Proteins within cells are highly dynamic across multiple dimensions of time and space, with many proteins being transported and communicated between different organelles or cells, mediating a variety of biological functions within the cell.

Microscopy-based protein imaging techniques can track the movement of proteins in living cells, but they can only study specific individual proteins; proteomics techniques based on mass spectrometry can simultaneously analyze tens of thousands of proteins in cell lysates, but they miss the dynamic information of these proteins in living cells. Therefore, the development of multidimensional proteomics methods helps to systematically decipher the life trajectories of different proteins within cells.

Assistant Professor Qin Wei at the School of Pharmacy, Tsinghua University, is committed to chemical biology research such as proximity labeling. He has developed functional proximity labeling techniques with spatial and temporal resolution, enabling large-scale analysis of specific types of proteins in subcellular regions; at the same time, he has developed a new proximity labeling technique for protein spatial dynamic transport called TransitID, and for the first time, he has used this method to achieve large-scale analysis of protein transport between different organelles and between cells.

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With the development of chemical-driven omics technology to systematically depict the traffic map of biomolecules, providing new ideas for the exploration of disease markers, Qin Wei has become one of the Chinese selected for the "35 Innovators Under 35" by MIT Technology Review in 2023.Bonding with Life Sciences, Achievements Published in Cell

The bond with life sciences began in the autumn of 2010. At that time, Qin Wei, who failed the college entrance examination, barely entered Beijing Institute of Technology and was transferred from explosives engineering to bioengineering. As soon as he entered college, Qin Wei took the initiative to join Professor Qinghong's laboratory at Beijing Institute of Technology. "I felt that I was not good at cultural and sports activities, and could only sleep in the dormitory." The experience in Professor Qinghong's laboratory enlightened Qin Wei's scientific research thinking, not only laying a solid foundation but also opening the prelude to his subsequent research journey.

In 2014, Qin Wei was admitted to Peking University for doctoral studies through an interview without examination. While establishing chemical biology as the research direction, he chose Professors Xing Chen and Chu Wang as his doctoral supervisors, combining the advantages of the two laboratories to carry out research in the field of chemical proteomics analysis and the functional study of protein glycosylation. Since then, Qin Wei has embarked on more than ten years of chemical biology research.

During his doctorate, Qin Wei developed a series of chemical proteomics strategies to systematically evaluate the regulation of protein stability and function by O-GlcNAc modification and itaconic acid modification. "Self-disciplined, diligent, efficient, passionate about science, and with profound insight... I firmly believe that he will become a future leader in the field of chemical biology..." Xing Chen and Chu Wang commented, unable to conceal their appreciation for Qin Wei.

In 2019, Qin Wei went to Stanford University in the United States for postdoctoral research, under the guidance of Professor Alice Ting, a member of the American Academy of Sciences, focusing on the development of new proximity proteomics technologies to achieve dynamic spatiotemporal analysis of the proteome in living cells. The research projects in Alice Ting's laboratory are roughly divided into three areas: (1) molecular recorders for scalable single-cell recording of past cellular events; (2) molecular editors for precise manipulation of cellular biomolecules, pathways, and organelles; (3) proximity labeling for unbiased discovery of functional molecules.In it, Proximity Labeling (PL) is widely used to study intracellular protein-protein interactions and their dynamic changes. This technique uses specific enzymes (such as biotin ligases or peroxidases) to label in the vicinity of the target protein, thereby identifying and capturing molecules that interact with the target protein.

In fact, before going to the United States, Qin Wei had thoroughly discussed postdoctoral topics with Alice Ting. Qin Wei's research experience at Peking University filled him with confidence and naturally led him to start research related to protein dynamics. Prior to this, Alice Ting had developed and iterated Proximity Labeling technology multiple times. She expressed that she had been preparing to gradually fade out of this research field, but her conversation with Qin Wei showed her new possibilities and rekindled her interest in Proximity Labeling technology. Although the existing Proximity Labeling technology is widely used to identify compositional proteins in specific cellular regions, it is limited to static information at a single time point.

Based on the foundation of Alice Ting's laboratory, Qin Wei developed a Proximity Labeling technology that can resolve the spatiotemporal dynamics of proteins within living cells, laying the foundation for a precise understanding of the dynamic regulation of protein functions. In 2023, this research achievement was officially published in the journal Cell, which was also his first time publishing a paper in Cell as the first author.

