Browsing by Author "Machado, Rui Sotero Rodrigues"
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- Analysis of the transcriptional regulatory network: underlying heart developmentPublication . Machado, Rui Sotero Rodrigues; Futschik, Matthias E.; Bragança, JoséHeart development is a highly complex process with a series of precisely spatially and temporally ordered events on molecular level. To understand how these events are controlled and coordinated, it is necessary to study the underlying gene expression and its regulation. While many studies have been carried out in the examination of single genes and their expression patterns, comprehensive analyses of genome-wide expression profiles associated with cardiomyogenesis (i.e. the differentiation of stem cells into cardiomyocytes) are still rare. In fact, no study exists to date which compares and consolidates the publicly available genome-wide measurement for cardiomyogenesis. Such endeavour however is important, as it is well known that individual microarray studies can be seriously compromised by artefacts. In contrast, the combination of various expression studies, which was performed in my study, can lead to more reliable results and help elucidate the different aspects of heart development and repair. Furthermore, a brief study was performed regarding the potential risk of originating cancer or teratomas from stem cell therapy. Finally, I carried out a network-based analysis, to identify regulatory actions between genes, based on published interaction data. This type of analysis can also help to identify novel genes with a role in heart development and provide new valuable targets to future experimental laboratorial analysis. The combination of the multiple dataset is thus an important approach to gain better insights of the different heart development processes as well as regenerative medicine applied to the heart.
- Identification of novel key factors of heart development using a systems biology approachPublication . Machado, Rui Sotero Rodrigues; Futschik, Matthias E.; Bragança, JoséHeart diseases are the leading cause of death worldwide. Although surgical interventions can provide valuable options for treatment, current therapies in cardiovascular medicine only delay disease progression. A main reason for this shortcoming is the limited regenerative capacity of the adult human heart. In contrast to many other tissues and organs, the mammalian heart has very limited regenerative capacity. However, it has been observed that neonatal hearts in mice show remarkable capacity to regenerate lost functional muscle tissue, a capacity that rapidly disappears after the first post-natal week. Therefore, the study of heart development might give crucial cues for cardiac regenerative medicine. Heart development or cardiogenesis is a highly complex process with many components that are finely tuned in a precise manner across time and space. Regulation of gene expression plays an important role in this process. To capture this level of regulation, technologies such as microarrays or next generation sequencing provide powerful tools, as they enable the simultaneous measurement of expression levels of thousands of coding and non-coding genes. Although, it is possible to obtain the expression information of several thousand of genes, there is a clear lack of platforms in which research can scan through this information to develop or generate insightful biological questions in the field of heart study. Hence, this doctoral research work has tried to provide different systems biology approaches in order to offer new insights into gene expression events that occur mainly during heart development. These approaches include: (i) the integration of more than 20 published microarray studies related to cardiogenesis and the development of the HeartEXpress database (http://heartexpress.sysbiolab.eu/) to provide an easy and public access to the integrated data; (ii) the integrative analysis of a genome-wide study profiling coding and noncoding genes during embryonic heart development in vivo; (iii) the assessment of transcription factors and miRNAs previously associated to heart development; (iv) the integration and prioritisation of miRNA-mRNA interactions to identify novel miRNAs, mRNAs or miRNAinteractions with potential impact on cardiogenesis; (v) the development of a web-server called HeartmiR (http://heartmir.sysbiolab.eu/), which enables independent query and visualisation of miRNA-mRNA interactions obtained from the in vivo study; and (vi) comparative analysis of in vivo and in vitro studies to obtain further insights into mRNA, miRNA and miRNA-mRNA interactions during embryonic stem cell differentiation and to clarify how the in vitro experiment can be used as a faithful model to study embryonic heart formation. The main contributions of this research work for the study in the heart field are: 1. The development of HeartEXpress, which is a database that integrates the expression of more than 16400 genes and 130 experimental conditions in both human and mouse; 2. The development of HeartmiR, which is a database profiling the expression of 9211 mRNA and 386 microRNAs during the heart development period (from E10.5 to E19.5) and additionally in adult and old murine heart tissue; 3. Identification of the potential of 165 miRNAs to be involved in heart development using different methods of miRNA candidate prioritisation; 4. Identification of 102 miRNA and 214 putative novel miRNA-mRNA interactions relevant for cardiac cell development in vivo and in vitro. Furthermore, from the top20 miRNA with most interactions, 12 of the miRNA (60%) had been already associated to heart related events, indicating promising results for the remaining 8 miRNAs (40%) In summary, I have developed, implemented and applied different systems biology approaches to analyse both publicly available and new generated experimental data. As result, I was able to identify potential novel coding and non-coding key factors important for cardiogenesis that might be utilised as markers or targets in future cardiac regenerative medicine strategies.