Repopulation of decellularized retinas with hiPSC-derived retinal pigment epithelial and ocular progenitor cells shows cell engraftment, organization and differentiation

The retinal extracellular matrix (ECM) provides architectural support, adhesion and signal guidance that controls retinal development. Decellularization of the ECM affords great potential to tissue engineering; however, how structural retinal ECM affects in vitro development, differentiation and maturation of ocular cells remains to be elucidated. Here, mouse and porcine retinas were decellularized and the protein profile analyzed. Acellular retinal ECM (arECM) scaffolds were then repopulated with human iPSC-derived retinal pigment epithelial (RPE) cells or ocular progenitor cells (OPC) to assess their integration, proliferation and organization. 3837 and 2612 unique proteins were identified in mouse and porcine arECM, respectively, of which 93 and 116 proteins belong to the matrisome. GO analysis shows that matrisome-related proteins were associated with the extracellular region and cell junction and KEGG pathways related to signalling transduction, nervous and endocrine systems and cell junctions were enriched. Interestingly, mouse and porcine arECMs were successfully repopulated with both RPE and OPC, the latter exhibiting cell lineage-specific clusters. Retinal cells organized into different layers containing well-defined areas with pigmented cells, photoreceptors, Müller glia, astrocytes, and ganglion cells, whereas in other areas, conjunctival/limbal, corneal and lens cells re-arranged in cell-specific self-organized areas. In conclusion, our results demonstrated that decellularization of both mouse and porcine retinas retains common native ECM components that upon cell repopulation could guide similar ocular cell adhesion, migration and organization

Proteomics Analysis of Extracellular Matrix Remodeling During Zebrafish Heart Regeneration

Adult zebrafish, in contrast to mammals, are able to regenerate their hearts in response to injury or experimental amputation. Our understanding of the cellular and molecular bases that underlie this process, although fragmentary, has increased significantly over the last years. However, the role of the extracellular matrix (ECM) during zebrafish heart regeneration has been comparatively rarely explored. Here, we set out to characterize the ECM protein composition in adult zebrafish hearts, and whether it changed during the regenerative response. For this purpose, we first established a decellularization protocol of adult zebrafish ventricles that significantly enriched the yield of ECM proteins. We then performed proteomic analyses of decellularized control hearts and at different times of regeneration. Our results show a dynamic change in ECM protein composition, most evident at the earliest (7 days postamputation) time point analyzed. Regeneration associated with sharp increases in specific ECM proteins, and with an overall decrease in collagens and cytoskeletal proteins. We finally tested by atomic force microscopy that the changes in ECM composition translated to decreased ECM stiffness. Our cumulative results identify changes in the protein composition and mechanical properties of the zebrafish heart ECM during regeneration

Methods and Models for the Analysis of Biological Signifïcance Based on High­Throughput Data

