A Quantitative Systems Pharmacology Platform Reveals NAFLD Pathophysiological States and Targeting Strategies

Abstract

Non-alcoholic fatty liver disease (NAFLD) has a high global prevalence with a heterogeneous and complex pathophysiology that presents barriers to traditional targeted therapeutic approaches. We describe an integrated quantitative systems pharmacology (QSP) platform that comprehensively and unbiasedly defines disease states, in contrast to just individual genes or pathways, that promote NAFLD progression. The QSP platform can be used to predict drugs that normalize these disease states and experimentally test predictions in a human liver acinus microphysiology system (LAMPS) that recapitulates key aspects of NAFLD. Analysis of a 182 patient-derived hepatic RNA-sequencing dataset generated 12 gene signatures mirroring these states. Screening against the LINCS L1000 database led to the identification of drugs predicted to revert these signatures and corresponding disease states. A proof-of-concept study in LAMPS demonstrated mitigation of steatosis, inflammation, and fibrosis, especially with drug combinations. Mechanistically, several structurally diverse drugs were predicted to interact with a subnetwork of nuclear receptors, including pregnane X receptor (PXR; NR1I2), that has evolved to respond to both xenobiotic and endogenous ligands and is intrinsic to NAFLD-associated transcription dysregulation. In conjunction with iPSC-derived cells, this platform has the potential for developing personalized NAFLD therapeutic strategies, informing disease mechanisms, and defining optimal cohorts of patients for clinical trials.

Modeling mechanisms underlying differential inflammatory responses to COVID-19 in type 2 diabetes using a patient-derived microphysiological organ-on-a-chip system

“…14,25 Conversely, LDH levels were higher in T2D media as compared to non, consistent with NASH induced cellular damage to liver. The secretome measurements in non-diabetic media were consistent with prior published reports 14,18 suggesting a functionally competent liver model that can be modified further to develop T2D-COVID-19-LAMPS.…”

“…As previously reported, 14,17,18 LAMPS is constituted using four predominant liver cell types – hepatocytes, liver sinusoidal endothelial cells (LSECs), macrophages, and stellate cells, in the ratio normally present in the human liver. Here, we modified the LAMPS to incorporate macrophages differentiated from patient-derived PBMCs that expressed S-protein to model SARS-CoV2 infection and perfused it with either Non or T2D media (schematic in Fig.…”

“…LAMPS offers tremendous potential for a customizable liver-on-a-chip model. It has been used to mimic disease progression and test drugs in non-alcoholic fatty liver disease (NAFLD), test fluorescent biosensors that track the progression of NAFLD, 14,18 and to screen drugs for hepatotoxicity. 55,56 In this study, we modified LAMPS by introducing T2D patient-derived primary macrophages from PBMCs and LSECs, over-expressing Spike protein, and culturing them in T2D mimicking media and demonstrate their contribution in the development of a hyperimmune state in the context of T2D.…”

“…LAMPS assembly and culture LAMPS were assembled as previously described. 13,14,17,18 Briefly, a single chamber commercial microfluidic device (HAR-V single-channel device, SCC-001, Nortis, Inc. Seattle, WA) was used for LAMPS studies. For all steps involving injection of media and/or cell suspensions into LAMPS devices, 100-150 μl per device was used to ensure complete filling of fluidic pathways, chamber, and bubble traps.…”

Opportunities and considerations for studying liver disease with microphysiological systems on a chip

“…To combat this, a recent focus has been developing microphysiological systems that can be used to study hepatocellular diseases such as NAFLD/NASH and DILI. 203,204 As both NAFLD and ALD have multifactorial etiologies, deciphering the correct biomimetic model to use will depend on the question. Comprehension of how genetic variants confer disease susceptibility is best answered using a sinusoidal focused chip model, comparable to what was accomplished with the sinusoid liver chip, 101 NASH-on-achip, 149 and NAFLD-on-a-chip.…”