During a recent conversation with a proteomics researcher, we agreed that proteomics is expected to be the next big “ome.” Nodding, she promptly encouraged me to attend the U.S. HUPO 2024 Conference, which was scheduled for the second week of March. U.S. HUPO, which stands for U.S. Human Proteome Organization, is based in Portland, OR. Notoriously rainy Portland. So, was the meeting to be held there? As it happened, yes—even though U.S. HUPO tends to host meetings elsewhere.
Undeterred by the chance of a little rain, I decided to attend the meeting. Indeed, I looked forward to marking two firsts—my first visit to Portland, and my first attendance of a proteomics meeting. And I was so prepared for inclement weather that I would have been disappointed by sunshine. Well, no worries there. I was greeted by cloudy skies and a cold steady rain.
I also had expectations about being deluged with information about proteomics. These expectations were most definitely fulfilled. Although U.S. HUPO is a small conference—with just under 600 attendees—it represents a tight community of researchers who are passionate about their field. Moreover, U.S. HUPO manages to span both academic research and industry-led technology. Finally, as I maintain in this article, U.S. HUPO lives up to its motto of “from genes to function.”
A distinct personality
U.S. HUPO has everything you would expect of a science and technology event. It has seminars, poster sessions, workshops, breakfast and lunch talks, exhibitors, and networking opportunities. But it also has an intimate feeling. Partly that’s because the meeting is fairly small. (The exhibit hall included about 30 companies.) But it’s also because U.S. HUPO has a distinct personality.
Although the people at U.S. HUPO are leaders in the proteomics field, they do not take themselves too seriously. For example, one session each day is dedicated to fun, creative, and entertaining presentations of each poster. It’s a pitch session, of sorts, for poster presenters to draw attention to their work and encourage people to stop by. Each presenter is given only one minute.
At this year’s event, some posters got pitches that were routine explanations; others got pitches that were much more creative. There were poems, costumes, and songs. In fact, one poster presenter, Pratik D. Jagtap, PhD, a research assistant professor of biochemistry, molecular biology, and biophysics at the University of Minnesota, sang his pitch to the tune of “Ice Ice Baby” by Vanilla Ice. Here is a snippet of his rap:
U.S. HUPO, Let’s kick it!
Nice nice data
It’s nice nice data
………………………….
Alright stop, collaborate, and listen
Detecting cancer is our mission
Searching for biomarkers, so cool
Variants and microbes, break the rule
Will it ever stop? Yo, I don’t know
Turn on the PASEF, and we will know
………………………….
If there was a problem, yo, I’ll solve it
Check out the poster while PDJ resolves it
Entertaining presentations weren’t limited to raps celebrating proteomics research. One evening, there was a workshop that had the playful title, “Proteomics Show LIVE!” I wandered in with no idea what to expect. I soon learned that “LIVE” referred to the live recording of a proteomics podcast.
The podcast’s hosts were Benjamin Neely, PhD, research chemist at the National Institute of Standards and Technology, and Renã A.S. Robinson, PhD, associate professor of chemistry at Vanderbilt University (standing in for Ben C. Orsburn, PhD, instructor of pharmacology and molecular sciences at Johns Hopkins University School of Medicine).
Besides being informative, the podcast was, like many things at U.S. HUPO, relaxed and fun. The guest—who was selected by pulling a name from a hat—was Olga Vitek, PhD, professor and director of the Barnett Institute for Chemical and Biological Analysis, Khoury College of Computer Sciences, Northeastern University. Vitek told her story and shared her wisdom, not only about data science but also about navigating a career in science as a woman and a mother. It was a terrific way to spend an hour, and it was yet another example of how U.S. HUPO brings pleasure to proceedings and rises above the routine.
Tried and true technology providers
Besides providing a showcase for the latest mass spectrometry (MS) technologies from companies such as Bruker, Thermo Fisher Scientific, SCIEX, Biognosys, and Seer, U.S. HUPO hosted researchers who delivered presentations describing how MS technologies were enabling research advances. For example, Fan Liu, PhD, group leader for structural interactomics and head of the proteomics research platform at Leibniz-Forschungsinstitut für Molekulare Pharmakologie, described how her team uses crosslinking MS to map interactomes and obtain remarkable findings about the viral-host interactome. She reported that her team’s work reveals how the virus “drags the host proteins, through protein-protein interactions, into the virion.”
