Browsing by Author "Chen, Tianyi"
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Item Open Access Chromatin remodeling in peripheral blood cells reflects COVID-19 symptom severity.(bioRxiv, 2020-12-05) Giroux, Nicholas S; Ding, Shengli; McClain, Micah T; Burke, Thomas W; Petzold, Elizabeth; Chung, Hong A; Palomino, Grecia R; Wang, Ergang; Xi, Rui; Bose, Shree; Rotstein, Tomer; Nicholson, Bradly P; Chen, Tianyi; Henao, Ricardo; Sempowski, Gregory D; Denny, Thomas N; Ko, Emily R; Ginsburg, Geoffrey S; Kraft, Bryan D; Tsalik, Ephraim L; Woods, Christopher W; Shen, XilingSARS-CoV-2 infection triggers highly variable host responses and causes varying degrees of illness in humans. We sought to harness the peripheral blood mononuclear cell (PBMC) response over the course of illness to provide insight into COVID-19 physiology. We analyzed PBMCs from subjects with variable symptom severity at different stages of clinical illness before and after IgG seroconversion to SARS-CoV-2. Prior to seroconversion, PBMC transcriptomes did not distinguish symptom severity. In contrast, changes in chromatin accessibility were associated with symptom severity. Furthermore, single-cell analyses revealed evolution of the chromatin accessibility landscape and transcription factor motif occupancy for individual PBMC cell types. The most extensive remodeling occurred in CD14+ monocytes where sub-populations with distinct chromatin accessibility profiles were associated with disease severity. Our findings indicate that pre-seroconversion chromatin remodeling in certain innate immune populations is associated with divergence in symptom severity, and the identified transcription factors, regulatory elements, and downstream pathways provide potential prognostic markers for COVID-19 subjects.Item Open Access Chromatin Remodeling of Colorectal Cancer Liver Metastasis is Mediated by an HGF-PU.1-DPP4 Axis.(Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2021-10) Wang, Lihua; Wang, Ergang; Prado Balcazar, Jorge; Wu, Zhenzhen; Xiang, Kun; Wang, Yi; Huang, Qiang; Negrete, Marcos; Chen, Kai-Yuan; Li, Wei; Fu, Yujie; Dohlman, Anders; Mines, Robert; Zhang, Liwen; Kobayashi, Yoshihiko; Chen, Tianyi; Shi, Guizhi; Shen, John Paul; Kopetz, Scott; Tata, Purushothama Rao; Moreno, Victor; Gersbach, Charles; Crawford, Gregory; Hsu, David; Huang, Emina; Bu, Pengcheng; Shen, XilingColorectal cancer (CRC) metastasizes mainly to the liver, which accounts for the majority of CRC-related deaths. Here it is shown that metastatic cells undergo specific chromatin remodeling in the liver. Hepatic growth factor (HGF) induces phosphorylation of PU.1, a pioneer factor, which in turn binds and opens chromatin regions of downstream effector genes. PU.1 increases histone acetylation at the DPP4 locus. Precise epigenetic silencing by CRISPR/dCas9KRAB or CRISPR/dCas9HDAC revealed that individual PU.1-remodeled regulatory elements collectively modulate DPP4 expression and liver metastasis growth. Genetic silencing or pharmacological inhibition of each factor along this chromatin remodeling axis strongly suppressed liver metastasis. Therefore, microenvironment-induced epimutation is an important mechanism for metastatic tumor cells to grow in their new niche. This study presents a potential strategy to target chromatin remodeling in metastatic cancer and the promise of repurposing drugs to treat metastasis.Item Open Access Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion.(Res Sq, 2022-04-07) Giroux, Nicholas S; Ding, Shengli; McClain, Micah T; Burke, Thomas W; Petzold, Elizabeth; Chung, Hong A; Rivera, Grecia O; Wang, Ergang; Xi, Rui; Bose, Shree; Rotstein, Tomer; Nicholson, Bradly P; Chen, Tianyi; Henao, Ricardo; Sempowski, Gregory D; Denny, Thomas N; De Ussel, Maria Iglesias; Satterwhite, Lisa L; Ko, Emily R; Ginsburg, Geoffrey S; Kraft, Bryan D; Tsalik, Ephraim L; Shen, Xiling; Woods, ChristopherSARS-CoV-2 infection triggers profound and variable immune responses in human hosts. Chromatin remodeling has been observed in individuals severely ill or convalescing with COVID-19, but chromatin remodeling early in disease prior to anti-spike protein IgG seroconversion has not been defined. We performed the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and RNA-seq on peripheral blood mononuclear cells (PBMCs) from outpatients with mild or moderate symptom severity at different stages of clinical illness. Early in the disease course prior to IgG seroconversion, modifications in chromatin accessibility associate with mild or moderate symptoms are already robust and include severity-associated changes in accessibility of genes in interleukin signaling, regulation of cell differentiation and cell morphology. Furthermore, single-cell analyses revealed evolution of the chromatin accessibility landscape and transcription factor motif accessibility for individual