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Chakravarty, K.

Publications and source records attributed to Chakravarty, K..

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Combinatorial approaches using an AI/ML-driven drug development platform targeting insulin resistance, lipid dysregulation, and inflammation for the amelioration of metabolic syndrome in patients

Dysregulations of key signaling pathways leading to metabolic syndrome (MetS) are complex eventually leading to cardiovascular events and type 2 diabetes. Dyslipidemia induces progression of insulin resistance and provokes release of proinflammatory cytokines resulting in chronic inflammation, acceleration of lipid peroxidation with further development of atherosclerotic alterations and diabetes. We have proposed a novel combinatorial approach using FDA approved compounds targeting IL-17a and DPP4 to ameliorate a significant portion of the clustered clinical risks in patients with MetS. As MetS is considered a multifactorial disorder, the treatment measures cannot be focused on the specific pathway because other metabolic changes keep the pathological processes in progression. In our present research we have modeled an outcomes of metabolic syndrome treatment using two distinct drug classes. Targets were chosen based on the clustered clinical risks in MetS; dyslipidemia, insulin resistance, impaired glucose control, and chronic inflammation. The AI/ML platform, BIOiSIM, was used in narrowing down two different drug classes with distinct mode of action and modalities. Preliminary studies demonstrated that the most promising drugs belong to DPP-4 inhibitors and IL-17A inhibitors. Alogliptin was chosen to be a candidate for regulating glucose control with long term collateral benefit of weight loss and improved lipid profiles. Secukinumab, IL-17A sequestering agent used in treating psoriasis, was selected as a candidate to address inflammatory disorders. Our analysis suggests this novel combinatorial approach has a high likelihood of ameliorating a significant portion of the clustered clinical risk in MetS. Author summaryMetabolic syndrome is a global epidemic affecting a significant population worldwide. This syndrome is the manifestation of clustered clinical conditions that cannot be fully ameliorated with monotherapies. No therapeutic approaches were confirmed to be effective in deceleration of the metabolic syndrome progression. Artificial intelligence driven computation methods were used to predict efficacy of innovative combinatorial therapy using IL-17A sequestering agent and a DPP-4 inhibitor. They are expected to mitigate a significant portion of the clustered risks in metabolic syndrome disrupting key pathological pathways playing important role in development of this syndrome. The main therapeutic effects are related to reduction of the elevated lipid level and high glucose concentration. Combinatorial treatment could potentially stop or reverse a significant portion of the clinical risks in metabolic syndrome globally. Repurposing of approved FDA drugs can have increased likelihood of approval of the new therapeutic regimens and can reach patients faster with reduced costs of treatment.

pharmacology and toxicology

Transient response of basal ganglia network in healthy and low-dopamine state

The basal ganglia (BG) are crucial for a variety of motor and cognitive functions. Changes induced by persistent low-dopamine (e.g. in Parkinsons disease), result in aberrant changes in steady-state population activity ({beta}-band oscillations) and transient response of the BG. Typically, brief cortical stimulation results in a triphasic response in the substantia nigra pars reticulata (SNr, output of the BG). The properties of the triphasic responses are shaped by dopamine levels. While it is relatively well understood how changes in BG result in aberrant steady state activity, it is not clear which BG interactions are crucial for the aberrant transient responses in the BG. Moreover, it is also not clear whether the same or different mechanisms underlie the aberrant changes in steady-state activity and aberrant transient response. Here we used numerical simulations of a network model of BG to identify the key factors that determine the shape of the transient responses. We show that an aberrant transient response of the SNr in low-dopamine state, involves changes in both, the direct pathway and the recurrent interactions within the globus pallidus externa (GPe) and between GPe and sub-thalamic nucleus. We found that the connections from D2-type spiny projection neurons to GPe are most crucial in shaping the transient response and by restoring them to their healthy level, we could restore the shape of transient response even in low-dopamine state. Finally, we show that the changes in BG that result in aberrant transient response are also sufficient to generate pathological oscillatory activity. Significance statementTo understand how changes induced by low-dopamine (e.g. in Parkinsons disease, PD) affect basal ganglia (BG) function, we need to identify the factors that determine the shape of BG responses to brief cortical stimuli. We show that transient response of the BG is also affected by recurrent interactions within the subnuclei of the BG, and not just feedforward pathways. We found that input and local connectivity within the globus pallidus externa are crucial for shaping the transient response. We also show that the same network changes may underlie both, pathological {beta}-band oscillations and aberrant transient responses. Our results highlight the importance of the recurrent connectivity within the BG and provide a coherent view of emergence of pathological activity in PD.

neuroscience

RNAseq analysis of rodent spaceflight experiments is confounded by sample collection techniques

To understand the physiological changes that occur in response to spaceflight, mice are transported to the International Space Station (ISS) and housed for variable periods of time before euthanasia on-orbit or return to Earth. Sample collection under such difficult conditions introduces confounding factors that need to be identified and addressed. We found large changes in the transcriptome of mouse tissues dissected and preserved on-orbit compared to tissues from mice euthanized on-orbit, preserved, and dissected after return to Earth. Changes due to preservation method eclipsed those between flight and ground samples making it difficult to identify spaceflight-specific changes. Follow-on experiments to interrogate the roles of euthanasia methods, tissue and carcass preservation protocols, and library preparation methods suggested that differences due to preservation protocols are exacerbated when coupled with polyA selection. This has important implications for the interpretation of existing datasets and the design of future experiments.

systems biology