Role of enteroendocrine cells in intestinal homeostasis and ageing.

The Intestine is a large and dynamic organ with a defined population of stem cells (ISCs) that are capable of giving rise to different differentiated cell types. The enteroendocrine cells (EEs) in the gut are responsible for producing different hormones which affect physiological and cellular processes locally and systemically throughout the body. In the intestine of the fruit fly (Drosophila melanogaster), EEs cumulatively produce 12 different prohormones that give rise to more than 20 hormone peptides. Despite their physiological importance, not much is known about the role that EEs and their products play in intestinal homeostasis during ageing in Drosophila. In the first part of my thesis, I investigated the mechanism by which the transcription factor Klumpfuss (Klu) determines the choice between enterocyte (EC) versus EE differentiation in the Drosophila intestine. We demonstrated that Klu acts in a cell-autonomous manner to restrict enteroblast (EB) cell fate to EC differentiation. Inhibition of klu expression by RNA interference resulted in excess EE differentiation. Ectopic expression of klu in ISCs reduces their proliferative capacity and blocked differentiation. Lastly, we showed that Klu acts down stream of Notch signaling in determining EC cell fate decision. In the second part of my thesis I employed a combination of bulk and single cell RNA sequencing (scRNA-seq) to investigate the changes in EE cells during ageing in both males and females. We observed significant changes in transcript-level for different EE hormones in our bulk RNA sequencing dataset. We examined the functional consequence of knocking down these hormones on ISC-proliferation and discovered that several EE-derived hormones play a role in promoting ISC-proliferation after infection. Moreover, we observed upregulation of pathways that are related to cell cycle and differentiation in old EEs, signifying changes in EE differentiation in the aged intestine. Analyzing our scRNA-seq dataset using Seurat algorithm and supervised clustering confirmed several of the changes from our bulk RNA-seq experiment, while expanding our knowledge on EE subtype change with age. We identified 4 major EE clusters in all conditions: NPF, AstA, AstC and EE progenitor cells, and observed increases in EE progenitor and AstA cell types in old female samples. Moreover, we observed a decrease of cells in the NPF cluster in old versus young female samples. This change was confirmed by Gal4 reporter line analysis for this hormone. Interestingly, the reduction of NPF-producing EEs in old flies happened in both male and female samples, but in different anatomical regions of the intestine. Finally, we showed that transcript of the transcription factor Escargot, which was thought to be restricted solely to the ISC and EB, is unexpectedly present in almost all EE clusters. With this study I have increased our understanding of ISC differentiation and cell fate determination in Drosophila intestine, and documented the changes that EE cells sustain during the ageing process. These results will be of crucial importance to better understand the role of EE cells in gut health and disease in an increasingly ageing population

AI Knowledge Transfer from the University to Society

AI Knowledge Transfer from the University to Society: Applications in High-Impact Sectors brings together examples from the "Innovative Ecosystem with Artificial Intelligence for Andalusia 2025" project at the University of Seville, a series of sub-projects composed of research groups and different institutions or companies that explore the use of Artificial Intelligence in a variety of high-impact sectors to lead innovation and assist in decision-making. Key Features Includes chapters on health and social welfare, transportation, digital economy, energy efficiency and sustainability, agro-industry, and tourism Great diversity of authors, expert in varied sectors, belonging to powerful research groups from the University of Seville with proven experience in the transfer of knowledge to the productive sector and agents attached to the Andalucía TECH Campu

AI Knowledge Transfer from the University to Society

AI Knowledge Transfer from the University to Society: Applications in High-Impact Sectors brings together examples from the "Innovative Ecosystem with Artificial Intelligence for Andalusia 2025" project at the University of Seville, a series of sub-projects composed of research groups and different institutions or companies that explore the use of Artificial Intelligence in a variety of high-impact sectors to lead innovation and assist in decision-making. Key Features Includes chapters on health and social welfare, transportation, digital economy, energy efficiency and sustainability, agro-industry, and tourism Great diversity of authors, expert in varied sectors, belonging to powerful research groups from the University of Seville with proven experience in the transfer of knowledge to the productive sector and agents attached to the Andalucía TECH Campu

Correction to: RNA Bioinformatics.

