1. Members

Project leader	ADACHI Jun
Adjunct Project Leader	ISHIHAMA Yasushi
Senior Researcher	MURAOKA Satoshi, KANAO Eisuke
Researcher	ISHIDA Mayumi, HIRANO Masayo
Technical assistant	TAKADA Yoko, TAKAAI Narimi
Collaborative Research Scientist	ABE Yuichi, HIRANO Hidekazu, KUGA Takahisa, MATSUBARA Misako, HARA Yasuhiro, SHIROMIZU Takashi, MURAKAMI Ken, GUNJI Daigo
Visiting Researcher	OKADA Mariko, TOMONAGA Takeshi
Trainee	SHINKURA Akina, KAMIHATA kyohei, HANADA Toshiki
Administrative Assistant	HYODO Seiko

2. Background and objectives

Currently, new drug development is stagnant globally, especially new drugs originating in Japan are fewer than in the West and the present situation of drug discovery research in Japan is not satisfactory. One reason for the delay of drug discovery is the depletion of drug targets. In recent years, with the advent of the next-generation sequencer, many disease-related gene mutations have been identified and understanding of etiology of many diseases seems deepened. However, genetic mutation does not often lead to the discovery of drug targets and a comprehensive analysis of disease related proteins, which are potential drug targets, is important.

This project aims to discover new drug targets with state-of-the-art proteomics technology mainly using clinical specimens. At the same time, we aim to develop a method that provides personalized medicine by identifying proteins that can predict the sensitivity of drugs to individual patient. Furthermore, by investigating the mechanism of action of drugs whose pharmacological effects are not well understood, we will pursue the possibility of re-purposing the drugs for various diseases.

3. Overview of our research

3-1．Proteomics technology development

One of the major breakthroughs in proteomics in recent years is the development technologies for quantification of proteins and identification of posttranslational modifications using mass spectrometry. Regarding quantitative proteomic technology, not only comparative quantification of proteins between specimens but absolute quantification of proteins in specimens by the Selected / Multiple Reaction Monitoring (SRM / MRM) method became possible with stable isotope labeling method. Our laboratory has a world-leading proteomic technology to identify and quantitate proteins (1). Moreover, the detection sensitivity of trace amounts of blood proteins in our laboratory is at the top level in the world (2).

Although only a few phosphorylation sites were able to be identified ten years ago, it is now possible to identify tens of thousands of phosphorylation sites in a single experiment owing to recent advance in pretreatment methods and analytical tools for phosphorylated proteins. In our laboratory, we developed a novel technology in identification of tyrosine phosphorylation site which is most challenging, and succeeded in identifying about 1,800 tyrosine phosphorylation sites, which is more than three times compared to the previously reported identified number (3).

References:

1. Wilhelm M, et al. Mass-spectrometry-based draft of the human proteome. Nature 2014, 509:582-7.
2. Sano S, et al. Absolute quantitation of low abundance plasma APL1β peptides at sub fmol/mL level by SRM/MRM without immunoaffinity enrichment.J Proteome Res 2014, 13:1012-20.
3. Abe Y, et al. Deep phosphotyrosine proteomics by optimization of phosphotyrosine enrichment and MS/MS parameters. J Proteome Res 2017 16, 1077-1086.

3-2．Discovery of novel drug targets using proteomics technology - Novel drug targets for colorectal cancer -

Currently, one of the most promising proteins as drug target is membrane proteins. In our laboratory, we searched for biomarker candidate proteins by quantitative proteomic technology using membrane proteins of colon cancer tissues. As a result, 44 membrane proteins were finally identified as candidates for colorectal cancer drug target protein (4).

In addition, our laboratory is also searching for new target proteins useful for diagnosis of colorectal cancer, and recently we have identified new diagnostic markers to detect early stage colorectal cancer using serum exosomes. Exosomes are small vesicles secreted from cells and they contain important factors involved in cell-to-cell communication. Thus, exosomes have recently been receiving particular attention. We have identified about 20 biomarker candidate proteins useful for early detection of colorectal cancer in the exosomes of patient sera and some of the proteins can diagnose early stage of colorectal cancer very accurately (AUC> 0.95 of ROC curve) (5).

References:

4. Kume H, et al. Discovery of colorectal cancer biomarker candidates by membrane proteomic analysis and subsequent verification using selected reaction monitoring and tissue microarray analysis. Mol Cell Proteomics 2014,13:1471-84.
5. Shiromizu T., et al. Quantitation of putative colorectal cancer biomarker candidates in serum extracellular vesicles by targeted proteomics. Sci Rep　2017, 7, 12782.

3-3．Discovery of novel drug targets using phosphoproteomics

Another promising protein as a drug target is a kinase. The reason is that most diseases such as cancer and lifestyle related diseases are caused by aberrant intracellular signalings and kinases are responsible for the signal transduction cascades. Therefore, once you know the kinases involved in the development of diseases, they could be the drug targets. Indeed, the mainstream of new molecular targeted drugs for cancer is kinase inhibitors, and cancer therapy has advanced dramatically thanks to the emergence of the drugs. However, only a fraction of the kinases is now druggable target, and if new kinases related to diseases can be identified, they are highly likely to be new drug targets.

Therefore, we are searching for new drug target kinases using the state-of-the-art large-scale phosphoproteomic technology and bioinformatics for predicting kinase activation. Phosphoproteomics is performed using cells derived from patients. Based on the identified tens of thousands of phosphorylation site data, activated kinases are predicted using a kinase-substrate database. Then, predicted kinases are verified by suppression of the kinases using their siRNA and/or inhibitors. For example, we discovered 17 kinases that are predicted to be specifically activated in cetuximab-resistant colon cancer cells, and revealed that the proto-oncogene tyrosine protein kinase (SRC kinase) is effective target against cetuximab-resistant colon cancer cells (6). In addition to cultured cells, we also developing analysis methods compatible with various clinical samples, such as cancer organoids (7). Furthermore, we have developed a method to obtain phosphorylation information with high sensitivity from microscopic endoscopic biopsy specimens and to quantitate the difference between patients for precision medicine (8).

In this way, phosphoproteomics and prediction of kinase activity using bioinformatics is an excellent method for discovering new drug targets, which might lead to development of new drugs for the diseases whose effective treatment are currently not available.

References:

6. Abe Y, et al. Deep Phospho- and Phosphotyrosine Proteomics Identified Active Kinases and Phosphorylation Networks in Colorectal Cancer Cell Lines Resistant to Cetuximab. Sci Rep　2017, 7, 10463.
7. Abe Y, et al. Improved phosphoproteomic analysis for phosphosignaling and active-kinome profiling in Matrigel-embedded spheroids and patient-derived organoids. Sci Rep　2018, 8, 11401.
8. Abe Y, et al. Comprehensive characterization of the phosphoproteome of gastric cancer from endoscopic biopsy specimens. Theranostics 2020, 10(5), 2115.

Laboratory of Proteomics for Drug Discovery

Website	https://www.nibiohn.go.jp/proteome/
E-mail	jun_adachi*nibiohn.go.jp (replace * by @)