Key Points
- Proteins are essential for biological processes and key to understanding health and disease. The human proteome (the full set of proteins) is immensely complex and has been challenging to decode.
- HuProt™ is the world’s largest protein microarray. It represents over 81% of the human proteome, offering unmatched capabilities for studying protein functions and interactions.
- HuProt builds on decades of proteomics advancements, from early ELISA tests to large-scale protein arrays. Developed in 2009 by Heng Zhu’s team at Johns Hopkins University, HuProt revolutionized the study of human proteins using high-quality, functional protein arrays.
- CDI Labs is enhancing HuProt with complementary technologies like HuScan® PhIP-Seq for epitope-level proteome analysis and VirScan® for analyzing past viral exposures through antibody testing.
Unlocking the Secrets of Proteins
The human proteome – a vast and dynamic constellation of proteins, serves as the backbone for nearly every biological process in the body. From enabling cellular communication to driving metabolic function, proteins are critical players in health and disease. But unlocking the secrets of the proteome, with its immense complexity and diversity, has always been a daunting challenge for scientists.
Enter HuProt™, the world's most comprehensive protein microarray. This revolutionary proteomics technology offers researchers a powerful, high-throughput platform to investigate protein functions and interactions on an unprecedented scale. HuProt microarrays have transformed our ability to study proteins, making it possible to unravel their role in diseases, identify biomarkers, and accelerate drug discovery.
FIGURE: HuProt Human Proteome Microarray
How did this innovative proteomics technology come to be? Let's look at the journey that led to the development and widespread adoption of HuProt microarrays.
The Foundation: From ELISA to Early Array Concepts
Protein array technology is rooted in the principle of specific antigen-antibody interactions, foundational to the ELISA technique developed by Eva Engvall and Peter Perlmann in 1971. ELISA's ability to immobilize molecules on a surface to capture binding partners set the stage for protein microarrays. A pivotal advancement came in 1983 when Tse Wen Chang patented the "antibody microarray," demonstrating how matrix-like arrays could analyze multiple analytes simultaneously on small glass surfaces. This innovation introduced multiplexed biosensor surfaces, paving the way for breakthroughs in proteomics, diagnostics, systems biology, and drug discovery.
Early Days of Protein Analysis: From Gels to Microarrays
High-throughput protein analysis has long been a key goal in biological research. Early methods like 2D gel electrophoresis, though groundbreaking, were labor-intensive and limited in sensitivity, especially for low-abundance proteins. The success of DNA microarrays in the 1990s inspired efforts to develop similar platforms for proteins, but challenges arose due to their diverse properties and the difficulty of maintaining functionality during immobilization.
2000s: Pioneering Efforts and the Dawn of Proteome Microarrays
The late 1990s and early 2000s saw significant progress in protein microarrays, though early versions faced issues like protein instability and limited availability of purified proteins. In 2001, Heng Zhu and Michael Snyder developed the groundbreaking yeast proteome array, featuring nearly 5,800 purified yeast proteins printed at high density. This array enabled large-scale functional studies, uncovering protein-protein and protein-lipid interactions, enzyme substrates, and binding motifs, proving the feasibility and potential of proteome arrays for advanced biological research.
The Genesis of HuProt: From Transcription Factors to the Entire Human Proteome
Following the success of the yeast proteome array, Heng Zhu advanced to studying human protein interactomics at Johns Hopkins University. Shaohui Hu, Heng Zhu and their collaborators developed a human transcription factor (TF) array containing ~4,200 proteins, enabling high-throughput analysis of protein-DNA interactions and uncovering regulatory mechanisms in gene expression, immunity, and disease. This work identified ERK2 (MAPK1) as a repressor of interferon signaling, showcasing the potential of specialized human protein arrays. Heng Zhu, along with Seth Blackshaw and Jef Boeke, aimed to create a comprehensive human proteome array. Using a robust system to express and purify thousands of full-length, active human proteins in yeast while maintaining their native structure, they developed the HuProt Human Proteome V1.0 Array in 2009, marking a major milestone in human proteomics research.
