notably reduced compared to that of the endogenous form found in normal cells. TcUBP1mut-knockdown epimastigotes exhibited normal growth and differentiation into infective metacyclic trypomastigotes and were capable of infecting mammalian cells. RESULTS: We analyzed the RNA-Seq expression profiles of these parasites and identified 276 up- and 426 downregulated genes with respect to the wildtype control sample. RNA-Seq comparison across distinct developmental stages revealed that the transcriptomic profile of these TcUBP1mut-knockdown epimastigotes significantly differs not only from that of epimastigotes in the stationary phase but also from the gene expression landscape characteristic of infective forms. This is both contrary to and consistent with the results of our recent study involving TcUBP1-overexpressing cells. CONCLUSION: Together, our findings demonstrate that the genes exhibiting opposite changes under overexpression and knockdown conditions unveil key mRNA targets regulated by TcUBP1. These mostly encompass transcripts that encode for trypomastigote-specific surface glycoproteins and ribosomal proteins, supporting a role for TcUBP1 in determining the molecular characteristics of the infective stage.

RNA-seq data exploration after trypanosome RNA-binding protein UBP1 expression is altered by CRISPR-Cas9 gene editing and overexpression.

Previous studies have shown that overexpression of the Trypanosoma cruzi U-rich RNA-binding protein 1 (TcUBP1) in insect-dwelling epimastigotes results in a gene expression pattern resembling that of the infective form of the pathogen. Here, we used CRISPR-Cas9-induced edition of TcUBP1 and full-length protein overexpression in epimastigote cells to monitor transcriptomic changes during the epimastigote-to-metacyclic trypomastigote stage transition of T. cruzi. This dataset includes the bioinformatics analysis of three different RNA-seq samples, each with three biological replicates, showing differential mRNA abundances. The current transcriptome report has the potential to shed light on the quantitative variances in the expression of significant up- or down-regulated mRNAs as a consequence of the levels of the UBP1 protein. Raw data files were deposited at the NCBI Sequence Read Archive - SRA at http://ncbi.nlm.nih.gov/Traces/sra/sra.cgi with accession numbers PRJNA907231 and PRJNA949967.

Proteomic data of the Trypanosoma cruzi insect-dwelling epimastigotes overexpressing the RNA-binding protein UBP1.

We present data on the proteome of the Trypanosoma cruzi epimastigote cells overexpressing the U-rich RNA-binding protein 1 (UBP1). The role of this regulatory protein during the epimastigote-to-metacyclic trypomastigote stage transition was clearly established by our group at the transcriptome level; nevertheless, the impact of UBP1 overexpression on protein synthesis is not known. To address this question, we performed shotgun label-free quantification proteomics using an in vitro system based on the tetracycline-inducible expression of TcUBP1 and epimastigote wildtype cells. Using tryptic peptide digestion and LC-MS/MS analysis with Orbitrap technology, this data file describes the proteome of three biological samples per condition and yields 1637 correctly quantified proteins. The statistical comparisons of the two analyzed groups within the Proteome Discoverer platform identified 379 differentially expressed proteins, with 207 being up-regulated and 172 being down-regulated. In addition, profile plots and heatmap analysis to visualize the distribution of protein abundances within replicates are also presented. Data are available via ProteomeXchange with identifier PXD047761.

RNA-Seq reveals that overexpression of TcUBP1 switches the gene expression pattern toward that of the infective form of Trypanosoma cruzi.

