Spatial transcriptomic profiling to identify mesoderm progenitors with precision genomic screening and functional confirmation

Abstract

Objectives: Mesoderm, derived from a new layer between epiblast and hypoblast during gastrulation, can differentiate into various tissues, including muscles, bones, kidneys, blood, and the urogenital system. However, systematic elucidation of mesoderm characteristics and specific markers remains a challenge. This study aims to screen and identify candidate genes important for mesoderm development.Materials and Methods: Cells originating from the three germ layers were obtained by laser capture microdissection, followed by microcellular RNA sequencing. Mesoderm-specific differentially expressed genes (DEGs) were identified by using a combination of three bioinformatics pipelines. Candidate mesoderm-specific genes expression were verified by real-time quantitative polymerase chain reaction analysis and immunohistochemistry. Functional analyses were verified by ESCs-EBs differentiation and colony-forming units (CFUs) assay.Results: A total of 1962 differentially expressed mesoderm genes were found, out of which 50 were candidate mesoderm-specific DEGs which mainly participate in somite development, formation of the primary germ layer, segmentation, mesoderm development, and pattern specification process by GO analysis. Representative genes Cdh2, Cdh11, Jag1, T, Fn-1, and Pcdh7 were specifically expressed in mesoderm among the three germ layers. Pcdh7 as membrane-associated gene has hematopoietic-relevant functions identified by ESCs-EBs differentiation and CFUs assay.Conclusions: Spatial transcriptomic profiling with multi-method analysis and confirmation revealed candidate mesoderm progenitors. This approach appears to be efficient and reliable and can be extended to screen and validate candidate genes in various cellular systems.Guanghui Liu and Guanheng Yang contributed equally to this study.

Transcriptome analysis to identify candidate genes related to mammary gland development of Bactrian camel (Camelus bactrianus)

“…Differential expression analysis was performed between the two groups of camels using the DESeq2 package in R (version 4.2.1), based on negative binomial distribution. Considering previous studies ( 19 , 20 ) and our specific experimental situation, adjusted p -values ( p adjust ) < 0.01 and |log2FoldChange| >2 were established as the thresholds for significance. p -values were adjusted for multiple testing using the Benjamini and Hochberg methods.…”