Application of gene expression profiling to the study of placental and fetal function
Piedrahita, Jorge A
Background: One of the key biological principles that differentiate mammals from other phyla is the presence of the placenta. This is a unique and complex tissue that plays an essential role in the development of the fetus and has both short terms effects in terms of reproductive efficiency, and long term effects in terms of adult onset diseases exacerbated by an inadequate fetal environment. Yet in spite of decades of intense study there is still a large number of unanswered questions regarding the function of this organ. This is true for both humans and domestic animals species. Review: In the past, studies focused on placental function and placental/fetal interactions have examined at most a few genes/ proteins at a time; what is commonly referred to as the candidate gene approach. While this approach has been quite successful, and has helped develop the knowledge base that we have at present, it is also limiting in scope. New genomic technologies allow simultaneous analysis of most, if not all, of the genes expressed in placental and fetal tissues. However these technologies also present significant challenges due to the massive amount of information that is generated. This entails not just how to handle the generated data, but also how to properly analyze it and interpret it. Fortunately, a large number of computer algorithms have been, and continued to be, developed that permit not just the identification of which genes are disregulated in the system being studied, but perhaps more importantly, permits the identification of which biological pathways are affected. This in effect convert a list of genes that in most cases defy interpretation, into a more biologically-oriented set of results that provide a better understanding of the system. This knowledge can then be used to design direct biochemical and physiological experiments that, in essence, allow the investigator to move from the gene level to the system level. This review will cover some of the fundamental aspects of gene expression profile data capture, and the different approaches that are used to analyze the data generated, including brief descriptions of some of the most commonly used web-based gene expression profiling analysis programs. In addition, methods for searching and downloading dataset of interest that can help complement your own data will be reviewed. In particular, focus will be placed on how this technology can be utilized to study placental and fetal growth abnormalities in humans, with an emphasis on fetal growth restriction and preeclampsia. Additionally, similar approaches will be described that helped to elucidate the conservation and possible function of imprinted genes in swine. Conclusion: This manuscript describes methods for capturing and analyzing gene expression profiles with an emphasis of how this technology was applied to the study of placental function in humans and swine. In addition, it provides a description of web-based systems that can be used to analyze data generated by your own studies as well as method for searching and downloading data generated by others.
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