A genomic approach to smooth muscle differentiation and diversity

Abstract: Smooth muscle cells (SMCs) are a broad class of contractile cells that are found in a number of organs systems, including the vasculature, the urogenital system, the bronchi and the gastrointestinal tract. The two main functions exerted by SMCs are to provide contractile force and to synthesize structural components of the extracellular matrix. SMCs are not terminally differentiated, but have a capacity to adjust their cellular phenotype to meet crucial physiological needs. Examples include repair of blood vessels, and uterine growth during pregnancy. In addition, SMC plasticity may be important in human diseases such as asthma, pre-term delivery, atherosclerosis, and hypertension. A great challenge in smooth muscle biology is therefore to identify molecular mechanisms that mediate SMC phenotypic differences. The aim of the present study is to examine SMC differentiation and diversity in terms of global gene expression. In general terms, we ask how genome sequences and large-scale observations of gene expression patterns together can be used to define and understand SMC differentiation and diversity. Three lines of investigation are followed. First, we examine gene expression patterns of SMC subpopulations using gene chip technology, which results in a transcription atlas of SMC diversity (I, IV). Second, we propose a general approach to the functional and regulatory interpretation of such data, based on the biological concept of gene batteries defined as sets of genes that are co-regulated and functionally linked (II, III). This approach is general, and applicable beyond SMC biology. Third, we use this framework to interpret our exploration of SMC phenotypes, and to postulate regulators of SMC phenotypic diversity (III, IV). We find evidence that that several gene batteries are synchronously regulated during vascular SMC maturation and neointima formation, suggesting that distinct features of the vascular SMC phenotype are encoded by individual gene batteries (IV). Among regulated gene batteries, a lipid metabolism battery and a vascular-selective extracellular matrix battery are found. Regulatory sequence analysis was performed on a whole-genome scale with respect to 266 DNA-binding transcription factors, and results were used to predict cis regulatory elements of importance for gene batteries and vascular SMC marker genes (III, IV). Specific findings include novel SMC differentiation markers, including LPP, a potential SMC-selective transcriptional regulator (II). In summary, the work provides a genomic formulation of the SMC differentiation and diversity problem, and proposes a model for the SMC phenotype which is based on explicitly defined groups of genes.