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Computational approaches for improving the accuracy and efficiency of RNA-seq analysis

The past decade has seen tremendous growth in the area of high throughput sequencing technology, which simultaneously improved the biological resolution and subsequent processing of publicly-available sequencing datasets. This enormous amount of data also calls for better algorithms to process, extract and filter useful knowledge from the data. In this thesis, I concentrate on the challenges and solutions related to the processing of bulk RNA-seq data. An RNA-seq dataset consists of raw nucleotide sequences, drawn from the expressed mixture of transcripts in one or more samples. One of the most common uses of RNA-seq is obtaining transcript or gene level abundance information from the raw nucleotide read sequences and then using these abundances for downstream analyses such as differential expression. A typical computational pipeline for such processing broadly involves two steps: assigning reads to the reference sequence through alignment or mapping algorithms, and subsequently quantifying such assignments to obtain the expression of the reference transcripts or genes. In practice, this two-step process poses multitudes of challenges, starting from the presence of noise and experimental artifacts in the raw sequences to the disambiguation of multi-mapped read sequences. In this thesis, I have described these problems and demonstrated efficient state-of-the-art solutions to a number of them. The current thesis will explore multiple uses for an alternate representation of an RNA-seq experiment encoded in equivalence classes and their associated counts. In this representation, instead of treating a read fragment individually, multiple fragments are simultaneously assigned to a set of transcripts depending on the underlying characteristics of the read-to-transcript mapping. I used the equivalence classes for a number of applications in both single-cell and bulk RNA-seq technologies. By employing equivalence classes at cellular resolution, I have developed a droplet-based single-cell RNA-seq sequence simulator capable of generating tagged end short read sequences resembling the properties of real datasets. In bulk RNA-seq, I have utilized equivalence classes to applications ranging from data-driven compression methodologies to clustering de-novo transcriptome assemblies. Specifically, I introduce a new data-driven approach for grouping together transcripts in an experiment based on their inferential uncertainty. Transcripts that share large numbers of ambiguously-mapping fragments with other transcripts, in complex patterns, often cannot have their abundances confidently estimated. Yet, the total transcriptional output of that group of transcripts will have greatly-reduced inferential uncertainty, thus allowing more robust and confident downstream analysis. This approach, implemented in the tool terminus, groups together transcripts in a data-driven manner. It leverages the equivalence class factorization to quickly identify transcripts that share reads and posterior samples to measure the confidence of the point estimates. As a result, terminus allows transcript-level analysis where it can be confidently supported, and derives transcriptional groups where the inferential uncertainty is too high to support a transcript-level result

Development and application of methodologies and infrastructures for cancer genome analysis within Personalized Medicine

Programa de Doctorat en Biomedicina / Tesi realitzada al Barcelona Supercomputing Cener (BSC)[eng] Next-generation sequencing (NGS) has revolutionized biomedical sciences, especially in the area of cancer. It has nourished genomic research with extensive collections of sequenced genomes that are investigated to untangle the molecular bases of disease, as well as to identify potential targets for the design of new treatments. To exploit all this information, several initiatives have emerged worldwide, among which the Pan-Cancer project of the ICGC (International Cancer Genome Consortium) stands out. This project has jointly analyzed thousands of tumor genomes of different cancer types in order to elucidate the molecular bases of the origin and progression of cancer. To accomplish this task, new emerging technologies, including virtualization systems such as virtual machines or software containers, were used and had to be adapted to various computing centers. The portability of this system to the supercomputing infrastructure of the BSC (Barcelona Supercomputing Center) has been carried out during the first phase of the thesis. In parallel, other projects promote the application of genomics discoveries into the clinics. This is the case of MedPerCan, a national initiative to design a pilot project for the implementation of personalized medicine in oncology in Catalonia. In this context, we have centered our efforts on the methodological side, focusing on the detection and characterization of somatic variants in tumors. This step is a challenging action, due to the heterogeneity of the different methods, and an essential part, as it lays at the basis of all downstream analyses. On top of the methodological section of the thesis, we got into the biological interpretation of the results to study the evolution of chronic lymphocytic leukemia (CLL) in a close collaboration with the group of Dr. Elías Campo from the Hospital Clínic/IDIBAPS. In the first study, we have focused on the Richter transformation (RT), a transformation of CLL into a high-grade lymphoma that leads to a very poor prognosis and with unmet clinical needs. We found that RT has greater genomic, epigenomic and transcriptomic complexity than CLL. Its genome may reflect the imprint of therapies that the patients received prior to RT, indicating the presence of cells exposed to these mutagenic treatments which later expand giving rise to the clinical manifestation of the disease. Multiple NGS- based techniques, including whole-genome sequencing and single-cell DNA and RNA sequencing, among others, confirmed the pre-existence of cells with the RT characteristics years before their manifestation, up to the time of CLL diagnosis. The transcriptomic profile of RT is remarkably different from that of CLL. Of particular importance is the overexpression of the OXPHOS pathway, which could be used as a therapeutic vulnerability. Finally, in a second study, the analysis of a case of CLL in a young adult, based on whole genome and single-cell sequencing at different times of the disease, revealed that the founder clone of CLL did not present any somatic driver mutations and was characterized by germline variants in ATM, suggesting its role in the origin of the disease, and highlighting the possible contribution of germline variants or other non-genetic mechanisms in the initiation of CLL

