Clinical proteomics in Russia and my last pair of pants

An index to this series is found on its first post.

October 30, 2017

At last the first day of ClinProt 2017 had arrived! I set aside my now-muddy pairs of jeans in favor of my fresh and clean blue dress pants, laced up my shiny black shoes, and put on my enthusiastic green shirt. With a spot of breakfast downstairs (on my third morning eating there, I found that the milk jug was full for the first time!), I was ready to meet with the others for a shuttle van ride over to the conference.

Moscow traffic at 8:20 AM is a bit intense. The drivers here are a bit more careful of road laws than I have seen in other countries, but they still produce some pretty creative merges in their traffic jams. What would have been a few minutes on the subway was more like a half hour on the road, but my dress pants were still pristine when we arrived at the Congress Center at the I.M. Sechenov First Moscow State Medical University. The facility had a lovely central hall, with a graceful split staircase to the two main venues for our meeting. I hadn’t seen lecture halls in which an array of nine HDTVs replaced the more typical projector. It certainly produced a bright image, though the borders between screens were distracting.

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Why project when you can emit?

The Clinical Proteomics 2017 meeting was organized because a confluence of groups wanted to consolidate researchers in this country. EuPA, the European Proteomics Association, helps to integrate activities that span national proteomics societies. The Russian Human Proteomics Organization (RHUPO) sought to foster a sense of community among Russian research groups in this area. The Sechenov First Moscow State Medical University was happy to contribute a venue for the event, and many instrument, reagent, and other vendors agreed to take part, as well. I haven’t learned the total count of attendees yet, but I know that there are 87 research posters. For a first effort, I think it is clear that a great many things have gone well.

From the very first talk, it was apparent that Russian clinical proteomics researchers are grappling with challenges that became familiar to me as part of the National Cancer Institute (NCI) CPTAC program. Anna Kudryavtseva discussed her efforts to reconcile proteomics data with those that had been produced by NCI The Cancer Genome Atlas (TCGA), working in a particular sub-type of head and neck cancer. Prioritizing genes that were more frequent targets of mutation in tumors has value for understanding which proteins are most useful to monitor closely, for example. It was a great “plenary” (all attendees) talk to kick off these discussions.

As soon as we split to multiple sessions, I was on duty. I co-chaired the “Genomics and Beyond” panel with Sergey Moshkovskii. It was a bit odd to be fielding this panel while the Protein Informatics workshop was taking place in another room (that topic has been my bread and butter for two decades)! In this case, however, Sergey and I were not only chairing the session but also leading it with our two lectures, both in the field of proteogenomics.

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Photo credit: Olga Kiseleva

I defined the term by saying that we want to improve our interpretation of genomic data by integrating proteomics data, and we want to improve our interpretation of proteomics data by integrating genomic data (I was trying to be ecumenical). From there, I led the group through the new paper that I’ve published with Anzaan Dippenaar and Tiaan Heunis, in which we demonstrated our ability to recognize sequence variations and novel genes in Mycobacterium tuberculosis “bugs” that had been isolated from patient sputum in South Africa. Sergey followed up by finding evidence of RNA editing in fruit flies.

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Photo credit: Olga Kiseleva

The other speakers in the panel were also quite interesting. Matthias Schwab was visiting from Germany, and he educated the group on the current status of the field of pharmacogenomics. Vladimir Strelnikov, a geneticist, described the value of bisulfite sequencing for measuring DNA methylation in breast cancer. Sergey Radko outlined a SISCAPA-like strategy for using “aptamers” to enrich proteins prior to Selected Reaction Monitoring. Artem Muravev closed out the session to discuss the challenges of biobanking. This last talk was delivered in Russian, so I benefited quite a lot from real-time translation to English by Anastasia, one of two translators fielding our session (during my talk, she had been translating my words to Russian as I worked through my slides). Finally all the speakers came together for fifteen minutes of question and answer. I tweaked our pharmacogenomics speaker a little bit by saying that even if we had the complete sequences for every human on earth in our hands today, personalized medicine would not have arrived!

With the morning complete, everyone adjourned to a nearby restaurant. I was a little leery when I learned our destination was the Black Market, but I needn’t have worried; we wandered down the street to a lovely restaurant named “Black Market.” I had the Black Market Burger and felt thoroughly happy. I felt very grateful that the European Proteomics Association picked up the bill for that morning’s speakers!

Back in the conference, I enjoyed hearing my long-time friend David Goodlett discuss his long-term monitoring study of diabetes. He’s a careful guy, and it is good to see that he can make label-free proteomics sing in biofluids (a tough space to work), recognizing protein pairs for which expression can flag the onset of disease. It’s very reminiscent of the kind of study Stellenbosch University has produced in the space of tuberculosis. Our next speaker returned to the subject of biobanking, and he delivered his talk via Skype, not my favorite format. I am a big believer in contact with my audience.

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Did I mention it was my enthusiastic green shirt?

I threw all my remaining energy into the poster session. Interacting with researchers at the start of their careers is very rewarding, and people who stand beside their work without knowing whether or not anyone will take interest have a hard job. These students were even braver, since they were prepared to defend their work in English!

I started with a poster very near and dear to my heart. A.V. Mikurova was evaluating the different levels of sequence coverage achieved by database search (Mascot, X!Tandem) and de novo algorithms (PepNovo+, Novor, and PEAKS) when working with 27 LC-MS/MS experiments for a defined mixture of human proteins. We discussed the relative unresponsiveness of sequence coverage as a metric for performance evaluation and the challenge of ensuring the algorithms had comparable configuration. I asked S.E. Novikova about her choices of statistical model for a time-series measurement of proteomes in response to all-trans retinoic acid. I hope my statistics lectures online will be useful to her, though it sounds like she’s already on the right track. N.V. Kuznetsova taught me a few things I didn’t know about celiac disease! She had been evaluating the ability of Triticain-Α to degrade the most immunogenic peptide of gluten-family proteins. Finally, J. Bespyatykh was presenting a poster on the proteomics of Mycobacterium tuberculosis from a strain called Beijing B0/W148. Her work obviously had a strong relationship to what Tiaan and Anzaan had published with me, so we had a great conversation about the work. I hope we can help her find a sequence database that is a more ideal fit for her proteomes than the generic “H37Rv” protein database. I was really pleased to speak with so many students about their work at this meeting.

With that, I slumped onto a wall and didn’t move very much. The other conference attendees had flowed back into the conference room for an afternoon round of talks. I let my mind wander for a bit, though I did have some nice conversations with the vendors. Soon, though, I heard some odd noises echoing through the entry hallway. Was there a music practice room somewhere in the building? Was that a tuba?

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Dixieland music in Moscow! Photo credit: Olga Kiseleva

My questions were answered when I eventually joined everyone downstairs for a catered closing reception. The organizers had invited a Dixieland band to perform for our reception! The group was really solid. I particularly liked one of their trumpeters, since he had a smooth Chuck Mangione vibe going on. I kept recognizing songs only part of the way, since they were singing many of the lyrics in Russian! I finally got a solid hit on “Mack the Knife!” I sat up close to enjoy the show.

With the evening at an end, I declined invitations to go hit a bar and walked to the nearby Frunzenskaya subway station. Two stops later, I was in my neighborhood. I trudged up the paved driveway to the street with my hotel. As I awaited the green light at my last crosswalk before the hotel entrance, a car drove too close to the curb where I was waiting, and dirty rainwater soaked my last clean pair of pants.

 

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One thought on “Clinical proteomics in Russia and my last pair of pants

  1. Pingback: Russia: acquiring a tourist visa for the world’s largest country | Picking Up The Tabb

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