Antibodies for profiling the human proteome—The Human Protein Atlas as a resource for cancer research

Abstract

In this review, we present an update on the progress of the Human Protein Atlas, with an emphasis on strategies for validating immunohistochemistry-based protein expression patterns and on the possibilities to extend the map of protein expression patterns for cancer research projects. The objectives underlying the Human Protein Atlas include (i) the generation of validated antibodies toward a major isoform of all proteins encoded by the human genome, (ii) creating an information database of protein expression patterns in normal human tissues, in cells, and in cancer, and (iii) utilizing generated antibodies and protein expression data as tools to identify clinically useful biomarkers. The success of such an effort is dependent on the validity of antibodies as specific binders of intended targets in applications used to map protein expression patterns. The development of strategies to support specific target binding is crucial and remains a challenge as a large fraction of proteins encoded by the human genome is poorly characterized, including the approximately one-third of all proteins lacking evidence of existence. Conceivable methods for validation include the use of paired antibodies, i.e. two independent antibodies targeting different and nonoverlapping epitopes on the same protein as well as comparative analysis of mRNA expression patterns with corresponding proteins.

Combining docking site and phosphosite predictions to find new substrates: Identification of smoothelin-like-2 (SMTNL2) as a c-Jun N-terminal kinase (JNK) substrate

“…7A). The mouse mRNA data agrees with human protein data obtained from the Human Protein Atlas [26], which shows strong expression of SMTNL2 in many human tissues, including muscle (Fig. 7A).…”

“…The human protein atlas and GEO database [26, 27] report that SMTNL2 is most abundantly expressed in skeletal muscle, but is also expressed in many other tissues including brain, liver, lung, and kidney. Recently, the first putative function for SMTNL2 emerged in a screen for regulators of epithelial cell architecture and morphogenesis in 3D culture [28].…”

“…A) Smtnl2 mRNA expression from adult mouse tissues, as measured by qPCR, and matching human tissue expression from the Human Protein Atlas [26]. B) Immunohistochemistry of Smtnl2 protein in embryonic day 18.5 mouse skeletal muscle.…”

The prognostic values of the peroxiredoxins family in ovarian cancer

“…This database offered the cell-specific localization information across 44 different normal tissues and organs, as well as 20 most common types of cancer [30]. In addition, IHC-based protein expression patterns in normal human tissues and tumor tissues were used to generate an expression map by using data from HPA [31]. In the present study, we utilized this database to comprehensively explore the protein expression of the PRDX family genes in normal ovarian tissues and ovarian cancer tissues.…”

The Use of Antibodies in Small-Molecule Drug Discovery

“…Paired antibody approaches have also been applied in which two independent antibodies targeting different and nonoverlapping epitopes on the same protein are used, thus allowing improved specificity of detection. 23 As described above, there remain a number of drawbacks with both antibody-based technologies and MS platforms. These might be overcome by combining the two technologies, for example, the use of stable isotope standards and capture by antipeptide antibodies method, 24 which has been described as providing a multiplexed, specific, and standardized alternative to conventional immunoassays.…”