A time-resolved multi-omic atlas of the developing mouse stomach

Abstract

The mammalian stomach is structurally highly diverse and its organ functionality critically depends on a normal embryonic development. Although there have been several studies on the morphological changes during stomach development, a system-wide analysis of the underlying molecular changes is lacking. Here, we present a comprehensive, temporal proteome and transcriptome atlas of the mouse stomach at multiple developmental stages. Quantitative analysis of 12,108 gene products allows identifying three distinct phases based on changes in proteins and RNAs and the gain of stomach functions on a longitudinal time scale. The transcriptome indicates functionally important isoforms relevant to development and identifies several functionally unannotated novel splicing junction transcripts that we validate at the peptide level. Importantly, many proteins differentially expressed in stomach development are also significantly overexpressed in diffuse-type gastric cancer. Overall, our study provides a resource to understand stomach development and its connection to gastric cancer tumorigenesis.

Data‐Independent Acquisition‐Based Quantitative Proteomics Analysis Reveals Dynamic Network Profiles during the Macrophage Inflammatory Response

“…Recently, significant advances have been made in MS‐based proteomics, from sample preparation to liquid chromatography and instrumentation, making the identification of more expressed proteins in cells or tissues possible with good accuracy and reproducibility . Data‐independent acquisition (DIA) has been widely employed in proteomics analysis because of enhanced protein coverage and reliable data acquisition .…”

Integrative analysis reveals pathways associated with sex reversal in Cynoglossus semilaevis

“…These results suggest that changes in mRNA levels provide limited insight into changes in protein expression, and this result builds an evidence that mRNA expression is not sufficient to fully understand expression changes. The discrepancies between mRNA and protein may be related to complex post-transcriptional regulatory mechanisms, different kinetics of RNA or protein degradation, and detection limits or biases of instruments that measure mRNA and protein, among other origins (Li et al, 2018).…”

“…Sequences were assembled based on alignment results and used for further analysis. Gene expression levels were further normalized using the fragments per kilobase of transcript per million mapped reads (FPKM) method to eliminate the influence of differences in gene lengths and the amount of sequencing data on calculations of gene expression (Wang et al, 2018). Differentially expressed genes (DEGs) between females and pseudomales were identified with an absolute log2FC ≥ 2 and a false discovery rate-adjusted P (q value) <0.05 using the ballgown package (https://www.rdocumentation.org/packages/ballgown).…”

“…A set of sex-biased genes potentially associated with growth and reproduction in tongue sole were identified by brain transcriptome analysis (Wang et al, 2016) and transcriptomic analysis revealed candidate networks and genes for sexual dimorphism of body size for C. semilaevis (Wang et al, 2018). The process of sex reversal is accompanied with many changes in transcription and translation of certain genes.…”

“…The integrative analysis of the transcriptome and proteome is an efficient tool for identifying differential expressed genes at the whole-genome level. Comparative transcriptomic and proteomic analysis was successfully used to study the development of the mouse stomach and its relationship with the development of gastric cancer at the whole-genome level (Li et al, 2018). However, the relationship between mRNA and protein levels did not follow a simple correlation in which higher mRNA levels always associate with higher protein levels (Becker et al, 2018).…”