vision & plans

My independent research program will leverage my expertise in molecular biology, genomics, epigenomics, metabolomics, and transgenic animal modeling to deepen our understanding of the dysregulated clock and metabolic pathways in metabolic diseases, cancer, and aging. The primary objective is to uncover hitherto unappreciated regulators and mechanisms that interconnect biological clocks and metabolism in response to a variety of nutritional and environmental challenges. My aim is to provide insights into new drug development and fundamental aspects of metabolic diseases and cancer metabolism. To achieve this, I propose the following aims to gain molecular-level insights into metabolic physiology and diseases.

In addition to the well-known 24-hour circadian clock, my recent research has uncovered a distinct 12-hour clock that plays a pivotal role in coordinating metabolic and stress rhythms. Through an extensive analysis of over 3,000 12-hour cycling genes using temporal bulk and single cell RNA-Seq and ChIP-Seq experiments, I have identified novel 12-hour clock transcriptional factors (TFs) and nuclear receptors (NRs) that constitute the machinery of this unique clock. To investigate their roles, I plan to conduct real-time luciferase 12-hour reporter assays in combination with RNAi knockdown and/or CRISPR-knockout techniques. Moreover, I will employ high-resolution microscopy to investigate the spatio-temporal changes occurring in the endoplasmic reticulum (ER), Golgi apparatus, mitochondria, P bodies, and stress granules. This comprehensive analysis will provide valuable insights into the dynamic remodeling of both membrane and membraneless organelles at cellular and physiological levels under metabolic and environmental stresses.

Furthermore, I will develop transgenic animal models to further understand the in vivo roles of these key players and their regulation. By focusing on the novel 12-hour rhythmic control of lipid homeostasis, I aim to shed light on its significance not only in liver diseases, where metabolic stresses reprogram multiple cell functions and interactions, but also in a broader spectrum of metabolic diseases such as type 2 diabetes mellitus (T2DM), obesity, and cancer metabolism. This research holds immense potential to uncover fundamental mechanisms underlying various metabolic diseases and could pave the way for developing novel therapeutics.

While the genetic drivers underlying Non-Alcoholic Fatty Liver Disease (NAFLD) and Hepatocellular Carcinoma (HCC) are still not fully understood, there is a growing recognition of the importance of hepato-immune-sympathetic crosstalk and the fundamental mechanisms governing hepatic fat accumulation, metabolic dysfunction, and inflammatory damage. Additionally, Non-Alcoholic Steatohepatitis (NASH) impairs anti-tumor surveillance in immunotherapy-treated HCC and non-viral NASH-HCC. Currently, our understanding of the hepato-immune-sympathetic crosstalk that regulates normal liver physiology and contributes to NASH development is incomplete. It is crucial to elucidate the constituents and regulatory factors underlying this unknown crosstalk in liver physiology and to decipher the tripartite communication in different liver pathologies.

Leveraging my expertise in multi-omics studies and bioinformatics, I aim to identify drivers and pathways that govern these elusive communications and reprogramming events using various animal models. Firstly, I have already established several mouse models that simulate different forms of human NASH-HCC development, including high-fructose corn syrup (HFCS) feeding, high-fat/low-choline diet, and inorganic arsenic feeding models. Furthermore, I will employ obese (ob/ob) and diabetic (db/db) mouse models to represent metabolic challenges associated with deficient leptin signaling. Secondly, I will integrate single-cell RNA-Seq and ATAC-Seq with immune profiling, iDISCO(+) 3D assessment of sympathetic innervation, and advanced quantitative bioinformatic methods. This integrative approach will enable the identification of transcriptional components responsible for the currently unknown yet critically important hepato-immune-sympathetic crosstalk. Regulator candidates identified in nutritional or toxin stress animal models will undergo comprehensive post-hoc analysis, utilizing publicly available human disease datasets at GEO, protein interaction databases, mouse and human tissue atlases, and the human TCGA Pan-Cancer resources. Thirdly, I will employ a small-molecule library-based strategy to screen for novel drugs targeting NAFLD (dHepaRG cells), HCC cell lines (HepG2 & Huh6/7), and patient-derived xenograft (PDX)-derived organoid models for the treatment of steatosis, steatohepatitis, and HCC. The functional roles of the identified small molecule inhibitors/activators will be determined using single-cell omics with metabolic assays. The efficacy of novel drugs will be evaluated in vivo using the aforementioned nutritional and environmental stress animal models.

The outcomes of this research project will directly contribute to the development of therapeutic interventions for metabolic diseases and associated cancers. By shedding light on the intricate hepato-immune-sympathetic crosstalk and its regulation, this study will pave the way for targeted treatments and improved management of these complex metabolic diseases.

Non-alcoholic fatty liver disease (NAFLD) has emerged as a global epidemic affecting both children and adults. Currently, there are no approved drugs or effective treatments available. This lack of therapeutic options stems from a limited understanding of the metabolic and transcriptional regulation underlying the chronic progression of steatosis and steatohepatitis. The primary objective of this project is to uncover novel transcriptional factors (TFs), nuclear receptors (NRs), and epigenetic regulators that control lipid homeostasis and inflammation in the context of steatosis and steatohepatitis. To achieve this objective, I will employ a comprehensive three-fold approach. First, leveraging my expertise in CRISPR-engineering and NAFLD modeling, I have already established in vitro human cell models for steatosis (dHepaRG+FA) and steatohepatitis (dHepaRG+FA+IL17A) as proof-of-principle. Using a lentiviral-based CRISPR library strategy, I will screen for new TFs, NRs, and epigenetic regulators to identify key drivers/modulators that promote or protect against steatosis and steatohepatitis. Second, I will develop a single-cell metabolomics combined with lipidomics methodology to precisely identify and quantify lipid metabolites and rate-limiting metabolic pathways regulated by the novel targets upon knockout, knockdown, rescue, or inducible expression. In addition to stable human cell lines, I will generate transgenic mouse models targeting these novel regulators (including whole-body, conditional, and inducible animal models) to systematically examine their roles in the initiation and progression of NAFLD in vivo. Furthermore, I will investigate the underlying regulatory mechanisms in lipid metabolism at both cellular organelle levels (membrane and membraneless processes) and the epigenetic and chromatin levels (DNA methylation, histone modification, and chromatin remodeling). Third, I will establish collaborations with clinical facilities/labs to evaluate the extent and nature of these uncharacterized targets in different NAFLD subtypes in situ, as well as in patient-derived xenografts and organoids under various metabolic stress conditions.

The successful identification of novel regulators that promote or protect against NAFLD will not only pave the way for pathway discovery but also hold the potential for the development of effective treatments. I firmly believe that technological advancements and conceptual breakthroughs, combined with rigorous experimental and bioinformatic analyses, offer a timely opportunity to yield exciting findings that will drive progress towards finding a cure for many metabolic diseases.