This technology, named TransitID, can simultaneously map the migration paths of thousands of endogenous proteins in living cells, revealing biological landscapes that current methods cannot see. During the research, Qin Wei applied this technology to identify proteins that run from the cytoplasm to the mitochondria; at the same time, he distinguished mitochondrial proteins that start from the outer membrane of the mitochondria and the cytoplasm; in addition, he applied this method to analyze the dynamic changes of transport proteins from the cytoplasm to the nucleus under oxidative stress conditions; and further applied TransitID to analyze the protein exchange between stress granules and nucleoli under different stress conditions.

In addition to intracellular protein transport, Qin Wei also expanded TransitID to analyze protein transport between cells. He successfully identified more than 60 proteins that were transferred from the cytoplasm of cancer cells to the cytoplasm of macrophages, and at the same time distinguished their potential transport pathways.The technology we have developed, in addition to understanding the fundamental biological laws within living organisms, can also be used to discover drug targets and biomarkers in the process of disease occurrence, and has a very promising prospect for translation. For example, the development of biomarker detection kits for early diagnosis of cancer, etc.

This 4-year study also left Qin with a lot of emotion, "In the 4 years, about 2.5 years were spent on establishing the technology, constantly trying and making mistakes; in addition, during the postdoctoral research period, it coincided with the COVID-19 pandemic, and there were requirements for the number of people and time control in the laboratory. The whole year of 2020 was carried out under the shift work mode of the project."

It is reported that the above research is based on in vitro cultured cells, and in the future, it is planned to be carried out in animals to understand which proteins communicate between different organs and the signal transduction pathways involved.

Joining Tsinghua full-time to promote the innovation of proteomics technology.

There are only about 20,000 proteins encoded by human genes, but due to post-translational modifications, protein complexes, and subcellular localization, the proteome within cells is far more complex than theoretically. The life trajectory of a protein includes its dynamic experiences in time, space, function execution, and interactions from generation to degradation. Understanding the life trajectory of every protein in the cell is of great significance for accurately understanding the complex network and dynamic regulation of the proteome.The process of protein transport and the cell-to-cell communication it mediates are crucial for the proper execution of physiological functions, such as the transmission of many signaling proteins between the brain and the gut. However, there is currently a lack of systematic, unbiased omics methods to mine communication proteins in living organisms. Solving this global challenge will promote research and development in various fields of biology.

The TransitID technology has experimented with the analysis of transport between cultured cells in vitro, taking a small step towards the aforementioned goal. However, there are still significant technical challenges in mapping the protein exchange in living organisms.

Now, Qin Wei has joined Tsinghua University as a full-time researcher to carry out independent research, continuing to use chemical biology and proteomics technology, as well as exploring the dynamic modification and interaction of biomacromolecules at the host-pathogen interaction interface. His long-term research goal is to promote the technological innovation of proteomics from one-dimensional to four-dimensional, depicting the life trajectory of every protein in the cell in the four dimensions of time, space, function, and interaction, so as to accurately understand the dynamic regulation of protein functions.

In the next stage, Qin Wei plans to apply the developed technology to the field of tumor immunology, exploring the different communication mechanisms between tumor cells and immune cells in the microenvironment, providing new ideas for the development of new tumor immunotherapies. At the same time, he will focus on the direct interaction between tumor cells and immune cells, identifying key proteins at the interaction interface, thereby exploring new targets for immune intervention. In addition, he will also develop new immunopeptidomics, identifying functional new antigens presented on the surface of tumors that can recruit T cells, providing technical support for the realization of personalized T cell therapy.

"First, we will systematically depict the communication proteins between tumor cells and different immune cells (macrophages, T cells, etc.), as well as distinguish their transport pathways (exosomes, nanotubes, migrasomes, etc.)," said Qin Wei.It is worth noting that the two neighboring labeling enzymes used in the TransitID technology both have issues such as poor specificity and high toxicity in living organisms. To address these issues, the research team will develop a new type of living-compatible neighboring labeling enzyme through a combination of directed evolution and theoretical design in the future, and establish methods for labeling and identifying transport proteins in living organisms.