Clock-infection Biology, Sleep, and Chronomedicine 

“No problem can be solved from the same level of consciousness that created it”

 Albert Einstein

  • Circadian clocks and sleep

  • Infectious diseases

  • Quantitative proteomics

  • Mass spectrometry  

  • Mechanism of drug action

  • Systems biology

  • Metabolism

  • Post-translational modifications

Project 1. Investigation on Host and Parasite Circadian Rhythms in Malaria to Decipher Disease Pathogenesis and Efficacy of Antimalarials

Circadian clocks have profound impacts on human health as they play a central role in coordinating daily physiological processes including innate and adaptive immune functions. Our immune system often responds more effectively during the active period causing the disease symptoms less severe when the infections occur in the daytime, while the pathogens intend to modulate our body clocks to facilitate their own replication. Importantly, we are more susceptible to infections at certain times of the day and many parasitic and viral infections show daily rhythmic patterns. Malaria is by far the world’s most significant tropical infectious disease with an estimated 228 million malaria cases worldwide in 2018, leading to around 0.5 million deaths (World malaria report 2019). In particular, the cyclical nature of malaria infections is well recognized, as the cell cycles across parasite species last a multiple of approximately 24-hour. Perturbing the timing of the murine malaria parasite cell cycle relative to the host’s circadian rhythm causes reduced replication and transmission. However, the mechanism driving the rhythmic host-parasite interactions in malaria and how the molecular circadian clockwork in the host is disrupted by Plasmodium is not clear.

              In this project, we are investigating the temporal regulation of the host-parasite interactions in malaria and the possible diurnal variation in the pharmacokinetics and efficacy of the most commonly used antimalarial drugs. We want to evaluate whether the malaria parasite Plasmodium and its host exhibit 24-hour oscillations of the proteome, and metabolome during the infection and how such molecular rhythmicity contributes towards the overall outcome of the disease in cellular and mice models as well as in humans. We will further investigate the dynamics of selected proteins and metabolites in actual clinical samples of falciparum malaria and vivax malaria patients (including complicated severe malaria patients).

Project 2. Deciphering the Mechanisms of Action of Pharmacological Agonists of Circadian Clocks for Developing New Anticancer Strategies

Pharmacological modulation of the circadian machinery could be an effective therapeutic strategy for combating chronic diseases associated with circadian misalignments such as cancers, diabetes, and cardiovascular diseases. This project’s goal is to determine how drug-like compounds, which can enhance circadian clock (in particular the agonists of REV-ERBα and REV-ERBβ) and thereby repress the expression of genes aberrantly activated in cancer cells, work at the molecular level. Drugs with such effects can be beneficial in developing novel anticancer strategies. However, in order to develop highly effective and less toxic new drug molecules, we need an inclusive understanding of how these agonists of REV-ERBs specifically work to exhibit their effects so that we can accurately target those aspects of cell functions and physiological processes. The circadian regulator REV-ERBα and REV-ERBβ (also known as NR1D1 and NR1D2, respectively) are emerging as promising targets for controlling tumorigenesis. Pharmacological modulators of these circadian clock components such as agonists of REV-ERBs - SR9009 and SR9011 exhibit specific lethal effects to cancer cells by triggering apoptosis. Multi-target activity for these promising REV-ERB agonists is not studied earlier.  

              We are interested to obtain a comprehensive landscape of the mechanisms of action of REV-ERB agonists in a variety of cancer cell lines including brain, breast, and colon cancers, melanoma, and leukemia. The research strategy will center on elucidating the mechanisms of action of these drugs by interrogating the multi-dimensional proteomes of cells and tissues treated with these drugs, employing cutting-edge quantitative mass spectrometry methodology. An approach integrating multipronged proteomics approaches including global proteome, and phosphoproteome, and proteome-wide profiling of thermal stability (TPP) will be applied to decipher the molecular mechanisms for multiple REV-ERB agonists (SR9009, SR9011, and GSK4112). Effects of RNA interference (RNAi)-mediated inhibition of the identified targets will be carried out to validate the findings of mass spectrometry-based methods. Cross-linking mass spectrometry (CLMS) will be applied to identify the interacting proteins of REV-ERBs for obtaining an inclusive picture for such pharmacological activation of the circadian clock and to investigate the effects of the clock pharmacologic modulation on cancer cell viability. This project can address a critical knowledge gap at the interface of basic research and its clinical application.  

Project 3. Mechanistic Study on Circadian Aberrations Due to Sleep Deficiency and Aging

Sleep-related disorders are increasing rapidly in modern society and are considered a serious public health issue. The molecular mechanisms driving sleep and the effects of sleep deprivation on circadian clocks are largely unidentified. Aging-related sleep disruption, as well as different sleeping disorders, can cause circadian misalignments. Circadian misalignments due to sleep deficiency, old age, and even shift-work are an increasing cause of considerable morbidity. Several studies have provided valuable information regarding the neural circuitry conducting the regulation of sleep-wake states and circadian rhythmicity and established the vital roles of circadian and homeostatic processes in the regulation of the sleep-and arousal-promoting circuitry. Phosphorylation–dephosphorylation cycle represents a major regulatory mechanism that underlies sleep-wake homeostasis. Sleep disorders and aging both disrupt circadian regulation of normal body physiology and metabolism and thereby increase the risk for diverse chronic diseases. Importantly, recent studies have provided some critical links between circadian clocks, sleep, and immune function. However, the exact mechanism by which sleep deficiency and aging affect our body clocks are not precisely established. 

              In this project, we are intending to illustrate the effects of sleep deprivation (SD) on circadian rhythmicity at a tissue/cell-type-specific proteome scale in two complementary model organisms (Mus musculus and Drosophila melanogaster). We are also intending to decipher whether the adversity of these SD-related effects is also influenced by aging. Moreover, the proposed research project aims to identify the blood markers for sleep deprivation in mice and eventually to investigate those molecular signatures of SD in the patients suffering from chronic sleeping disorders. Using multiplexed highly sensitive quantitative proteomics pipeline we will systematically investigate the plasma proteome alterations in patients for a comprehensive mapping of the sleep deprivation-induced alterations in body clock with aging. The expected outcome of this research will be a better understanding regarding the interconnectivity among the body clocks, sleep-need, and aging.  

Dr. Sandipan Ray, Ph.D., MRSB
Department of Biotechnology, Indian Institute of Technology Hyderabad,
Kandi, Sangareddy 502285, Telangana, India