Digital Gene Expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea

The freshwater planarian Schmidtea mediterranea is recognised as a valuable model for research into adult stem cells and regeneration. With the advent of the high-throughput sequencing technologies, it has become feasible to undertake detailed transcriptional analysis of its unique stem cell population, the neoblasts. Nonetheless, a reliable reference for this type of studies is still lacking. Taking advantage of digital gene expression (DGE) sequencing technology we compare all the available transcriptomes for S. mediterranea and improve their annotation. These results are accessible via web for the community of researchers. Using the quantitative nature of DGE, we describe the transcriptional profile of neoblasts and present 42 new neoblast genes, including several cancer-related genes and transcription factors. Furthermore, we describe in detail the Smed-meis-like gene and the three Nuclear Factor Y subunits Smed-nf-YA, Smed-nf-YB-2 and Smed-nf-YC. DGE is a valuable tool for gene discovery, quantification and annotation. The application of DGE in S. mediterranea confirms the planarian stem cells or neoblasts as a complex population of pluripotent and multipotent cells regulated by a mixture of transcription factors and cancer-related genes

Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality

Proliferative and positional instructions underliying planarian regeneration and tissue renewal = Instrucciones proliferativas y posicionales subyacentes a la regeneración y el recambio tisular en planaria

[eng] Some animals have incredible regenerative abilities which kept researchers fascinating during decades. How these animals are able to regenerate missing parts and restore damaged tissues can give researchers insights in the regenerative medicine field. Here, we use the planarian Schmidtea mediterranea, specie which is able to fully regenerate every missing part, to deeper understand the regeneration and the tissue renewal processes. Both processes share several mechanisms which are essentials for their correct development. In this Thesis, we described some aspect of the balance between proliferation and apoptosis, the stem cell differentiation and the positional instructions required all of them to properly regenerate any structure and produce the tissue turn over required during the normal homeostasis of the animals. To study the balance between proliferation and apoptosis, we were focused in the description of Krüppel-like factor 10/11, which in other organisms is also involved in these mechanisms. Here we show that klf10/11 is required for the proper regulation of proliferation and apoptosis in regeneration and that they are essential for the correct remodelling of the organism structures, probably downstream c-Jun N-terminal kinase. On the other hand, we have been focused on the study of the transcriptional complex Nuclear Factor Y in order to understand its role during differentiation events in planarian. We have shown that planarian NF-Y is essential for regeneration and homeostasis and that its inhibition generates neoblast accumulation and absence of epidermal progenitors which demonstrates that NF-Y is involved in the early differentiation of epidermal lineage progenitors. Finally, the positional instructions which are essential for the correct positioning of cells and organs during regeneration and homeostasis have been studied. Here, we have been focused in the control of the medio-lateral organization of the central nervous system in planarian, where Wnt5 and Slit play an essential role. Wnt5, Slit and their receptors create a self-regulatory system to establish the medio-lateral pattern in planarians which guide the CNS to be positioned in this axis[spa] Algunos animales tienen habilidades regenerativas increíbles, las cuales han mantenido a los investigadores fascinados durante décadas. Cómo estos animales son capaces de regenerar partes perdidas y recuperar los tejidos dañados podría dar a los investigadores claves en el campo de la medicina regenerativa. Aquí, nosotros usamos la planaria Schmidtea mediterránea, una especie que es capaz de regenerar completamente cada parte perdida, para entender más profundamente el proceso de regeneración y recambio tisular. Ambos procesos comparten varios mecanismos los cuales son esenciales para su correcto desarrollo. En esta Tesis, describimos algunos aspectos del balance entre la proliferación y la apoptosis, la diferenciación de células madre y las instrucciones posicionales, requeridas todos ellos para regenerar cualquier estructura y producir el recambio tisular requerido durante la homeostasis normal de los animales. Para estudiar el balance entre la proliferación y la apoptosis, nos hemos centrado en la descripción del factor Krüppel-like 10/11, el cual se ha relacionado con estos procesos en otros organismos. Aquí hemos visto que, klf10/11 se requiere durante la regeneración para la correcta regulación de la proliferación y de la apoptosis y que es necesario para el correcto remodelaje de las estructuras del organismo, probablemente aguas abajo de la kinasa c-Jun N-terminal. Por otra parte, nos hemos centrado en el estudio del complejo transcripcional Nuclear Factor Y para así comprender su papel durante los eventos de diferenciación en la planaria. Hemos visto que el NF-Y presente en planaria es esencial para la regeneración y homeostasis y que su inhibición produce la acumulación de neoblastos y la pérdida de progenitores epidérmicos, lo cual demuestra que NF-Y está involucrado en la diferenciación temprana de los progenitores tempranos epidérmicos. Finalmente, se han estudiado las instrucciones posicionales, las cuales son esenciales para el correcto posicionamiento de las células y órganos durante la regeneración y homeostasis. Aquí, nos hemos centrado en el control de la organización medio-lateral del sistema nervioso central en la planaria, donde Wnt5 y Slit juegan un papel esencial. Wnt5, Slit y sus receptores crean un sistema auto-regulativo para establecer el patrón medio-lateral en las planarias, el cual guía al SNC para ser posicionado en este eje

Hippo signaling controls cell cycle and restricts cell plasticity in planarians.

Constant cell renewal is required to maintain healthy organs during adult homeostasis. The highly conserved Hippo signaling pathway is essential for the regulation of basic cell behaviors that underlie tissue renewal, including cell proliferation, cell differentiation, and cell death. The Hippo protein has been implicated in several human cancers, and its inhibition in mouse and Drosophila promotes the formation of overgrowths. Nonetheless, its biological function remains poorly understood. To address this issue, we studied the role of Hippo in planarians, flatworms that continuously alter their size depending on nutrient availability, and therefore have a high rate of cellular turnover. This ability is sustained by an abundant population of adult totipotent stem cells. We show that hippo inhibition in planarians decreases apoptotic cell death, impairs cell progression through the cell cycle, and causes instability of the differentiated cell fate. These events ultimately lead to the formation of overgrowths consisting of undifferentiated cells. We propose that the main role of Hippo in planarians is not to promote proliferation but to control the cell cycle and maintain a stable differentiated cell fate

Digital Gene Expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea

The freshwater planarian Schmidtea mediterranea is recognised as a valuable model for research into adult stem cells and regeneration. With the advent of the high-throughput sequencing technologies, it has become feasible to undertake detailed transcriptional analysis of its unique stem cell population, the neoblasts. Nonetheless, a reliable reference for this type of studies is still lacking. Taking advantage of digital gene expression (DGE) sequencing technology we compare all the available transcriptomes for S. mediterranea and improve their annotation. These results are accessible via web for the community of researchers. Using the quantitative nature of DGE, we describe the transcriptional profile of neoblasts and present 42 new neoblast genes, including several cancer-related genes and transcription factors. Furthermore, we describe in detail the Smed-meis-like gene and the three Nuclear Factor Y subunits Smed-nf-YA, Smed-nf-YB-2 and Smed-nf-YC. DGE is a valuable tool for gene discovery, quantification and annotation. The application of DGE in S. mediterranea confirms the planarian stem cells or neoblasts as a complex population of pluripotent and multipotent cells regulated by a mixture of transcription factors and cancer-related genes