Integration of transcriptomics and antibody-based proteomics for exploration of proteins

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Extending the proteome analysis on specialized tissues using immunohistochemistry.

Approximately 11% of the human proteins are defined as missing proteins. These proteins lack experimental data on the protein level. In an investigation led by Sjöstedt et al, an integrated omics approach was applied to explore and identify missing proteins.

Over the last years, many drafts of the human proteome have been published with the aim to describe the proteomic landscape in normal human tissues. Now, there is an ongoing effort to validate and refine all the generated data, and to deepen the analysis in order to present an even more complete and curated map of the human proteome.

A significant number of human proteins are referred to as missing proteins. They are defined as proteins with an unconfirmed genetic sequence for which a protein product is not yet detected, and "protein-coding genes that lack experimental data on the protein level due to factors such as temporal expression, expression in tissues that are difficult to sample or with low availability, or they do not encode functional proteins" as the authors state in the investigation published in the Journal of Proteome Research. Missing proteins are classified based on evidence of protein existence (PE) in a 1-5 tier system in an effort led by HUPO and the Human Proteome Project.

Transcriptomics data from three different sources; the Human Protein Atlas (HPA), the GTEx consortium, and the FANTOM5 consortium, were used to identify genes selectively expressed in wide array of extended tissue samples. Complementing and validating the analysis, the authors proceeded with immunohistochemical profiling to investigate the cell type-specific expression patterns. The authors profiled more than 300 genes and identified tissue-specific expression of nine proteins previously listed as missing proteins (POU4F1, FRMD1, ARHGEF33, GABRG1, KRTAP2-1, BHLHE22, SPRR4, AVPR1B, and DCLK3), as well as several proteins with evidence of existence on the protein level that previously lacked information on cell type-specific expression pattern.

In summary, the applied methods combining transcriptomics with antibody-based proteomics is a comprehensive strategy for identification and exploration of missing proteins.

1. Uhlen et al (2015) "Proteomics. Tissue-based map of the human proteome" Science. 347 (6220).
2. Sjöstedt et al (2017) "Integration of Transcriptomics and Antibody-Based Proteomics for Exploration of Proteins Expressed in Specialized Tissues" Journal of Proteome Research. DOI: 10.1021/acs.jproteome.8b00406.