Heart Disease Biomarker Discovery Using Nanoproteomics

Significance 

Measuring low-concentration proteins in the blood like cTnI is a classic needle-in-a-haystack problem. Rare, meaningful biomarkers of disease are completely overwhelmed by common and diagnostically useless proteins in the blood. Current methods use antibodies to enrich and capture proteins in a complex sample to identify and quantify proteins. But antibodies are expensive, have batch-to-batch variations, and can generate inconsistent results.

To capture cTnI and overcome some of the limitations of antibodies, the researchers designed nanoparticles of magnetite, a magnetic form of iron oxide, and linked it to a peptide of 13 amino acids long designed to specifically bind to cTnI. The peptide latches onto cTnI in a blood sample, and the nanoparticles can be collected together using a magnet. Nanoparticles and peptides are easily made in the lab, making them cheap and consistent. Doctors currently use an antibody-based ELISA test to help diagnose heart attacks based on elevated levels of cTnI in the patient’s blood sample. While the ELISA test is sensitive, patients can have high levels of cTnI in the blood without having heart disease, which can lead to expensive and unnecessary treatments for patients.

Scientists at the University of Wisconsin-Madison say they have developed a technique combining sticky nanoparticles with high-precision protein measurement to capture and analyze a common marker of heart disease to reveal details that were previously inaccessible. In a new research published in Nature Communications led by Professor Ying Ge, professor Song Jin, and graduate students Timothy Tiambeng and David Roberts. The new method—nanoproteomics—effectively captures and measures various forms of the protein cardiac troponin I, or cTnI, a biomarker of heart damage currently used to help diagnose heart attacks and other heart diseases, according to the team which maintains that an effective test of cTnI variations could one day provide doctors with a better ability to diagnose heart disease, the leading cause of death in the United States.

Top-down mass spectrometry (MS)-based proteomics provides a comprehensive analysis of proteoforms to achieve a proteome-wide understanding of protein functions. However, the MS detection of low-abundance proteins from blood remains an unsolved challenge due to the extraordinary dynamic range of the blood proteome. The research team developed an integrated nanoproteomics method coupling peptide-functionalized superparamagnetic nanoparticles with top-down MS for the enrichment and comprehensive analysis of cardiac troponin I (cTnI), a gold-standard cardiac biomarker, directly from serum.

The designed nanoparticles would enable the sensitive enrichment of cTnI (<1 ng/mL) with high specificity and reproducibility, while simultaneously depleting highly abundant proteins such as human serum albumin (>1010 more abundant than cTnI). They demonstrated that top-down nanoproteomics can provide high-resolution proteoform-resolved molecular fingerprints of diverse cTnI proteoforms to establish proteoform-pathophysiology relationships.

The research team developed a new nanoproteomics system to look into more details at various modified forms of this protein rather than just measuring its concentration. This will help reveal molecular fingerprints of cTnI from each patient for precision medicine. They were able to effectively enrich cTnI in samples of human heart tissue and blood. Then they used advanced mass spectrometry, which can distinguish different proteins by their mass, to not only get an accurate measurement of cTnI, but also to assess the various modified forms of the protein.

Like many proteins, cTnI can be modified by the body depending on factors like an underlying disease or changes in the environment. In the case of cTnI, the body adds various numbers of phosphate groups, small molecular tags that might change the function of cTnI. These variations are subtle and hard to track.

The method was able to associate a pattern of cTnI variations with heart health that the researchers hope could one day produce a new diagnostic tool to help when patients come to the hospital with suspected heart disease. The researchers have filed a patent application on the new innovation. The researchers now plan to use their new method to associate the various forms of cTnI with specific heart diseases as a step toward developing a new diagnostic test.

Heart Disease Biomarker Discovery Using Nanoproteomics - Medicine Innovates

About the author

Ying Ge, PhD

Professor, Department of Cell and Regenerative Biology
Professor, Department of Chemistry
Director of Mass Spectrometry
Human Proteomics Program
School of Medicine and Public Health
University of Wisconsin-Madison

Professor Ying Ge research is trans-disciplinary that cuts across the traditional boundaries of chemistry, biology, and medicine. We aim to develop and apply cutting-edge ultra high-resolution mass spectrometry (MS)-based top-down comparative proteomics and metabolomics technologies for systems biology combined with functional studies to gain a better understanding of the molecular and cellular mechanisms underlying cardiovascular diseases.

Cardiovascular disease is the leading cause of morbidity and mortality in developed countries and is reaching epidemic proportions.  Transformative insights from a holistic approach at the systems level have great potential to elucidate disease mechanisms and to develop new therapeutic treatments.  Proteins and metabolites are important molecular entities of the cell downstream of genes.  Hence in the post genomic era, proteomics and metabolomics (the large-scale global analysis of proteins and metabolites in a cell, organism, tissue, and biofluid) are essential for deciphering how molecules interact as a system and for understanding the functions of cellular systems in health and disease.  However, there are tremendous challenges in proteomics and metabolomics due to the extreme complexity and dynamic nature of the proteome and metabolome.

To address such challenges, we are developing novel ultra high-resolution MS-based top-down comparative proteomics and metabolomics platforms with high efficiency, specificity, sensitivity, and reproducibility.  We globally identify, characterize, and quantify intact proteins and metabolites extracted from tissues/cells/biofluids and reveal all changes in the proteome and metabolome in response to extrinsic and intrinsic stresses.  We then employ these technology platforms to study cardiovascular diseases in conjunction with biochemical and physiological functional assays.  Success in my proposed research will provide innovative tools to advance our understanding of the molecular basis of diseases and foster the development of new strategies for early diagnosis, prevention and better treatment of cardiovascular diseases

About the author

Song Jin

Professor, Department of Chemistry, University of Wisconsin-Madison
1101 University Avenue, Madison, Wisconsin 53706
Phone: (608)262-1562, FAX: (608)262-0453, E-mail: [email protected]
homepage: http://www.chem.wisc.edu/users/jin
research group webpage: http://jin.chem.wisc.edu/

Research in the Jin group is centered on the chemistry and physics of nanomaterials. We develop rational strategies for chemical synthesis, assembly and integration of nanomaterials, and investigate fundamental synthesis-structure-property relationships, especially through device fabrication and characterization, and finally develop  them for various applications. We apply vapor-phase, solution-phase and solid-state nanomaterials synthesis, as well as “traditional” inorganic synthesis of single source precursors.  We are interested in nanomaterials for renewable energy conversion, such as photovoltaic and thermoelectric energy conversion, and the applications of nanomaterials in biotechnology.

Reference

Timothy N. Tiambeng, David S. Roberts, Kyle A. Brown, Yanlong Zhu, Bifan Chen, Zhijie Wu, Stanford D. Mitchell, Tania M. Guardado-Alvarez, Song Jin & Ying Ge. Nanoproteomics enables proteoform-resolved analysis of low-abundance proteins in human serum. Nature Communications volume 11, Article number: 3903 (2020)

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