PBMC cell types over time. The most extensive remodeling occurred in CD14+ monocytes, where sub-populations with distinct chromatin accessibility profiles were observed prior to seroconversion. Mild symptom severity is marked by upregulation classical antiviral pathways including those regulating IRF1 and IRF7, whereas in moderate disease these classical antiviral signals diminish suggesting dysregulated and less effective responses. Together, these observations offer novel insight into the epigenome of early mild SARS-CoV-2 infection and suggest that detection of chromatin remodeling in early disease may offer promise for a new class of diagnostic tools for COVID-19.Item Open Access Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion.(Scientific reports, 2022-07-09) Giroux, Nicholas S; Ding, Shengli; McClain, Micah T; Burke, Thomas W; Petzold, Elizabeth; Chung, Hong A; Rivera, Grecia O; Wang, Ergang; Xi, Rui; Bose, Shree; Rotstein, Tomer; Nicholson, Bradly P; Chen, Tianyi; Henao, Ricardo; Sempowski, Gregory D; Denny, Thomas N; De Ussel, Maria Iglesias; Satterwhite, Lisa L; Ko, Emily R; Ginsburg, Geoffrey S; Kraft, Bryan D; Tsalik, Ephraim L; Shen, Xiling; Woods, Christopher WSARS-CoV-2 infection triggers profound and variable immune responses in human hosts. Chromatin remodeling has been observed in individuals severely ill or convalescing with COVID-19, but chromatin remodeling early in disease prior to anti-spike protein IgG seroconversion has not been defined. We performed the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and RNA-seq on peripheral blood mononuclear cells (PBMCs) from outpatients with mild or moderate symptom severity at different stages of clinical illness. Early in the disease course prior to IgG seroconversion, modifications in chromatin accessibility associated with mild or moderate symptoms were already robust and included severity-associated changes in accessibility of genes in interleukin signaling, regulation of cell differentiation and cell morphology. Furthermore, single-cell analyses revealed evolution of the chromatin accessibility landscape and transcription factor motif accessibility for individual PBMC cell types over time. The most extensive remodeling occurred in CD14+ monocytes, where sub-populations with distinct chromatin accessibility profiles were observed prior to seroconversion. Mild symptom severity was marked by upregulation of classical antiviral pathways, including those regulating IRF1 and IRF7, whereas in moderate disease, these classical antiviral signals diminished, suggesting dysregulated and less effective responses. Together, these observations offer novel insight into the epigenome of early mild SARS-CoV-2 infection and suggest that detection of chromatin remodeling in early disease may offer promise for a new class of diagnostic tools for COVID-19.Item Open Access Single-cell Transcriptome Profiling Reveals Hedgehog Critically Regulates Hepatocyte Resiliency(2022) Chen, TianyiAs the largest organ in the body, liver is responsible for maintaining systemic metabolic homeostasis, and also plays an important role in immune functions. Nutrients absorbed through the gastrointestinal tract are processed by the liver and are either stored or distributed to other organs to provide energy. When these metabolic processes become unbalanced, fat builds up in the liver and hepatic steatosis may ensue. Current global estimates indicate non-alcoholic fatty liver disease (NAFLD) afflicts at least 25% of adults worldwide and is the leading cause of cirrhosis and liver cancer. It remains challenging to individualize treatment for NAFLD because its prevalence and severity vary considerably among patients depending on their age, gender, inheritable traits, and even environmental factors. For the past several decades, substantial resources have been devoted to studying this disease and our understanding of its pathogenesis has advanced. Nevertheless, there are currently no effective therapies approved specifically for preventing or treating non-alcoholic steatohepatitis (NASH; the inflammatory liver injury that develops when fatty hepatocytes experience lipotoxicity) or cirrhosis (the end result of maladaptive efforts to repair NASH that replace lipotoxic hepatocytes with scar).Hence, it is critical to improve understanding of the mechanisms that cause hepatic steatosis (NAFL) to progress to steatohepatitis (NASH), as well as the mechanisms that determine whether NASH resolves, stabilizes or progresses to cirrhosis. In the work presented here I focused on Hedgehog, a lipid-sensing developmental morphogenic pathway, and uncovered how its regulation mediates multiple hepatocyte functions in adult livers, including metabolic homeostasis and the regenerative response to liver injury. These findings not only clarify why hepatocytes lose their resiliency as NAFLD advances