Commercialization of the HuProt Human Proteome Microarray
In 2009, Heng Zhu and his collaborators at Johns Hopkins University made a major leap with the creation of the first HuProt Human Proteome Microarray (v1.0). This innovation was made possible through an ingenious system for expressing and purifying thousands of full-length, functional human proteins. Leveraging yeast expression systems, Zhu’s team ensured that the proteins retained their native structure and functionality, critical for ensuring reliable experimental results. Soon, HuProt became the most comprehensive protein array available, offering unmatched coverage of the human proteome. In 2012, CDI Labs took the baton and began manufacturing the HuProt microarray, continuously improving its performance. Today, the HuProt array represents over 81% of the human genome, a testament to its scale and precision.
FIGURE: Timeline of the HuProt Human Proteome Microarray
How HuProt is Driving Discovery
The adoption of HuProt microarrays in research has revolutionized how scientists study proteins and their interactions. Here’s how HuProt has made groundbreaking contributions in various fields:
- Autoimmune Disease Research: HuProt has played a pivotal role in identifying autoantibody profiles in diseases like multiple sclerosis and autoimmune thyroid disorders. For example, researchers used HuProt microarrays to uncover molecular mimicry between Epstein-Barr virus proteins and host antigens in multiple sclerosis, shedding light on new mechanisms driving the disease.
- Cancer Immunology: In ovarian cancer research, HuProt enabled the identification of antibodies that target specific cancer antigens. This finding provided crucial insights into protective immune responses in patients and pointed to new therapeutic possibilities.
- Biomarker Discovery: Researchers have utilized HuProt technology to identify protein biomarkers for early disease detection and prognosis in conditions like cardiovascular disease, cancer, and infectious diseases.
- Drug Discovery: HuProt microarrays have accelerated drug development by screening small molecules for interactions with target proteins, ensuring more precise and efficient drug validation.
Looking to the Future
CDI Labs is building on the success of HuProt with complementary technologies like HuScan PhIP-Seq, which probes the proteome at the peptide level, and VirScan, offering insights into an individual’s viral exposure history. Together, these advancements are ushering in a new era of "seromics"—global studies of the immune system. As researchers unlock more of the human proteome’s secrets, HuProt will remain at the forefront, empowering discoveries that bring us closer to personalized medicine.
The journey that started with a simple lab test has given us a powerful window into the workings of the human body and may unlock the potential for individualized diagnostics and treatments. By watching our proteins at work, we're getting closer than ever to understanding, diagnosing, and conquering disease.
REFERENCES
Chang TW. Binding of cells to matrixes of distinct antibodies coated on solid surface. J Immunol Methods. 1983;65(1-2):217-223. DOI: 10.1016/0022-1759(83)90318-6
Zhu H, Bilgin M, Bangham R, et al. Global analysis of protein activities using proteome chips. Science. 2001;293(5537):2101-2105.
Hu S, Xie Z, Onishi A, et al. Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell. 2009;139(3):610-622.
Jeong JS, Jiang L, Albino E, et al. Rapid identification of monospecific monoclonal antibodies using a human proteome microarray. Mol Cell Proteomics. 2012;11(6):O111.016253.
Venkataraman A, Yang K, Irizarry J, et al. A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors. Nat Methods. 2018;15(5):330-338.
Lanz TV, Brewer RC, Ho PP, et al. Clonally expanded B cells in multiple sclerosis bind EBV EBNA1 and GlialCAM. Nature. 2022;603(7900):321-327. https://doi.org/10.1038/s41586-022-04432-7.
Biswas S, Mandal G, Payne KK, et al. IgA transcytosis and antigen recognition govern ovarian cancer immunity. Nature. 2021;591(7850):464-470. https://doi.org/10.1038/s41586-020-03144-0.
Xu GJ, Kula T, Xu Q, et al. Viral immunology. Comprehensive serological profiling of human populations using a synthetic human virome. Science. 2015;348(6239):aaa0698.