Bioanalysis Zone

2012 Young Investigator Award Finalist: Eugene Ciccimaro


Gene Ciccimaro


Nominee: Eugene Ciccimaro, ThermoFisher Scientific, USA

Nominated By: Ian A Blair, University of Pennsylvania, USA


Supporting Comments: Eugene Ciccimaro is one of the most talented graduate students that I have trained. Initially, during his thesis research he developed a novel LC–MS approach for the quantification of phosphorylated proteins. This enabled him to analyze 29 phosphorylated and nonphosphorylated tryptic peptides from focal adhesion kinase. Aspects of this work were presented as posters at the American Society for Mass Spectrometry (ASMS) and Human Proteome Organization (HUPO) meetings. He then developed novel stable isotope dilution methodology, which made possible, for the first time, absolute quantification of phosphorylated proteins. These findings were published in a well-cited paper and the technique was used to monitor the effects of a Src inhibitor in vivo. Since graduating he has been a regular presenter at ASMS and HUPO meetings, and recently co-wrote an insightful review on quantitative biomarker analysis. Eugene was a key member of the team that developed new approaches to serum estrogen quantitation and synaptic protein expression in vivo. He is currently developing groundbreaking new methods for the quantification of proteins and biologically important serum sphingolipids. This latter study will provide technology for studying an underdeveloped and important area of bioanalysis. Therefore, I believe that this talented young scientist is an outstanding candidate for the Bioanalysis Young Investigator Award.

Bioanalysis Zone asked Gene to highlight one of his favorite published articles and explain his reasoning.

Ciccimaro E, Hanks SK, Yu KH, Blair IA. Absolute quantification of phosphorylation on the kinase activation loop of cellular focal adhesion kinase by stable-isotope dilution liquid chromatography–mass spectrometry. Anal. Chem. 81(9), 3304–3313 (2009).

What were the most difficult challenges encountered in this study? And how were they overcome?

The work I highlight describes the use of a full-length isotopically labeled protein used to measure, in a targeted LC–MS assay, endogenous phosphorylation on a group of residues within a key signaling protein. In a first-of-its-kind approach, the labeled full-length protein was expressed using an in vitro expression system and then phosphorylated on tryosin residues via an in vitro kinase reaction. The creation of this standard protein proved extremely difficult and required extensive experimentation in denaturing and refolding of the target protein before the recombinant protein appeared to behave similar to its native form, and reacted with its endogenous kinase target. I ultimately was able to create a suitable standard that could then be used to absolutely quantify endogenous phosphorylation and control for variation in immunoprecipitation.

Which areas of your research did you find the most interesting/enjoyable and why? By comparison, which were the least agreeable?

Learning and devising ways to optimize targeted peptide quantitation assays by LC–MS was (/is) very enjoyable. The speed of data collection and the immediacy with which hypotheses could be drawn and implemented played to my natural abilities as a problem solver, and were a great deal more exciting than my previous experiences in the laboratory, which was much slower paced. Having absolute amounts to work with when describing a biological system governed by phosphorylation was novel, and allowed us to design and conduct unique experiments. Furthermore, the ability to add control to a ‘messy’ experimental process was very rewarding.

In your opinion, how has the research conducted in this study advanced the field of bioanalysis (i.e., future implications)?

Absolute quantification of proteins is becoming a critical aspect of many analytical laboratories. Many critical proteins of interest are at biological concentrations that require some form of preconcentration. To accurately quantify a protein, losses accrued during this and other sample-handling steps should be accounted for. The experimental design highlighted not only shows a way to control for downstream sample preparation, but also allows for absolute quantification to be made on key post-translational modifications (PTMs) on the targeted protein. To my knowledge, this approach is the most analytically rigorous of its kind and, if protein standards were made readily available, could become the future gold standard methodology. The measurement of low level protein phosphorylation on key signaling molecules can serve as a sensitive and specific dosimeter of drug efficacy in cell culture (as we have shown), but may also be used in the future to monitor dose–response in a physiological system. In practice now, it is becoming a very popular technique to use isotopically labeled monoclonal antibody (mAb) to measure mAb targets, the next step in this work is to consider glycosylation and other PTMs on the mAb – this future possibility would build upon my initial work.

Colleague quotes

Here is what some of Gene’s friends and colleagues had to say about him.

Sumit Shah, University of Pennsylvania, USA

“Gene’s key attributes are his professionalism, scientific acumen, innovative thinking, diligence and calm temperament. He has a very calm and soothing personality, and has a natural talent of getting along with people around him. He leads by example. He is keen to try new experiments and never afraid to investigate novel ideas. He is open in discussing his ideas and taking inputs from colleagues, as well as equally open in sharing his knowledge with others. And above all, he does this in a very calm, gracious and professional manner. Gene is definitely a role-model for young and budding scientists.”

Tara Schroeder, ThermoFisher Scientific, USA

“Gene is dedicated, very well rounded and extremely personable. Outside work, Gene clears his head by spear fishing and working in his garden. He is also super excited to become a dad this coming fall. I would say Gene’s most original characteristic is his sense of humor. The combination of being witty and sarcastic always keeps morale high in the laboratory.”

Matt MacDonald, University of Pennsylvania, USA

“Gene is constantly seeking to utilize any technology at his disposal to its limit. He is constantly tinkering, ensuring that every instrument is in top shape. When planning an experiment, he methodically considers all confounds. Gene is highly ambitious in the direction he chooses to take his research, while remaining thoroughly grounded in the limits of the instrumentation and informatics capabilities at his disposal. These attributes have, and will continue to, serve him well as he is often correct in his estimations of what can be accomplished while continuing to live on the leading edge of the field.”



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