Press Release – Large-scale analysis of protein arginine methylation by mass spectrometry

The article by Dr. Tiziana Bonaldi et al. is published in Current Protein & Peptide Science, 2020

Methylation (namely addition of a methyl group) of arginine amino acid residues of proteins is a post-translational modification (PTM) catalyzed by a family of nine enzymes called Protein Arginine Methyl-Transferases (PRMTs).

PRMTs have been gaining increasing attention in the scientific landscape due their role in several essential physiological processes and implication in various diseases, including cancer and neurological disorders; loss of PRMT1 is lethal at the early developmental stages, while overexpression is frequently observed in different tumor types and correlates with poor patient prognosis, suggesting that inhibition of PRMTs may represent an effective therapeutic approach in oncology. Moreover, PTM levels are deregulated in different tumor types, and both local and global changes in PTM of the DNA-associated proteins – the histones – are linked to Amyotrophic Lateral Sclerosis. Due to the large body of scientific evidence indicating their role in cell pathophysiology, several PRMT inhibitors have been designed and developed as a potential new class of drugs. For instance, a potent, reversible type I PRMT inhibitor has been shown to have anti-tumor effects in human cancer models and some of the molecular candidates have entered clinical trials for solid tumors and lymphomas.

“Although it was first described in 1968,” says Dr Tiziana Bonaldi, Group Leader at the European Institute of Oncology, “for almost 30 years, very little was known about the extent of protein arginine methylation, its effect on protein activity, and its biological role. The first PRMT, capable of catalyzing arginine methylation, was discovered in 1996 and, since then, nine proteins exerting the same functions have been discovered. However, inefficient analytical approaches have largely limited a comprehensive understanding of their biological function. Quantitative Mass spectrometry has emerged as the ideal analytical strategy to study the extent of protein arginine-methylation in model systems and identify PRMT targets, thus contributing substantial knowledge in this field.”

In their article published in Current Protein & Peptide Science, Dr. Bonaldi and co-workers offer an overview on state-of-the-art arginine methyl-proteomics, describing the innovations that led – from the description by Mathias Mann’s group of the first high-quality methyl-proteome in 2004 – to the latest studies that profile protein-methylation events occurring on hundreds of cellular proteins. Throughout this review, the authors describe the implementations both in the biochemical methods and in the computational methods for Mass spectrometry data analysis or the identification of sites of arginine methylation, discussing the pros and cons of the most common strategies employed.

Furthermore, relevant issues related to protein-arginine methylation analysis that are still under development are also discussed, such as the discrimination of symmetric and asymmetric arginine-di-methylation from Mass spectrometry fragmentation spectra. “These two modifications have identical mass, yet they are catalyzed by different PRMTs and have substantially different biological outcomes,” explains Bonaldi; “Indeed, even though, for instance, both have a role in regulation of transcription, while asymmetric di-methylation is activating, symmetric di-methylation is repressive. Therefore, being able to distinguish between the two processes is crucial.”

Finally, major emphasis is devoted to the heavy methyl SILAC strategy, a variation of the more conventional SILAC (Stable Isotope Labelling with Amino acids in Cell culture). “The heavy methyl SILAC strategy was designed to increase the confidence of in vivo arginine methyl-peptides identification by Mass spectrometry,” – continues Bonaldi – “and the use will be facilitated by the recent development of ad hoc algorithms tailored for processing of heavy methyl SILAC datasets, such as MethylQuant and hmSEEKER.”

Importantly, the authors conclude that optimization of the currently available analytical approaches and their systematic application will play a key role in the future research on the involvement of protein methylation in biological processes, providing critical insights in the related cellular biology processes and likely offering potential novel targets to be exploited in a clinical context. Read the full Press Release to find out more: https://www.eurekalert.org/pub_releases/2020-05/bsp-lao052220.php

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To get the full-text article, please visit the following link: http://www.eurekaselect.com/181344/article

Press Release | Computational advances in the label-free quantification of cancer proteomics data

 

In recent years, proteomics research has become a popular method for characterizing the functional proteins driving the transformation of malignancy, tracing the large-scale protein alterations induced by anti-cancer drug, as well as discovering the innovative targets and first-in-class drugs for oncologic disorders. Proteomics became popular due to its ability to provide quantitative and dynamic information on tumor genesis and development by directly profiling protein expression. Label-free Quantification (LFQ) is an important method for quantifying protein expression in cancer proteomics. However, the main challenge in using this method for discovering anti-cancer targets and drugs is the low precision, poor reproducibility, and inaccuracy of the LFQ of proteomics data.