Trypanosomes regulate gene expression mainly by using posttranscriptional mechanisms. Key factors responsible for carrying out this regulation are RNA-binding proteins, affecting subcellular localization, translation, and/or transcript stability. Trypanosoma cruzi U-rich RNA-binding protein 1 (TcUBP1) is a small protein that modulates the expression of several surface glycoproteins of the trypomastigote infective stage of the parasite. Its mRNA targets are known, but the impact of its overexpression at the transcriptome level in the insect-dwelling epimastigote cells has not yet been investigated. Thus, in the present study, by using a tetracycline-inducible system, we generated a population of TcUBP1-overexpressing parasites and analyzed its effect by RNA-Seq methodology. This allowed us to identify 793 up- and 371 downregulated genes with respect to the wildtype control sample. Among the upregulated genes, it was possible to identify members coding for the TcS superfamily, MASP, MUCI/II, and protein kinases, whereas among the downregulated transcripts, we found mainly genes coding for ribosomal, mitochondrial, and synthetic pathway proteins. RNA-Seq comparison with two previously published datasets revealed that the expression profile of this TcUBP1-overexpressing replicative epimastigote form resembles the transition to the infective metacyclic trypomastigote stage. We identified novel cis-regulatory elements in the 3'-untranslated region of the affected transcripts and confirmed that UBP1m, a signature TcUBP1 binding element previously characterized in our laboratory, is enriched in the list of stabilized genes. We can conclude that the overall effect of TcUBP1 overexpression on the epimastigote transcriptome is mainly the stabilization of mRNAs coding for proteins that are important for parasite infection.

Terapias biológicas del cáncer: un enfoque a favor de la accesibilidad / Biological cancer therapies: an approach towards accessibility

RESUMEN Los anticuerpos monoclonales son una poderosa herramienta para el diagnóstico de laboratorio y un instrumento cada vez más utilizado en el tratamiento de diversas enfermedades, siendo uno de los grupos más importantes de drogas en el tratamiento del cáncer. La revolución en el mundo de los anticuerpos ocurre en 1975 cuando Milstein y Köhler desarrollan la técnica de las hibridomas en Cambridge. Objetivo Hacer una revisión del uso de anticuerpos monoclonales en medicina y, en particular, en el tratamiento del cáncer. Se busca aportar una visión generalizada del concepto de anticuerpo monoclonal para explicar su aplicabilidad terapéutica y abordar un enfoque económico y sociosanitario de la obtención y acceso a las nuevas terapias. Método En la caracterización del fenómeno de investigación se empleó el estudio descriptivo, de recolección de datos documental y la correlación entre las distintas fuentes. Discusión Son aún elevados los costos tanto para el paciente como para los sistemas de salud pública, y se ha de optimizar la valoración costo-efectividad de modo que la rentabilidad y el acceso a tiempo para los pacientes puedan ser compatibles. Se deja abierto el reto del desarrollo de nuevos mAbs dirigidos a nuevas dianas, mejorar el perfil de seguridad, evitando o reduciendo las reacciones adversas inmunes y conseguir el abaratamiento del coste de producción mediante mejoras en la biotecnología.(AU)

ABSTRACT Monoclonal antibodies are a useful tool for laboratory diagnosis and an instrument used in the treatment of various diseases and represent one of the most important groups of new drugs for the treatment of cancer. The revolution in the world occured in 1975 when Milstein and Köhler discovered monoclonal antibodies in Cambridge. Objective To review the use of monoclonal antibodies in medicine and in the treatment of cancer. To provide a generalized vision of the concept of monoclonal antibody to explain its therapeutic applicability, and to approach an economic, health-care approach to obtaining and accessing new therapies. Method In the characterization of the research phenomenon, the descriptive study, the collection of documentary data and the correlation between the different sources were used. Discussion However, the costs for both the patient and the public health systems are still high, and the cost-effectiveness assessment must be optimized so that cost-effectiveness and access to time for patients can be compatible. And the challenge of developing new mAbs aimed at new targets, improving the safety profile, avoiding, or reducing adverse immune reactions and achieving lower production costs through improvements in biotechnology, is left open.(AU)

The RNA-binding protein TcUBP1 up-regulates an RNA regulon for a cell surface-associated Trypanosoma cruzi glycoprotein and promotes parasite infectivity.

