Research focus of Kasumov’s lab

Kasumov’s laboratory applies high-throughput unbiased system biology approaches, i.e. metabolomics, proteomics, and fluxomic to understand the pathogenesis of metabolic disorders, including alcoholic liver disease (ALD), nonalcoholic fatty liver disease (NAFLD) and diabetes, and their cardiovascular and neurodegenerative complications.

Current work

Our current projects include:

1. Mechanisms of diet- and alcohol-induced liver injury
2. Development of methods for quantification of temporal and spatial acetylome dynamics;
3. Studies on the mechanisms involved in hyperglycemia-induced dementia and Alzheimer’s disease in diabetic patients.

Mechanisms of alcohol-induced liver injury: Alcoholic liver disease (ALD) is a major cause of liver-related death. There is growing evidence that the dysfunction of mitochondria (the part of the cell that converts food into energy) plays a key role in disease propagation. Alcohol intake is associated with hyperacetylation of hepatic mitochondrial proteins. This project studies the role of alcohol-induced changes in acetylome dynamics in mitochondrial dysfunction. The rationale is that hepatic mitochondria may respond to alcohol-induced stress via acetyl-transfer dependent enzymatic inhibition and/or the regulation of protein stability via acetylation. To assess the impact of these acetylation-mediated changes, we will quantify mitochondrial acetylome dynamics in ALD mice liver in vivo using a stable isotope-resolved high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS).

Methods of temporal and spatial acetylome dynamics: Dysregulated post-translational protein acetylation at the lysine side chain by acetyl-CoA plays a critical role in the pathogenesis of various diseases, such as cancer, neurodegeneration, and metabolic disorders. In addition to modulating metabolic processes by affecting transcription and enzyme activity, acetylation regulates multiple facets of proteostasis, including protein stability. However, the lack of suitable techniques for studying acetylation dynamics in vivo poses a significant obstacle in developing effective therapies for acetylation-related disorders. To overcome this limitation, we are developing innovative techniques to accurately measure the rates of acetylation and deacetylation, as well as the effect of acetylation on protein stability in different organs and cell compartments. To achieve these goals, we will be leveraging the advancements of our 2H2O-based proteome dynamics method in conjunction with ultra-high-resolution Orbitrap mass spectrometer.

Acetylome dynamics in NAFLD:  Protein acetylation links nutrient metabolism and enzymes involved in this process through reversible acetylation of proteins by acetyl-CoA, a key node in nutrient metabolism. In addition to acetyl-CoA availability, acetylation of proteins is regulated by adenine dinucleotide (NAD+), the redox cofactor and a substrate for family deacetylase sirtuins, including mitochondrial Sirt3. The objective of this project is to assess the mechanisms linking diet-induced dysregulated acetylation and altered substrate metabolism. We will quantify acetylation dynamics, and the role of acetylation on mitochondrial protein stability in Sirt3-/- mice characterized by hepatic mitochondrial hyperacetylation. Then, we will use this method to assess the role of acetylation in hepatic substrate metabolism in a high-fat diet (HFD)-induced mouse model of NAFLD.

Type 2 Diabetes and Preclinical Alzheimer’s Disease: Diabetes-related cardiovascular risk factors have been associated to higher risk of dementia and Alzheimer’s Disease (AD) in late life. The large number of younger diabetics among both the general population and veterans is vulnerable to a significant future risk of dementia. T2DM is associated with systemic metabolic changes including low levels of HDL cholesterol and ApoA1, the major protein of HDL involved in reverse cholesterol transport function of HDL. Our preliminary study in T2DM patients shows that glycation of plasma ApoA1 results in reduced stability of ApoA1 and inefficient cholesterol transport function of HDL. Dr. Pillai, our collaborator from Cleveland Clinic, observed that baseline plasma ApoA1 levels are associated with poorer memory scores and CSF baseline ApoA1 levels predicts future cognitive decline among cognitively normal subjects. In collaboration with Dr. Pillai, we will evaluate the relationship between plasma ApoA1 (total and glycated) and CSF biomarkers related to cognition.