 

 

This article by Dr. Feng Zhu et al. is published in Current Pharmaceutical Design, 2018. To obtain the article, please visit: http://www.eurekaselect.com/166976

Read full press release to find out more at: https://www.eurekalert.org/pub_releases/2018-12/bsp-cai122718.php

Focus On Research With Rakesh Rathore, PhD

One of our respected Editorial Board Members of  Bentham Science journal ‘Combinatorial Chemistry & High Throughput Screening’ , Rakesh Rathore, has contributed to the implementation of mass spectrometry-based high-throughput screening technologies to identify drug leads and made us all very proud of him:

Focus On Research With Rakesh Rathore, PhD

After a receiving his PhD in biochemistry from Govind Ballabh Pant University and his master’s degree from Cancer Hospital & Research Institute, both in India, Rakesh Rathore conducted postdoctoral research in the Department of Biochemistry & Biophysics at Göteborg University in Sweden and then the Center for Cardiovascular Sciences at Albany Medical Center. Rathore is currently working as a research scientist within the Proteomics & Mass Spectrometry Core Laboratory and the Department of Cancer Biology at UC.He is involved in implementing mass spectrometry-based high-throughput screening technologies to identify drug leads. Mass spectrometry is a tool that can be effectively used to detect ionizable elements in a wide variety of sample types in the form of mass to charge ratio. Mass spectrometry-based assays offer a rapid, sensitive and direct approach to measure the effects on enzyme activity.He also oversees the operation of the UC diverse pharmaceutical compound repository, which consists of over 350,000 compounds. He serves as reviewer and editorial advisory board member in drug discovery and development journals, including the Combinatorial Chemistry & High Throughput Screening and the Journal of Bimolecular Screening.What brought you to UC?“I was looking for new technology development opportunities after several years of conducting calcium signaling basic research at Albany Medical Center, and at the same time, my wife assumed a fellowship at a Dayton-based health care system. So we decided to move to this area, where I obtained a research position in the Proteomics & Mass Spectrometry Laboratory with Ken Greis, PhD, on a drug discovery technology project which was funded by MDS Analytical Technologies in Canada. Since industry is currently taking part in many collaborative research efforts with academia, this unique position made my move to UC a great professional opportunity. This area turns out to be a great place to raise a family, and we have been here for about six years.”What is the focus of your research? What discoveries have you made?“My focus of research is on mass spectrometry-based enzyme assay development and high-throughput screening technologies for drug discovery applications, and we have developed a new mass spectrometry-based tool that provides more precise, cost-effective data collection for drug discovery. “Using robotics, data processing and control software, liquid handling devices, and sensitive detectors, high-throughput screening allows a researcher to quickly conduct millions of chemical, genetic or pharmacological tests. Through this process one can rapidly identify active compounds which modulate a particular biomolecular pathway. The results of these experiments provide starting points for drug design and for understanding the interaction or role of a particular biochemical process in biology. “Recently we have extended our capabilities to screen more than 30,000 compounds with mass spectrometry and compared our results with conventional fluorescence methods, which is part of a National Cancer Institute-funded Innovative Molecular Analysis Technologies grant with Dr. Greis. We obtained interesting data to help understand how one can improve the chances of obtaining hits more likely to succeed in clinical trials, which would have been missed using traditional methods of screening. This has the potential of changing the way drug discovery research is performed. “We further extended this technology to develop a fee for service model for other investigators that was demonstrated by 25,000 compounds screened for a group at Case Western Reserve University. Now, we can offer targeted screening of 1,000 to 5,000 compounds as a revenue source for core facility. “This year, the work was recognized as a finalist of the Waters Corporation poster award during the 2013 Association of Biomolecular Resource Facilities conference and in the ‘Gallery Of Excellence’ at UC Research Day 2013. “At UC, I worked on a Global Cardiovascular Innovation Center grant to the company CardioCeption, LLC, founded by Keith Jones, PhD, and part of the UC Tech Accelerator, which was involved in the pre-clinical studies in various cardiovascular conditions.” How will this impact patient care? “Drug discovery is the perfect bridge between basic and clinical research. We are one of very few research institutes to have a library of over 350,000 compounds, which enables us to screen many new and existing drug targets for new leads with the potential for new therapeutics. From our own data using this library, we obtained promising hits and are further evaluating the results, which may have the potential to impact patient care through the development of successful drugs in the future.” What do you like to do in your spare time? “I mainly enjoy spending time with my family and friends and traveling. I have a 3-year-old daughter who loves playing with me, thus my evening time is quite different from what I do at UC. I have been involved with United Way activities in the recent past and would like to continue such services to similar nonprofit organizations.”

Borrowed from http://healthnews.uc.edu/news/?/23525/