to cirrhosis, but also reveal novel therapeutic targets that we might manipulate to restore hepatocyte function, improve recovery from NASH, and prevent NAFLD-related cirrhosis and liver cancer. Hedgehog signaling plays a key role in tissue patterning during embryo development. Until recently, activity of this pathway was presumed to be silenced in healthy adults because dysregulated gain-of-function mutations and epigenetic activation of this pathway has been implicated in hepatocellular carcinoma and many other cancer types. To thoroughly investigate the role of Hedgehog in adult liver, we utilized a viral vector-based approach to study whether disruption of Hedgehog in healthy mature hepatocytes evokes any phenotype of interest. We discovered that mice with Hedgehog-deficient hepatocytes rapidly developed NAFLD within a week as characterized by hepatic accumulation of fatty acids, triglyceride and cholesterol, providing strong evidence that Hedgehog is active and broadly regulates lipid metabolism in adult liver. Using single-cell transcriptomic profiling, we demonstrated that Hedgehog activity was spatially restricted to hepatocytes localized in the mid-lobular area. By manipulating Hedgehog activity in hepatocytes of intact mice and challenging them with an acute intraportal injection of insulin, we demonstrated that disruption of Hedgehog induced steatohepatitis, and caused hepatic and systemic insulin resistance by stimulating the mTOR pathway. Further in silico analyses and in vitro studies revealed that Hedgehog pathway disruption evoked mitochondrial dysfunction and induced pre-mature aging. Importantly, analysis of human bulk RNA-seq datasets revealed an inverse relationship between Hedgehog activity and the severity of liver fibrosis, such that activity of this pathway declined progressively as lipotoxicity, and fibrosis severity worsened in NAFLD. These results suggest Hedgehog controls hepatocyte resiliency in adult livers. Loss of hepatocyte Hedgehog activity induces metabolic stress, disrupts energy homeostasis, and promotes NAFLD and its metabolic sequela. NAFLD encompasses a broad spectrum of fatty liver damage because both lipid-related injury (lipotoxicity) and responses to prevent and repair injury are quite dynamic. During the early stage of NAFLD (known as NAFL or hepatic steatosis), most people are asymptomatic. However, when excessive fat accumulation in hepatocytes is accompanied by recurrent bouts of lipotoxicity, inflammation and wound healing, hepatocyte death increases, marking the transition to NASH. When lipotoxicity persists and repair responses are maladaptive chronically, functional hepatocytes cannot be replaced and scarring (fibrosis) progresses; cirrhosis eventually results and risk for liver cancer is increased. Because our initial studies showed that Hedgehog is critical for maintaining liver metabolic homeostasis and thus, regulates susceptibility to NAFL and NASH, we also studied whether hepatocyte Hedgehog activity might be important for the liver to respond appropriately to a regenerative challenge and thereby, impact susceptibility to cirrhosis and/or liver cancer... Using single-cell technology, we first studied how individual hepatocytes with normal Hedgehog activity respond to liver injury to achieve robust regeneration. We discovered that when challenged to regenerate, mature hepatocytes functionally diversify. Some continue to fulfill liver specific functions, while others undergo dedifferentiation to give rise to a fetal-like progenitor population that can be further subdivided into hepatic, biliary and bipotent lineages. Work by us and others indicates that adult-to-fetal reprogramming is a reversible pre-requisite for effective liver regeneration and suggest that changes in Hedgehog signaling may be involved in the process. Remarkably, when we disrupted Hedgehog signaling in hepatocytes, formation of both hepatic and bipotent proliferative progenitors was abrogated; the dedifferentiation process became skewed towards biliary cells and liver regeneration was inhibited significantly. Together, these results demonstrate that hepatocyte Hedgehog activity is critical for effective liver repair and that failure to activate this signaling impairs hepatocyte regeneration by interrupting hepatic lineage specification during the adult-to-fetal reprogramming. Together, these studies reveal that Hedgehog has fundamental roles in regulating liver homeostasis and regeneration. My research uncovers hepatic and systemic responses that are orchestrated by Hedgehog. In particular, the single-cell transcriptome data provide a powerful resource that will enable discovery of unique hepatocyte states in both normal and diseased livers, including NAFLD. Importantly, the new data also have implications for pathology in other organs that become damaged due to metabolic stress.