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HUPO B/D-HPP Interview with HUPO President Yu-Ju Chen, PhD

25 Mar 2021 4:21 PM | Anonymous member (Administrator)

By Maggie Pui Yu Lam, B/D-HPP Executive Committee, USA

Q1: Can you please tell us about when did you first become involved in HUPO activities? I was interested in switching my research direction to biological mass spectrometry in my early career. After few years of learning basics of proteins and biology, I became really serious to devote my efforts in developing mass spectrometry-based proteomics methods and attended my first HUPO congress in Amsterdam in 2008. I was so attracted to the “race” between the proteome complexity, still mostly underexplored at that time, and the rapid advancement in mass spectrometry presented in the congress. When the Chromosome-centric Human Proteome Project (C-HPP) was launched, encouragement from Young-Ki Paik for Taiwan team to work on the Chromosome 4 made my first engagement to the HUPO initiative.

Q2: What made you interested in becoming a HUPO member? In my term as the President of the Taiwan Proteomics Society (TPS, 2009-2011), I started to learn more about the HUPO and HPP activities and enjoyed the team work to explore the proteome research and their impact to biology and medicine. I was subsequently involved in a few activities, including Publication Committee (2012-2016), Member-at-large (2014-2016), C-HPP (chromosome 4), Council Member (2014-2016), President-elect (2020) and President (2021-2022) of HUPO. It is truly a great honor and a big responsibility to serve as the HUPO president. I always believe that joint leadership and collaborative efforts can inspire new ideas with success beyond the expectation of a single mind. I look forward to working together to create an enabling environment for exploring the utility of proteomics to impact our life in the near future.

Q3: What is important for a successful collaboration with non-proteomics researchers? On the long term experiences to work with my non-proteomics colleagues, every collaboration is like a short-term intense course of a special topic. Mutual understandings on the specific biology to be studied as well as technical knowledge on the strength and limitation of the proteomics characterization are the most important criteria, which takes patience and time to align on the same page. It seems to be more challenging for non-proteomics scientist to learn the technical details of proteomics than the other way around. I found that learning to speak the same language of a biologist or physician is very helpful to jointly design the experiment and identify the novel findings. Validation of proteomic discovery also takes time, which will definitely train ourselves to be more patient to wait for fruitful results to come.

Q4: Could you please list three practical steps that all proteomics researchers can take in improving the visibility of proteomics globally? In the real world, such as the clinical community, people tend to see what has been achieved rather than what should be established. Only when we demonstrate utility with board level visibility and critical mass, proteomics can be appreciated as a powerful tool. Everyone can contribute to enhancing its visibility by the following actions: (1) In collaboration with non-proteomics scientist, we can try to maximize the value of proteomics finding to answer the key biology or clinical question beyond the existing knowledge; (2) Outreach to expand the proteomics applications for various topics can promote it into one of the major tools for life science community; (3) The proteomics technology of its current status has achieved high degree of maturity for practical application. It is time to transform proteomics into utilizes in various aspects of life, such as clinical care, precision agriculture and food safety.

Q5. What are the major hurdles that proteomics faces on the way to its integration into daily clinical practice? The clinical community has relatively conservative view to adapt well-established and cost-effective approach within existing clinical infrastructure. Adapting proteomics tool, a brand new concept in clinical setting, requires visible and valuable benefit to change the clinical practice. I would expect that demonstrating the clinical benefit of proteomics in large cohort beyond the publication is the most effective way. On the technical aspect, standardization (preferred to establish regulations and guidelines), highly robust sample handing pipeline with automation, rapid analysis workflows with high throughput, will facilitate acceleration of the transformation process for proteomics into clinical practice.

Q6: What advice would you give to Early Career "proteomics practitioners" to best set up themselves for a long and prosperous career? The field of proteomics has evolved in very fast paths. Even with the availability of many tools, the ability to develop new technology or implement methodology to best address a specific question is important. In the big data era, the advanced instrumentation easily allows high quality and large-scale dataset. Thus, the expertise to develop or apply computation tools is the key to explore the gold mine of new discovery. Finally, being able to enjoy the discovery from proteomics will keep our passion to proteomics in the long run.

Q7: Could you please list a few proactive steps that proteomics researchers can take to position proteomics in multi-omics studies (e.g., as has been done on a grand scale by CPTAC3 for proteogenomics of cancers)? As shown in the CPTAC efforts and achievements, proteomics has demonstrated complementary functionality to reflect new cancer subtypes and enhance our understanding on cancer biology. Compared to genomics, proteomics data has shown closer engagement of with clinical features. This new knowledge can be taken into action by validating biomarkers for future strategy in precision oncology. With rigorous assay optimization and validation on adequate size of cohort, the features of unprecedented accuracy on highly multiplexed analysis of mass spectrometry make them promising tools as a routine component of oncology clinic. I expect much faster path of proteomics discovery and validation in the near future.




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