Transcriptome analysis of pancreatic cells across distant species highlights novel important regulator genes

BMC Biology

Research Article

Bernard Peers¹  Arnaud Lavergne¹  Isabelle Manfroid¹  Alice Bernard¹  Estefania Tarifeño-Saldivia¹  Keerthana Padamata¹  David Bergemann¹  Marianne L. Voz¹ 

[1] Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l’Hôpital 1, B34, 4000 Sart Tilman, Liege, Belgium;

关键词: RNA-seq;    Comparative transcriptomics;    Pancreas;    Endocrine cells;    Acinar cells;    Ductal cells;   

DOI  :  10.1186/s12915-017-0362-x

 received in 2016-11-03, accepted in 2017-03-01,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundDefining the transcriptome and the genetic pathways of pancreatic cells is of great interest for elucidating the molecular attributes of pancreas disorders such as diabetes and cancer. As the function of the different pancreatic cell types has been maintained during vertebrate evolution, the comparison of their transcriptomes across distant vertebrate species is a means to pinpoint genes under strong evolutionary constraints due to their crucial function, which have therefore preserved their selective expression in these pancreatic cell types.ResultsIn this study, RNA-sequencing was performed on pancreatic alpha, beta, and delta endocrine cells as well as the acinar and ductal exocrine cells isolated from adult zebrafish transgenic lines. Comparison of these transcriptomes identified many novel markers, including transcription factors and signaling pathway components, specific for each cell type. By performing interspecies comparisons, we identified hundreds of genes with conserved enriched expression in endocrine and exocrine cells among human, mouse, and zebrafish. This list includes many genes known as crucial for pancreatic cell formation or function, but also pinpoints many factors whose pancreatic function is still unknown. A large set of endocrine-enriched genes can already be detected at early developmental stages as revealed by the transcriptomic profiling of embryonic endocrine cells, indicating a potential role in cell differentiation. The actual involvement of conserved endocrine genes in pancreatic cell differentiation was demonstrated in zebrafish for myt1b, whose invalidation leads to a reduction of alpha cells, and for cdx4, selectively expressed in endocrine delta cells and crucial for their specification. Intriguingly, comparison of the endocrine alpha and beta cell subtypes from human, mouse, and zebrafish reveals a much lower conservation of the transcriptomic signatures for these two endocrine cell subtypes compared to the signatures of pan-endocrine and exocrine cells. These data suggest that the identity of the alpha and beta cells relies on a few key factors, corroborating numerous examples of inter-conversion between these two endocrine cell subtypes.ConclusionThis study highlights both evolutionary conserved and species-specific features that will help to unveil universal and fundamental regulatory pathways as well as pathways specific to human and laboratory animal models such as mouse and zebrafish.

【 授权许可】

CC BY   
© Peers et al. 2017