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Loyola University Chicago Cell & Molecular Physiology
Stritch School of Medicine
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Jonathan Kirk, PhD

Associate Professor; Vice Chair

  • BS. Bioengineering, 2004. Washington State University; Pullman, WA
  • PhD, Bioengineering, 2009. University of Pittsburgh; Pittsburgh, PA

The Kirk lab studies cardiovascular disease from the perspective of the sarcomere, the force-generating unit in heart muscle cells. Our goal is to understand how changes in the sarcomere can lead to disease and how disease impacts the sarcomere, then harness this knowledge to develop therapies to treat cardiovascular disease. We use sophisticated biophysical assays to measure single-cell function from human samples and animal models, and state-of-the-art mass spectrometry to discover changes in sarcomere protein modifications that impact function. Specifically, we study heart failure, diabetes, cardiac dyssynchrony, cardiac ischemia, and genetic mutations.

Research Interests

Heart failure affects 5.7 million Americans and while it involves many complex and heterogeneous signaling pathways, it almost universally results in depressed contractile strength of the heart. The cardiac myofilament is a specialized protein lattice within heart cells (myocytes) that produces force, so much of what goes wrong in heart failure eventually ends up altering myofilament function. Discovering how to restore its function could represent a therapeutic approach applicable to the majority of the heart failure population. The Kirk lab uses sophisticated biophysical assays to study human and animal models of disease to understand the precise molecular mechanisms that cause the myofilament to malfunction. Heart failure often disrupts molecular “switches” on myofilament proteins that depress function. We use proteomics techniques, such as mass spectrometry, to identify these and whether they can be reversed to attempt to treat the disease.

Myofilament and Heart Failure

The myofilament generates force through the interaction of thick and thin filaments. The thick filament is composed of myosin, with the myosin heads extending towards the actin thin filaments. When the myosin heads attach to their binding spots on the actin thin filament, they can perform a POWERSTROKE which pulls the filaments past each other, generating force. When the heart is relaxed and filling with blood, the myosin binding sites on actin are blocked by a protein that wraps around actin called tropomyosin The troponin complex (consisting of troponin I, C, and T) acts as the “switch” that, when calcium ions bind to it, moves tropomyosin away from myosin’s binding spot. Thus, the whole cycle starts with a huge increase in calcium that floods the cell as the beginning of cardiac contraction.

The ability of the myofilament to generate force in response to calcium in a single cell is fundamental to the ability of the whole heart to pump blood. The Kirk lab has several instruments for measuring the function of single heart cells. One key instrument can expose the myofilament directly to controlled levels of calcium, to assay its functional response. This experiment can be done on very small pieces of tissue, including single biopsies taken from a human heart. Our underlying goal is to understand human disease, and while animal models are a necessary component, we always try to start with patients.       


Within the myofilament, there are only a handful of proteins that are directly responsible for generating force. Much work has been done on how these “core” proteins are altered in heart failure. There are many other proteins and structures that are part of the myofilament, however, and most of these have unknown roles. It is for this reason we use Proteomics, and specifically, mass spectrometry.

The real power of mass spectrometry is it’s ability to discover. Traditional approaches (western blots, etc.) will only tell you an answer to a question you purposefully asked: did protein X change? Mass Spectrometry, however, is unbiased, and can respond to the command: tell me every protein that changed with this disease. Thus, we can discover new targets, new signaling mechanisms, and hopefully new therapeutic targets for treating disease. One of the few drawbacks to mass spectrometry is the need for complex instrumentation and a high level of technical knowledge. The Kirk lab and the Department of Cell and Molecular Physiology have both, allowing us to use this technology on human and animal models of disease.

Cardiac Dyssynchrony and Resynchronization Therapy

Contraction of the left ventricle is precisely coordinated by the His-Purkinje system, which rapidly conducts electrical excitation to the heart muscle. This ensures shortening throughout the wall occurs synchronously to optimize the pumping efficiency of the heart. Diseases of the conduction system such as a left-bundle branch block (LBBB) lead to dyssynchrony, and occur in 30-50% of patients with heart failure. As a result, instead of ejecting blood efficiently to the body, the early and late activated regions waste energy “sloshing” blood back and forth within the ventricle. In the failing heart, where function is already reduced, dyssynchrony significantly worsens morbidity and mortality.

Studies in the 1990s showed that simultaneous bi-ventricular pacing applied to dyssynchronous hearts improved function and chamber efficiency, while concomitantly lowering morbidity and mortality. This ultimately led to Cardiac Resynchronization Therapy (CRT). To date, CRT remains the singular therapy for heart failure that simultaneously improves both acute and chronic systolic function, increases cardiac work, and yet also prolongs survival.

Traditionally, CRT has been viewed as a mechanical tuning of the heart. There was very little basic science on CRT reported prior to its use in the clinic. Recently, however, there have been efforts by ourselves and others to “reverse-engineer” CRT, exploring the cellular and molecular mechanisms that are involved. Indeed, dyssynchrony and CRT induce a wide range of changes, many unique to both the disease and the treatment.

Our work involves furthering this understanding, with the goal of improving CRT and discovering a way to bring its substantial benefits to the wider heart failure population.