[cat]L'aparició de les tecnologies d'alt rendiment ha generat una quantitat ingent de dades òmiques. Els resultats d'aquests experiment són llargues llistes de gens, que poden ser utilitzats com a biomarcadors. Un dels grans reptes dels investigadors experimentals és atribuir una interpretació o significació biològica a aquests biomarcadors potencials, ja be sigui extraient la informació bioblògica emmagatzemada en recursos com la Gene Ontology (GO) o la Kyoto Encyclopedia of Genes and Genomes (KEGG), o be combinant-les amb altres dades òmiques. Els objectius de la tesis eren: primer, estudiar les propietats matemàtiques de dos tipus de mesures de similaritat semàntica per a explorar categories GO, i segon, classificar i estudiar l'evolució de les eines GO per a l'anàlisi d'enriquiment. La primera mesura de similaritat semàntica considerada, proposada per en Lord et al., es fonamentava en la teoria de grafs, i la segona era un grup de pseudo-distàncies, proposades per Joslyn et al., fonamentades en la teoria dels Partially Ordered Sets (POSETs). L'estudi de les eines GO es va basar en les primeres 26 eines disponibles al web del The GO Consortium. S'ha vist que la mesura d'en Lord et al. és la mateixa mesura que la d'en Resnik, anteriorment publicada. S'ha observat una analogia en la forma de mapejar els gens a la GO via grafs i/o via POSETs. S'han proposat una propietat i un corol·lari que permeten calcular matricialment les la primera mesura de similaritat semàntica. S'ha demostrat que ambdues mesures estan associades a la distància mètrica. A'ha desenvolupat un paquet R, anomenat sims, que permet calcular similaritats semàntiques d'una ontologia arbitraria i comparar perfils de similaritat semàntica de la GO. S'ha proposat un Conjunt de Funcionalitats Estàndard per a classificar eines GO i s'ha desenvolupat un programari web, anomenat SerbGO, dirigit a seleccionar i comparar eines GO. L'estudi estadístic ha revelat que els promotors de les eines GO han introduït millores al llarg del temps, però no s'han detectat models ben definits. S'ha desenvolupat una ontologia, anomenada DeGOT, que proporciona un vocabulari als desenvolupadors per a introduir millores a les eines o dissenyar una de nova.[eng] Cerca avançada Restringir a TDX Inici | Què és? | Preguntes més freqüents (FAQ) | Contacte English | Castellano Consultar TDX Per universitats i departaments Per data de defensa Per autors/directors Per títols Per matèries Consultar departament Per data de defensa Per autors/directors Per títols Per matèries Estadístiques Per tesi Per departament Per universitat Tot TDX El meu TDX Registrat com [email protected] (Finalitza la sessió) Perfil Enviaments Alertes per correu-e Opcions administrador Edita aquest element Altres portals de tesis Tesis europees Tesis internacionals Novetats Pàgina inicial del TDX > Universitat de Barcelona > Departament d'Estadística > Visualitza tesi Logotip de la col·lecció Empreu aquest identificador per citar o enllaçar aquesta tesi: http://hdl.handle.net/10803/286465 Títol: Methods and Models for the Analysis of Biological Signifïcance Based on High­Throughput Data Autor/a: Mosquera Mayo, José Luís Director/a: Sànchez, Àlex (Sànchez Pla) Tutor/a: Oller i Sala, Josep Maria Departament/Institut: Universitat de Barcelona. Departament d'Estadística Abstract: The advent of high-throughput technologies has generated a huge quantity of omics data. The results of these experiments usually are long lists of genes that can be used as biomarkers. A major challenge for the researchers is to attribute a biological interpretation or significance to these list of potential biomarkers, by using biological information stored in bioinformatics resources such as the Gene Ontology (GO) or the Kyoto Encyclopedia of Genes and Genomes (KEGG), or combining them with other types of omics data. This dissertation had two main objectives. First, to study mathematical properties of two types of semantic similarity measures for exploring GO categories, and second, to classify and to study the evolution of GO tools for enrichment analysis. The first measure considered was a semantic similarity measure proposed by Lord et al. It is a node- based approach based on the Graph Theory. The second measure actually was a group pseudo- distances proposed Joslyn et al. They were edge-based approaches based on the algebraic point of view of the Partially Ordered Sets (POSET) Theory. So, in order of reaching our objectives, first of all a review and description of main methods about graph theory and POSET theory was carried out. This fact allowed us to realized that there are to ways for mapping objects (e.g. genes) in to the terms of an ontology (e.g. GO). First formulation is called Object-Ontology Complex (OOC). It was proposed by Carey in order to perform statistical computations. Second formulation is called POSET Ontology (POSO) and it was introduced by Joslyn et al. In order to classify the GO for enrichment analysis the first 26 GO available at the website of The GO Consortium were surveyed. These left us list of 205 features that were used for building an Standard Functionalities Set. Based on these functionalities the 26 GO tools were classified according to their capabilities. The study of the GO tools evolution was based on the monitoring of these 26 GO tools. So the statistical analysis consisted of a descriptive statistics, an inferential analysis and a multivariate analysis. With regard to the first objective, we have seen the Lord's measure is the same as the Resnik's measure, previously published. It has observed that there exists a certain level of analogy between the formalization of the OOC and the POSO for mapping genes to objects to terms of an ontology. A property and a corollary to calculate semantic similarity measures from node-based approaches based on a matrix point of view have been proposed. It has been proved that the Lord's measure and the Joslyn's measure can be redefined in terms of metric distance. An R package called sims for computing semantic similarity measures between terms of an arbitrary ontology and comparing semantic similarity profiles based on the GO terms associated with two lists of genes has been developed. Based on the classification of the GO programs a web-based tool called SerbGO devoted to select and compare GO tools stored in was developed. The statistical analysis about the evolution of GO tools suggested that the promoters have introduced improvements over time, but clear models of GO tools have been detected. According to the results of the statistical analysis an ontology called DeGOT was built in order to provide an structured vocabulary for the developers when they dealing with the task of introducing improvements in the existing GO tools for enrichment analysis or designing a new one program. DeGOT can be used for supporting queries and comparison results of SerbGO

Extramedullary multiple myeloma patient-derived orthotopic xenograft with a highly altered genome: combined molecular and therapeutic studies

Extramedullary multiple myeloma (EMM) has an overall survival of 6 months and occurs in 20% of multiple myeloma (MM) patients. Genetic and epigenetic mechanisms involved in EMM and the therapeutic role of new agents for MM are not well established. Besides, well-characterized preclinical models for EMM are not available. Herein, a patient-derived orthotopic xenograft (PDOX) was generated from a patient with an aggressive EMM to study in-depth genetic and epigenetic events, and drug responses related to extramedullary disease. A fresh punch of an extramedullary cutaneous lesion was orthotopically implanted in NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ(NSG) mouse. The PDOX mimicked histologic and phenotypic features of the tumor of the patient. Cytogenetic studies revealed a hyperploid genome with multiple genetic poor-prognosis alterations. Copy number alterations (CNAs) were detected in all chromosomes. The IGH translocation t(14;16)(q32;q23)IGH/MAF was already observed at the medullary stage and a new one, t(10;14)(p?11-12;q32), was observed only with extramedullary disease and could be eventually related to EMM progression in this case. Exome sequencing showed 24 high impact single nucleotide variants and 180 indels. From the genes involved, only TP53 was previously described as a driver in MM. A rather balanced proportion of hyper/hypomethylated sites different to previously reported widespread hypomethylation in MM was also observed. Treatment with lenalidomide, dexamethasone and carfilzomib showed a tumor weight reduction of 90% versus non-treated tumors, whereas treatment with the anti-CD38 antibody daratumumab showed a reduction of 46%. The generation of PDOX from a small EMM biopsy allowed us to investigate in depth the molecular events associated with extramedullary disease in combination with drug testing