The University of Colorado Department of Medicine has invested in an important disease research tool that brings the dynamics of proteins inside human cells into sharper focus.
A new Orbitrap Exploris 480 mass spectrometer was installed on the CU Anschutz Medical Campus in July and is now ready for use by researchers. It deepens the department’s resources in mass spectrometry, allowing for direct analyses of the structure and function of cellular proteins inside human cells on a large scale – a field known as proteomics – to give investigators more insight into protein changes that can cause many diseases.
The acquisition by the department and its Division of Cardiology was funded in part through a grant from the CU School of Medicine’s Strategic Infrastructure for Research Committee (SIRC), establishing an Advanced Proteomics Infrastructure program directed by Maggie Lam, PhD, associate professor of cardiology and affiliated faculty in the CU Department of Biochemistry and Molecular Genetics.
Lam and Edward Lau, PhD, her cardiology colleague and frequent research partner, plan to use the upgraded technology to follow up on their recent study, published in the journal Nature Communications. Their paper described a new technique using mass spectrometry for gathering various kinds of information simultaneously about protein dynamics within cells.
“Most of us are aware that cells are the basic units of life,” Lam says. “What may not be always as well appreciated is that cells are incredibly complex structures. Different parts of the cell, such as the nucleus and the mitochondria, perform different functions. Being able to pinpoint where proteins are located inside the cells is relevant to finding new strategies to combat diseases, including heart failure and myopathies, and understanding how patients’ hearts may be damaged by some cancer treatments,” Lam says.
Mass spectrometers are machines that give an electrical charge to sample molecules, turning them into ions. The ions can then be sorted using electric and magnetic fields and analyzed. The technology is used across many fields besides medicine, from detecting signs of petroleum in rocks to identifying the age of archaeological specimens.
“A mass spectrometer is a complex analytical instrument that can be used to weigh molecules very accurately,” Lam says of the new device. “Scientists can use this method to look inside a cell and see what kinds of proteins and components there are and what kinds of functions they might be doing. That helps us generate new hypotheses and make new discoveries about how cells regulate their function in response to changing environments, and how these processes sometimes go awry in disease.”
Mass spectrometry “has become an indispensable tool of discovery in our field.” Lam adds. “For example, using mass spectrometry analysis, researchers can take a patient’s blood or other biopsy sample, and find out what thousands of proteins are present inside, and whether there are differences between a sample from a person with disease versus a healthy person.”
Lam’s lab develops mass spectrometry techniques to help understand mechanisms underlying the onset and progression of disease. Lau’s lab seeks to understand how cells in the heart communicate through secreted proteins and nucleic acids, with an interest in harnessing cellular communication networks to monitor and influence cell differentiation, stress response, and disease.
In their recent paper, which relied on a previous generation of mass spectrometry equipment, Lam and Lau described a new method they created that uses mass spectrometry to simultaneously find the spatial location of proteins within cells as well as to distinguish between newer and older proteins – “something we call spatial-temporal proteomics,” Lau says.
They say their technique can also be used to determine the rate of recycling old proteins within cells, a process – known as protein turnover – that’s critical to maintaining cellular activity.
Using their method – called Simultaneous Proteome Localization and Turnover (SPLAT) – researchers for the first time are able to reveal the dynamics of proteins over space and time simultaneously, Lam and Lau say.
“Old and damaged proteins need to be effectively recycled by the cell, so that new proteins can take their place and maintain cellular function,” Lau says. “This process is so critical to the healthy wellbeing of cells and organs that cells have evolved separate complex machineries dedicated to maintaining a healthy protein pool within different parts of the cell. With this new method, we can now more fully understand how cells modulate protein degradation in different subcellular locations in response to stress,” Lau says.
To make use of SPLAT in further research, Lam and Lau recently received a new Research Project Grant (R01) from the National Institutes of Health. The newly installed mass spectrometry infrastructure is “a vital component” of the new method, Lam says.
“This new instrument being installed is an important step,” she says. “With the higher sensitivity and speed of this instrument, we will possess the resolution and speed to gain an even deeper look into the spatial and temporal changes of proteins within the proteome” – the assortment of proteins within a cell.
Says Lau: “In many instances, we can’t fully explain how diseases happen by looking at genes. With new mass spectrometry techniques, we have new opportunities to find out what happens to heart cells when they’re exposed to certain types of cancer drugs that function by inhibiting protein degradation, which is an important aspect of the functions that cells need in order to stay healthy. Certain cancer drugs that target that pathway also happen to be toxic to cells in the heart, which is why some cancer patients have side effects from these drugs, like heart failure and arrythmia.”
Lam and Lau predict the Department of Medicine’s new mass spectrometry investment, and their new SPLAT method, will be useful to collaborating investigators on campus who seek a closer look at the dynamics of proteins inside cells, including those developing treatments for various disease conditions such as fibrosis and heart failure.
These are exciting times in protein spatial-temporal dynamics, Lam and Lau say. With more investment and development into understanding the busy life of proteins, they add, investigators will be able to ask new questions that are broadly applicable to multiple disease models.
Photo at top: Maggie Lam, PhD, in her lab. Photo by Justin LeVett for the CU Department of Medicine.