SIP1 encodes a DNA-binding transcription factor that regulates multiple developmental processes, as highlighted by the pleiotropic defects observed in Mowat-Wilson Syndrome, which results from mutations in this gene. Further, in adults, dysregulated SIP1 expression has been implicated in both cancer and fibrotic diseases, where it functionally links TGFβ signaling to the loss of epithelial cell characteristics and gene expression. In the ocular lens, an epithelial tissue important for vision, Sip1 is co-expressed with epithelial markers, such as E-cadherin, and is required for the complete separation of the lens vesicle from the head ectoderm during early ocular morphogenesis. However, the function of Sip1 after early lens morphogenesis is still unknown. Here, we conditionally deleted Sip1 from the developing mouse lens shortly after lens vesicle closure, leading to defects in coordinated fiber cell tip migration, defective suture formation, and cataract. Interestingly, RNA-Sequencing analysis on Sip1 knockout lenses identified 190 differentially expressed genes, all of which are distinct from previously described Sip1 target genes. Furthermore, 34% of the genes with increased expression in the Sip1 knockout lenses are normally downregulated as the lens transitions from the lens vesicle to early lens, while 49% of the genes with decreased expression in the Sip1 knockout lenses are normally upregulated during early lens development. Overall, these data imply that Sip1 plays a major role in reprogramming the lens vesicle away from a surface ectoderm cell fate towards that necessary for the development of a transparent lens and demonstrate that Sip1 regulates distinctly different sets of genes in different cellular contexts.

Next-generation sequencing of the transcriptome (RNA-Seq) is a powerful method that allows for the quantitative determination of absolute gene expression, and can be used to investigate how these levels change in response to an experimental manipulation or disease condition. The sensitivity of this method allows one to analyze transcript levels of all expressed genes, including low abundance transcripts that encode important regulatory molecules, providing valuable insights into the global effects of experimental manipulations. However, this increased sensitivity can also make it challenging to ascertain which expression changes are biologically significant. Here, we describe a novel set of filtering criteria - based on biological insights and computational approaches - that were applied to prioritize genes for further study from an extensive number of differentially expressed transcripts in lenses lacking Smad interacting protein 1 (Sip1) obtained via RNA-Seq by Manthey and colleagues in Mechanisms of Development (Manthey et al., 2014). Notably, this workflow allowed an original list of over 7,100 statistically significant differentially expressed genes (DEGs) to be winnowed down to 190 DEGs that likely play a biologically significant role in Sip1 function during lens development. Focusing on genes whose expression was upregulated or downregulated in a manner opposite to what normally occurs during lens development, we identified 78 genes that appear to be strongly dependent on Sip1 function. From these data (GEO accession number GSE49949), it appears that Sip1 regulates multiple genes in the lens that are generally distinct from those regulated by Sip1 in other cellular contexts, including genes whose expression is prominent in the early head ectoderm, from which the lens differentiates. Further, the analysis criteria outlined here represent a filtering scheme that can be used to prioritize genes in future RNA-Seq investigations performed at this stage of ocular lens development.

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Disease or trauma-induced loss or dysfunction of neurons in any central nervous system (CNS) tissue will have a significant impact on the health of the affected patient. The retina is a multilayered tissue that originates from the neuroectoderm, much like the brain and spinal cord. While sight is not required for life, neurodegenerationrelated loss of vision not only affects the quality of life for the patient but also has societal implications in terms of health care expenditure. Thus, it is essential to develop effective strategies to repair the retina and prevent disease symptoms. To address this need, multiple techniques have been investigated for their efficacy in treating retinal degeneration. Recent advances in cell transplantation (CT) techniques in preclinical, animal, and in vitro culture studies, including further evaluation of endogenous retinal stem cells and the differentiation of exogenous adult stem cells into various retinal cell types, suggest that this may be the most appropriate option to replace lost retinal neurons. Unfortunately, the various limitations of CT, such as immune rejection or aberrant cell behavior, have largely prevented this technique from becoming a widely used clinical treatment option. In parallel with the advances in CT methodology, the use of electrical stimulation (ES) to treat retinal degeneration has also been recently evaluated with promising results. In this review, we propose that ES could be used to enhance CT therapy, whereby electrical impulses can be applied to the retina to control both native and transplanted stem cell behavior/survival in order to circumvent the limitations associated with retinal CT. To highlight the benefits of this dual treatment, we have briefly outlined the recent developments and limitations of CT with regard to its use in the ocular environment, followed by a brief description of retinal ES, as well as described their combined use in other CNS tissues.