The regulation of transcription in trypanosomes is unusual. To modulate protein synthesis during their complex developmental stages, these unicellular microorganisms rely largely on post-transcriptional gene expression pathways. These pathways include a plethora of RNA-binding proteins (RBPs) that modulate all steps of the mRNA life cycle in trypanosomes and help organize transcriptomes into clusters of post-transcriptional regulons. The aim of this work was to characterize an RNA regulon comprising numerous transcripts of trypomastigote-associated cell-surface glycoproteins that are preferentially expressed in the infective stages of the human parasite Trypanosoma cruzi. In vitro and in vivo RNA-binding assays disclosed that these glycoprotein mRNAs are targeted by the small trypanosomatid-exclusive RBP in T. cruzi, U-rich RBP 1 (TcUBP1). Overexpression of a GFP-tagged TcUBP1 in replicative parasites resulted in >10 times up-regulated expression of transcripts encoding surface proteins and in changes in their subcellular localization from the posterior region to the perinuclear region of the cytoplasm, as is typically observed in the infective parasite stages. Moreover, RT-quantitative PCR analysis of actively translated mRNAs by sucrose cushion fractionation revealed an increased abundance of these target transcripts in the polysome fraction of TcUBP1-induced samples. Because these surface proteins are involved in cell adherence or invasion during host infection, we also carried out in vitro infections with TcUBP1-transgenic trypomastigotes and observed that TcUBP1 overexpression significantly increases parasite infectivity. Our findings provide evidence for a role of TcUBP1 in trypomastigote stage-specific gene regulation important for T. cruzi virulence.

[Biological cancer therapies: an approach towards accessibility]. / Terapias biológicas del cáncer: un enfoque a favor de la accesibilidad.

OBJECTIVE: Monoclonal antibodies are a useful tool for laboratory diagnosis and an instrument used in the treatment of various diseases and represent one of the most important groups of new drugs for the treatment of cancer. The revolution in the world occured in 1975 when Milstein and Köhler discovered monoclonal antibodies in Cambridge. To review the use of monoclonal antibodies in medicine and in the treatment of cancer. To provide a generalized vision of the concept of monoclonal antibody to explain its therapeutic applicability, and to approach an economic, health-care approach to obtaining and accessing new therapies. METHOD: In the characterization of the research phenomenon, the descriptive study, the collection of documentary data and the correlation between the different sources were used. DISCUSSION: However, the costs for both the patient and the public health systems are still high, and the cost-effectiveness assessment must be optimized so that cost-effectiveness and access to time for patients can be compatible. And the challenge of developing new mAbs aimed at new targets, improving the safety profile, avoiding, or reducing adverse immune reactions and achieving lower production costs through improvements in biotechnology, is left open.

OBJETIVO: Los anticuerpos monoclonales son una poderosa herramienta para el diagnóstico de laboratorio y un instrumento cada vez más utilizado en el tratamiento de diversas enfermedades, siendo uno de los grupos más importantes de drogas en el tratamiento del cáncer. La revolución en el mundo de los anticuerpos ocurre en 1975 cuando Milstein y Köhler desarrollan la técnica de las hibridomas en Cambridge. Hacer una revisión del uso de anticuerpos monoclonales en medicina y, en particular, en el tratamiento del cáncer. Se busca aportar una visión generalizada del concepto de anticuerpo monoclonal para explicar su aplicabilidad terapéutica y abordar un enfoque económico y sociosanitario de la obtención y acceso a las nuevas terapias. MÉTODO: En la caracterización del fenómeno de investigación se empleó el estudio descriptivo, de recolección de datos documental y la correlación entre las distintas fuentes. DISCUSIÓN: Son aún elevados los costos tanto para el paciente como para los sistemas de salud pública, y se ha de optimizar la valoración costo-efectividad de modo que la rentabilidad y el acceso a tiempo para los pacientes puedan ser compatibles. Se deja abierto el reto del desarrollo de nuevos mAbs dirigidos a nuevas dianas, mejorar el perfil de seguridad, evitando o reduciendo las reacciones adversas inmunes y conseguir el abaratamiento del coste de producción mediante mejoras en la biotecnología.