Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of the endothelial cell microproteome. [ext234]

ABSTRACT: Non-canonical small open reading frames (smORFs) that encode microproteins (miPs; <100 amino acids) are present in the genome. However, the study of smORF-encoded miPs has been hampered by technical challenges associated with the detection of small peptides by mass spectrometry. Here we combined deep RNA sequencing of ribosome-associated transcripts and optimized bioinformatic pipelines for downstream proteomic studies to identify thousands of smORF-derived miPs in endothelial cells (human 2,256, murine 7,597). Profound alterations in smORF/miP expression were detected following human endothelial cell activation by interleukin 1beta (IL-1beta) in vitro and by hypercholesterolemia and altered blood flow in vivo (in mice). Genome-wide homology analyses revealed that human smORFs are highly conserved among primates, and poorly in rodents or zebrafish. Functional characterization of selected miPs demonstrated their physical interaction with proteins in different subcellular compartments and their involvement in the regulation of proliferation, cell death, gene expression and inflammation. Moreover, it was possible to demonstrate that miPs can be released into the blood stream following cellular damage in humans. These findings demonstrate the value of this proteo-genomic pipeline for smORF and miP identification and highlight that the potential impact of miPs on cell and tissue function is much larger than previously presumed.

ORGANISM(S): Mus musculus

PROVIDER: GSE195449 | GEO | 2026/07/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Identification of the endothelial cell microproteome. [ext224]

Project description:Non-canonical small open reading frames (smORFs) that encode microproteins (miPs; <100 amino acids) are present in the genome. However, the study of smORF-encoded miPs has been hampered by technical challenges associated with the detection of small peptides by mass spectrometry. Here we combined deep RNA sequencing of ribosome-associated transcripts and optimized bioinformatic pipelines for downstream proteomic studies to identify thousands of smORF-derived miPs in endothelial cells (human 2,256, murine 7,597). Profound alterations in smORF/miP expression were detected following human endothelial cell activation by interleukin 1beta (IL-1beta) in vitro and by hypercholesterolemia and altered blood flow in vivo (in mice). Genome-wide homology analyses revealed that human smORFs are highly conserved among primates, and poorly in rodents or zebrafish. Functional characterization of selected miPs demonstrated their physical interaction with proteins in different subcellular compartments and their involvement in the regulation of proliferation, cell death, gene expression and inflammation. Moreover, it was possible to demonstrate that miPs can be released into the blood stream following cellular damage in humans. These findings demonstrate the value of this proteo-genomic pipeline for smORF and miP identification and highlight that the potential impact of miPs on cell and tissue function is much larger than previously presumed.

2026-07-01 | GSE195448 | GEO

Identification of the endothelial cell microproteome. [ext187]

2026-07-01 | GSE195447 | GEO

Identification of the endothelial cell microproteome. [ext305]

2026-07-01 | GSE195451 | GEO

Identification of the endothelial cell microproteome. [ext284]

2026-07-01 | GSE195450 | GEO

Effect of miP-PSTPIP2 overexpression on endothelial gene expression in homeostasis and inflammation. [ext501]

Project description:Detecting microproteins (miPs) translated from small open reading frames (smORFs) by mass spectrometry poses major challenges. Here we report a high-throughput proteo-genomic pipeline that provides cumulative evidence for a large number of bona fide miPs in human and murine endothelial cells. Vascular inflammation in vitro and in vivo profoundly altered smORF expression and a large number of miPs was identified in the blood stream of patients following heart tissue damage. Human miPs presented high homology with other primates and their functional perturbation identified miPs that were essential for endothelial cell growth and viability. Moreover, combining gain/loss-of-function with multi-omic approaches demonstrated the involvement of an inflammation-regulated miP in the regulation of gene expression, proliferation and inflammation through interaction with proteins in different subcellular compartments. Thus, large numbers of uncharacterized miPs exist, play a major role in the regulation of cell function and may become biomarkers or therapeutic targets in cardiovascular disease. MiP-PSTPIP2 is upregulated in inflammatory conditions in vitro and in vivo. Therefore this study investigated global transcriptomic alterations following overexpression of FLAG-miP-PSTPIP2 in homeostatic conditions as well as after treatment with interleukin-1beta in human endothelial cells. As the overexpression of FLAG-miP-PSTPIP2 was achieved by adenoviral infection, infection with an adenovirus to express the small protein FLAG-miRFP670nano served as control. The analysis included non infected human endothelial cells under the same experimental conditions to control for infection-dependent effects.