Open positions

See open positions in this lab on the NEOMED careers site

Select publications

1. Agayev M., Alvarado A., Ilchenko S., Scott I, Chen Y-R., Zhang G., Tsai T-H. and Kasumov T. A high-fat diet increases mitochondrial turnover through restricted acetylation in NAFLD mouse model. Am J Physiol Endocrinol Metab. 2023, 325 (1), E83-E98. PMCID: PMC10312330.
2. Sadana P, Edler M., Agayev M., Alvarado A., Cohn E., Ilchenko S., Pillai J.A., Kashyap S., and Kasumov T. Metabolic labeling unveils alterations in the turnover of plasma proteins during diabetes progression in mice. Am J Physiol Endocrinol Metab. 2022, 323(6): E480-E491.
3. Ilchenko S, Haddad A., Racchia F, Sadana P., Sadygov R, Kasumov T. Calculation of the Protein Turnover Rate Using the Number of Incorporated 2H Atoms and Proteomics Analysis of a Single Labelled Sample. Analytical Chemistry, 2019, 91(22): 14340-51.
4. McCullough A, Previs SF, Dasarathy J, Lee K, Osme A, Kim C, Ilchenko S, Lorkowski SW, Smith JD, Dasarathy S, Kasumov T. HDL flux is higher in patients with nonalcoholic fatty liver disease. Am J Physiol Endocrinol Metab. 2019, 317(5): E852-E862.
5. Kashyap S., Ösme A., Golizeh M., Lee K., Ilchenko S., Bena J., Kasumov T. Increased Glycation Reduces the Stability of ApoAI and Increases HDL Dysfunction in Diet-controlled Type 2 Diabetes. 
6. Kasumov T, Li L, Li M, Gulshan K, Kirwan J, Liu X, Previs S, Willard B, Smith J, McCullough A, Ceramide as a Mediator of Non-alcoholic Fatty Liver Disease Associated Atherosclerosis. PLOSE ONE, 2015, 10(5):e0126910. doi: 10.1371/journal.pone.0126910. eCollection 2015.
7. Kasumov T, Willard B, Li L, Li M, Conger H, Buffa J A, Previs S, McCullough A, Hazen SL, Smith JD, 2H2O-based HDL turnover method for the assessment of dynamic HDL function in Mice. Arterioscl Thromb Vasc Biol, 2013, 33(8), 1994-2003.
8. Kasumov T, Dabkowski ER, Shekar KC, Li L, Ribeiro RF Jr, Walsh K, Previs SF, Sadygov RG, Willard B, Stanley WC, Assessment of cardiac proteome dynamics with heavy water: slower protein synthesis rates in interfibrillar than subsarcolemmal mitochondria. Am J Physiol Heart Circ Physiol. 2013; 304(9): H1201-1214.

Select collaborators

1. Dr. Guo-fang Zhang, Duke Medical School
2. Dr. Jeffrey Shelling, Case Western Reserve University
3. Dr. Elizabeth Parks, University of Missouri
4. Dr. Recchia Fabio, Temple University
5. Dr. Lora Nagy, Cleveland Clinic Foundation
6. Dr. Jagan Pillai, Cleveland Clinic Foundation

Previous lab members and what they are doing today

1. Ling Li, Ph.D., Assistant Professor at Lerner College of Medicine of Cleveland Clinic, Cleveland, OH
2. Makan Golizeh, Ph.D., Assistant Professor at Concordia University of Edmonton, Edmonton, Canada.
3. Aisha Feyza Keles, M.S., Forensic Chemist, Forensic Test for Alcohol Branch, Raleigh, NC

Equipment

Q Exactive Plus Orbitrap (Thermo Scientific)
Q Exactive Plus with normal flow and nano-flow chromatographic inlet offers untargeted metabolomics and proteomics studies. High resolution (up to 140,000), accurate mass (<1ppm) HRAM) and full-scan capabilities captures all sample data at all time points with confidence when analyzing samples in complex matrices. Selected ion monitoring (SIM) and parallel reaction monitoring (PRM) enables targeted analysis of hundreds of metabolites and peptides levels with high specificity and sensitivity. High resolving power eliminates isobaric interferences, increasing the sensitivity of metabolic flux and dynamic proteomics studies. Mass range to 6,000m/z enhances detection of singly charged small molecules and biomolecules. More than four orders of magnitude dynamic range, along with femtogram-level sensitivity, allow detection of trace-level and high-abundance compounds in the same scan.

GC-MS (Agilent)
This capillary gas chromatography coupled with a single quadrupole mass spectrometer is designated for the direct analyses of volatile small molecules or derivatized compounds. The electron ionization (EI) on this instrument induces fragmentation in the source and produces characteristic mass spectra that can be searched against the EI spectra library. Although the MassHunter software coupled with NIST library allows non-targeted metabolic profiling, the GC-MS instrument is best suited for the targeted metabolomics and stable isotope-based flux studies.

Grants

• Mitochondrial acetylation and acetylome dynamics in alcoholic liver disease assessed with heavy water. Awarded by National Institute of Alcohol Abuse and Addiction
• NRF2-ACSS2 Axis in Alcohol-associated Metabolic Reprogramming and Esophageal Pathology
  Awarded by National Institute of Alcohol Abuse and Addiction
• Apolipoprotein A1 Modifications Related to Cognitive Decline in Type 2 Diabetes and Preclinical Alzheimer’s Disease
  Awarded by Department of Defense
• Mechanisms of Tubular Atrophy in Renal Disease
  Awarded by National Institute of Diabetes, Digestive diseases, and Kidney.

Lab members

Serguei Ilchenko, Ph.D., research scientist
Victor Lufi, B.S., research technician
Andrea Aras-Alvarado, M.D., Ph.D. candidate
Mirjavid Aghayev, M.S., Ph.D. candidate