Development and application of methodologies and infrastructures for cancer genome analysis within Personalized Medicine

[eng] Next-generation sequencing (NGS) has revolutionized biomedical sciences, especially in the area of cancer. It has nourished genomic research with extensive collections of sequenced genomes that are investigated to untangle the molecular bases of disease, as well as to identify potential targets for the design of new treatments. To exploit all this information, several initiatives have emerged worldwide, among which the Pan-Cancer project of the ICGC (International Cancer Genome Consortium) stands out. This project has jointly analyzed thousands of tumor genomes of different cancer types in order to elucidate the molecular bases of the origin and progression of cancer. To accomplish this task, new emerging technologies, including virtualization systems such as virtual machines or software containers, were used and had to be adapted to various computing centers. The portability of this system to the supercomputing infrastructure of the BSC (Barcelona Supercomputing Center) has been carried out during the first phase of the thesis. In parallel, other projects promote the application of genomics discoveries into the clinics. This is the case of MedPerCan, a national initiative to design a pilot project for the implementation of personalized medicine in oncology in Catalonia. In this context, we have centered our efforts on the methodological side, focusing on the detection and characterization of somatic variants in tumors. This step is a challenging action, due to the heterogeneity of the different methods, and an essential part, as it lays at the basis of all downstream analyses. On top of the methodological section of the thesis, we got into the biological interpretation of the results to study the evolution of chronic lymphocytic leukemia (CLL) in a close collaboration with the group of Dr. Elías Campo from the Hospital Clínic/IDIBAPS. In the first study, we have focused on the Richter transformation (RT), a transformation of CLL into a high-grade lymphoma that leads to a very poor prognosis and with unmet clinical needs. We found that RT has greater genomic, epigenomic and transcriptomic complexity than CLL. Its genome may reflect the imprint of therapies that the patients received prior to RT, indicating the presence of cells exposed to these mutagenic treatments which later expand giving rise to the clinical manifestation of the disease. Multiple NGS- based techniques, including whole-genome sequencing and single-cell DNA and RNA sequencing, among others, confirmed the pre-existence of cells with the RT characteristics years before their manifestation, up to the time of CLL diagnosis. The transcriptomic profile of RT is remarkably different from that of CLL. Of particular importance is the overexpression of the OXPHOS pathway, which could be used as a therapeutic vulnerability. Finally, in a second study, the analysis of a case of CLL in a young adult, based on whole genome and single-cell sequencing at different times of the disease, revealed that the founder clone of CLL did not present any somatic driver mutations and was characterized by germline variants in ATM, suggesting its role in the origin of the disease, and highlighting the possible contribution of germline variants or other non-genetic mechanisms in the initiation of CLL

Following the trail of cellular signatures : computational methods for the analysis of molecular high-throughput profiles