2026-07-01 | GSE261982 | GEO

Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins [Ribo-seq]

Project description:The absence of thousands of recently annotated small open reading frame (smORF)-encoded peptides and small proteins (microproteins) from databases has precluded their analysis in metabolism and metabolic disease. Given the outsized importance of small proteins and peptides in metabolism—insulin, leptin, amylin, glucagon, and glucagon-like peptide-1 (GLP-1)—microproteins are a potentially rich source of uncharacterized metabolic regulators. Here, we annotate smORFs in primary differentiated brown, white, and beige mouse adipose cells. Ribosome profiling (Ribo-Seq) detected a total of 3,877 unannotated smORFs. Analysis of RNA-Seq datasets revealed diet-regulated smORF expression in adipose tissues, and validated the adipose translation of the feeding-neuron marker gene Gm8773. Gm8773 encodes the mouse homolog of FAM237B, a neurosecretory protein that stimulates food intake and promotes weight gain in chickens. Testing of recombinant mFAM237B produced similar orexigenic activity in mice further supporting a role for FAM237B a metabolic regulator and part of the brain-adipose axis. Furthermore, we showed that data independent acquisition mass spectrometry (DIA-MS) proteomics can provide a sensitive, flexible, and quantitative platform for identifying microproteins by mass spectrometry. Using this system led to the detection of 58 microproteins from cell culture and an additional 25 from mouse serum. The proteomics data established the anti-inflammatory microprotein AW112010 as a circulating factor, and found that serum levels of a microprotein translated from a FRS2 uORF is elevated in older obese mice. Together, the data highlight the value of this database in examining understudied smORFs and microproteins in metabolic research and identifying additional regulators of metabolism.

2022-12-13 | GSE197909 | GEO

Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins [RNA-seq]

2022-12-13 | GSE198107 | GEO

Accurate annotation of human protein-coding small open reading frames

Project description:Protein-coding small open reading frames (smORFs) are emerging as an important class of genes, however, the coding capacity of smORFs in the human genome is unclear. By integrating de novo transcriptome assembly and Ribo-Seq, we confidently annotate thousands of novel translated smORFs in three human cell lines. We find that smORF translation prediction is noisier than for annotated coding sequences, underscoring the importance of analyzing multiple experiments and footprinting conditions. These smORFs are located within non-coding and antisense transcripts, the UTRs of mRNAs, and unannotated transcripts. Analysis of RNA levels and translation efficiency during cellular stress identifies regulated smORFs and provides an approach for identifying smORFs for further investigation. Sequence conservation and signatures of positive selection indicate that encoded microproteins are likely functional. Additionally, proteomics data from enriched human leukocyte antigen complexes validates the translation of hundreds of smORFs and positions them as a source of novel antigens. Thus, smORFs represent a significant number of important, yet unexplored human genes.

2019-07-03 | GSE125218 | GEO

Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides

Project description:Computational, genomic, and proteomic approaches have been used to discover nonannotated proteincoding small open reading frames (smORFs). Some novel smORFs have crucial biological roles in cells and organisms, which motivates the search for additional smORFs. Proteomic smORF discovery methods are advantageous because they detect smORF-encoded polypeptides (SEPs) to validate smORF translation and SEP stability. Because SEPs are shorter and less abundant than average proteins, SEP detection using proteomics faces unique challenges. Here, we optimize several steps in the SEP discovery workflow to improve SEP isolation and identification. These changes have led to the detection of several new human SEPs (novel human genes), improved confidence in the SEP assignments, and enabled quantification of SEPs under different cellular conditions. These improvements will allow faster detection and characterization of new SEPs and smORFs.

2017-10-17 | PXD005643 | Pride

CRISPR-Cas9 Screening Reveals Microproteins Regulating Adipocyte Proliferation and Lipid Metabolism [RNA-seq]

Project description:Small open reading frames (smORFs) encode microproteins that play crucial roles in various biological processes, yet their functions in adipocyte biology remain largely unexplored. In a previous study, we identified thousands of smORFs in white and brown adipocytes derived from the stromal vascular fraction (SVF) of mice using ribosome profiling (Ribo-Seq). Here, we expand on this work by identifying additional smORFs related to adipocytes using the in vitro 3T3-L1 preadipocyte model. To systematically investigate the functional relevance of these smORFs, we designed a custom CRISPR/Cas9 guide RNA (sgRNA) library and screened for smORFs influencing adipocyte proliferation and differentiation. Through a dropout screen and fluorescence-assisted cell sorting (FACS) of lipid droplets, we identified dozens of smORFs that regulate either cell proliferation or lipid accumulation. Among these, we validated a novel microprotein as a key regulator of adipocyte differentiation. These findings highlight the potential of CRISPR/Cas9-based screening to uncover functional smORFs and provide a framework for further exploration of microproteins in adipocyte biology and metabolic regulation.

2025-08-27 | GSE297349 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data