In another standout talk about MS-driven research, presented during Bruker’s sponsored lunch, details were shared about interactions between jumbo phages and the pathogenic bacterium Pseudomonas aeruginosa. Specifically, certain protein interactions were shown to mediate phage attack. In the same session, research findings were presented about biomarkers for Mycobacterium tuberculosis infection in children.
Emerging technologies
Within and among the presentations about MS-driven research projects, the developers of next-generation proteomics technologies were making themselves heard. For example, SomaLogic sponsored a breakfast talk that was delivered by Towia Liebermann, PhD, associate professor of medicine at Beth Israel Deaconess Medical Center and associate professor of medicine at Harvard Medical School. Liebermann described how he used the SomaScan 11k platform to disentangle the proteomic network of irritable bowel syndrome. He explained how proteomic profiling can advance the discovery of biomarkers for differential diagnosis, clinical features, disease outcomes, and treatment selection.
Another breakfast talk was sponsored by Alamar Biosciences. Although Alamar was launched in 2018 and is thus fairly new to the proteomics scene, the company’s founder and CEO, Yuling Luo, PhD, is a biotechnology veteran, having started Panomics (which was acquired by Affymetrix) and Advanced Cell Diagnostics (which was acquired by Bio-Techne). Alamar announced Series C financing of $128 million in late February, bringing the company’s total funding to nearly $250 million.
Alamar’s vice president of sales, Alex Forrest-Hay, pulled no punches. He spent the first part of the breakfast talk giving a head-to-head comparison between Alamar’s NULISA (NUcleic acid–Linked Immuno-Sandwich Assay) technology and Olink’s proximity ligation immunoassay technology. He presented data that first appeared last fall in a Nature Communications paper (“NULISA: A proteomic liquid biopsy platform with attomolar sensitivity and high multiplexing”).
Forrest-Hay asserted that Alamar’s technology offered better sensitivity and specificity in the detection of differential expression of key inflammatory markers. Alamar not only has competition in the market from Olink, but is also in a legal battle, having been sued by Olink for patent infringement. (Olink did not have a presentation at the meeting, but the company told GEN that it is continuing to promote its Target 48 mouse cytokine panel, which was launched last September.)
Nautilus Biotechnology, which plans to launch its first product next year, had a strong presence at U.S. HUPO. Why assume such a high profile so far in advance? To educate the proteomics community on Nautilus’s technology, said Parag Mallick, PhD, the company’s founder and chief scientist. (He is also professor of radiology at the Canary Center at Stanford for Cancer Early Detection.)
Mallick noted that he has attended all the U.S. HUPO annual conferences except for the first one or two. That’s an impressive record, given that U.S. HUPO is marking its 20th anniversary. He added that he has learned throughout his career the importance of communicating, integrating, and building trust with the proteomics community.
Nautilus is building a platform that is focused on quantifying the whole proteome using Protein Identification by Short-epitope Mapping (PrISM), a method that uses hundreds of multi-affinity probes. According to Nautilus, the platform will quantify protein isoforms and post-translational modifications.
Within the emerging technologies being developed for proteomic analysis, there are companies focused on the sequence of proteins. Protein sequencing is so new that it was barely present at the U.S. HUPO event; Quantum-Si was the only company with a noticeable presence. At the Quantum-Si exhibition booth, the company discussed the latest improvements in its technology. First, the company has added a new amino acid recognizer to its existing set, bringing the total number of amino acids that can be sequenced to 13. In addition, the company told me about a new development, protein inferences, that allow a protein to be identified without requiring the entire protein sequence. Lastly, the company talked about its new peptide-barcoding technology. The company’s platform, the Platinum, enables single-molecule resolution of the short peptide barcodes—a useful capability in applications such as drug discovery and synthetic biology.
Altogether, my first U.S. HUPO meeting was hugely rewarding. And because proteomics is showing no signs of slowing down, I’m sure that GEN will be at the meeting next year. And now that I’m more familiar with U.S. HUPO’s atmosphere, I will start working on my proteomics-themed poetry.