Over the last three decades, high-throughput techniques, such as next-generation sequencing, microarrays, or mass spectrometry, have revolutionized biomedical research by enabling scientists to generate detailed molecular profiles of biological samples on a large scale. These profiles are usually complex, high-dimensional, and often prone to technical noise, which makes a manual inspection practically impossible. Hence, powerful computational methods are required that enable the analysis and exploration of these data sets and thereby help researchers to gain novel insights into the underlying biology. In this thesis, we present a comprehensive collection of algorithms, tools, and databases for the integrative analysis of molecular high-throughput profiles. We developed these tools with two primary goals in mind. The detection of deregulated biological processes in complex diseases, like cancer, and the identification of driving factors within those processes. Our first contribution in this context are several major extensions of the GeneTrail web service that make it one of the most comprehensive toolboxes for the analysis of deregulated biological processes and signaling pathways. GeneTrail offers a collection of powerful enrichment and network analysis algorithms that can be used to examine genomic, epigenomic, transcriptomic, miRNomic, and proteomic data sets. In addition to approaches for the analysis of individual -omics types, our framework also provides functionality for the integrative analysis of multi-omics data sets, the investigation of time-resolved expression profiles, and the exploration of single-cell experiments. Besides the analysis of deregulated biological processes, we also focus on the identification of driving factors within those processes, in particular, miRNAs and transcriptional regulators. For miRNAs, we created the miRNA pathway dictionary database miRPathDB, which compiles links between miRNAs, target genes, and target pathways. Furthermore, it provides a variety of tools that help to study associations between them. For the analysis of transcriptional regulators, we developed REGGAE, a novel algorithm for the identification of key regulators that have a significant impact on deregulated genes, e.g., genes that show large expression differences in a comparison between disease and control samples. To analyze the influence of transcriptional regulators on deregulated biological processes,, we also created the RegulatorTrail web service. In addition to REGGAE, this tool suite compiles a range of powerful algorithms that can be used to identify key regulators in transcriptomic, proteomic, and epigenomic data sets. Moreover, we evaluate the capabilities of our tool suite through several case studies that highlight the versatility and potential of our framework. In particular, we used our tools to conducted a detailed analysis of a Wilms' tumor data set. Here, we could identify a circuitry of regulatory mechanisms, including new potential biomarkers, that might contribute to the blastemal subtype's increased malignancy, which could potentially lead to new therapeutic strategies for Wilms' tumors. In summary, we present and evaluate a comprehensive framework of powerful algorithms, tools, and databases to analyze molecular high-throughput profiles. The provided methods are of broad interest to the scientific community and can help to elucidate complex pathogenic mechanisms.Heutzutage werden molekulare Hochdurchsatzmessverfahren, wie Hochdurchsatzsequenzierung, Microarrays, oder Massenspektrometrie, regelmäßig angewendet, um Zellen im großen Stil und auf verschiedenen molekularen Ebenen zu charakterisieren. Die dabei generierten Datensätze sind in der Regel hochdimensional und oft verrauscht. Daher werden leistungsfähige computergestützte Anwendungen benötigt, um deren Analyse zu ermöglichen. In dieser Arbeit präsentieren wir eine Reihe von effektiven Algorithmen, Programmen, und Datenbaken für die Analyse von molekularen Hochdurchsetzdatensätzen. Diese Ansätze wurden entwickelt, um deregulierte biologische Prozesse zu untersuchen und in diesen wichtige Schlüsselmoleküle zu identifizieren. Zusätzlich wurden eine Reihe von Analysen durchgeführt um die verschiedenen Methoden zu evaluieren. Zu diesem Zweck haben wir insbesondere eine Wilmstumor Studie durchgeführt, in der wir verschiedene regulatorische Mechanismen und dazugehörige Biomarker identifizieren konnten, die für die erhöhte Malignität von Wilmstumoren mit blastemreichen Subtyp verantwortlich sein könnten. Diese Erkenntnisse könnten in der Zukunft zu einer verbesserten Behandlung dieser Tumore führen. Diese Ergebnisse zeigen eindrucksvoll, dass unsere Ansätze in der Lage sind, verschiedene molekulare Hochdurchsatzmessungen auszuwerten und dabei helfen können pathogene Mechanismen im Zusammenhang mit Krebs oder anderen komplexen Krankheiten aufzuklären

Emerging Genomic Technologies for Agricultural Biotechnology: Current Trends and Future Prospects

Twenty years from now, the earth’s population will need 55% more food than it can currently produce. However, agriculture is facing severe challenges such as global climate change, exhausted resources, reduction of arable lands and various pathogen attacks. Advances in genomic technologies may offer potential solutions to these agricultural problems. Recent years have seen the rapid development of new genomic technologies such as CRISPR, TALENS and ODM (collectively gene editing), as well as doubled haploids, molecular markers and mapping populations. Together with the rapidly expanding availability of genome sequence data, these technologies have the potential to transform plant breeding. Cross breeding is a traditionally used technology to improve the crops with desirable traits such as nutritional quality, higher yields, abiotic and biotic stress tolerances. Nowadays, emerging genomic technologies (EGTs) are being used extensively in agriculture and life sciences by researchers all over the world to incorporate desirable genes in different crops such as cereals, pulses, oilseeds, fruits or vegetables. Application of these technologies in new crops is expected to play an important role towards faster growth in productivity so critical for meeting the sustainable development goals, in particular the goals of zero hunger and sustainable food, nutrition and environmental security in the world. This Research Topic will include papers that describe the application of cutting-edge technologies to improve various crops, vegetables and fruits. We aim to attract papers addressing targets from all over the world but not limited to the following: • CRISPR/Cas, ZFN, TALENs • Development of Molecular Markers • Markers Assisted Breeding • SNP Markers • Computer-Aided Drug Design (CADD) in plants • Genetic Engineering and Development of Transgenic (GMO) crops • Current status of regulatory frameworks controlling GMO crops in the world • Risk assessment of GMO crops • New other emerging genomic technologie