Browsing by Author "Wang, Ergang"
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Item Open Access Antagonizing the irreversible thrombomodulin-initiated proteolytic signaling alleviates age-related liver fibrosis via senescent cell killing.(Cell research, 2023-07) Pan, Christopher C; Maeso-Díaz, Raquel; Lewis, Tylor R; Xiang, Kun; Tan, Lianmei; Liang, Yaosi; Wang, Liuyang; Yang, Fengrui; Yin, Tao; Wang, Calvin; Du, Kuo; Huang, De; Oh, Seh Hoon; Wang, Ergang; Lim, Bryan Jian Wei; Chong, Mengyang; Alexander, Peter B; Yao, Xuebiao; Arshavsky, Vadim Y; Li, Qi-Jing; Diehl, Anna Mae; Wang, Xiao-FanCellular senescence is a stress-induced, stable cell cycle arrest phenotype which generates a pro-inflammatory microenvironment, leading to chronic inflammation and age-associated diseases. Determining the fundamental molecular pathways driving senescence instead of apoptosis could enable the identification of senolytic agents to restore tissue homeostasis. Here, we identify thrombomodulin (THBD) signaling as a key molecular determinant of the senescent cell fate. Although normally restricted to endothelial cells, THBD is rapidly upregulated and maintained throughout all phases of the senescence program in aged mammalian tissues and in senescent cell models. Mechanistically, THBD activates a proteolytic feed-forward signaling pathway by stabilizing a multi-protein complex in early endosomes, thus forming a molecular basis for the irreversibility of the senescence program and ensuring senescent cell viability. Therapeutically, THBD signaling depletion or inhibition using vorapaxar, an FDA-approved drug, effectively ablates senescent cells and restores tissue homeostasis in liver fibrosis models. Collectively, these results uncover proteolytic THBD signaling as a conserved pro-survival pathway essential for senescent cell viability, thus providing a pharmacologically exploitable senolytic target for senescence-associated diseases.Item Open Access Branched-Chain Amino Acid Accumulation Fuels the Senescence-Associated Secretory Phenotype.(Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2023-11) Liang, Yaosi; Pan, Christopher; Yin, Tao; Wang, Lu; Gao, Xia; Wang, Ergang; Quang, Holly; Huang, De; Tan, Lianmei; Xiang, Kun; Wang, Yu; Alexander, Peter B; Li, Qi-Jing; Yao, Tso-Pang; Zhang, Zhao; Wang, Xiao-FanThe essential branched-chain amino acids (BCAAs) leucine, isoleucine, and valine play critical roles in protein synthesis and energy metabolism. Despite their widespread use as nutritional supplements, BCAAs' full effects on mammalian physiology remain uncertain due to the complexities of BCAA metabolic regulation. Here a novel mechanism linking intrinsic alterations in BCAA metabolism is identified to cellular senescence and the senescence-associated secretory phenotype (SASP), both of which contribute to organismal aging and inflammation-related diseases. Altered BCAA metabolism driving the SASP is mediated by robust activation of the BCAA transporters Solute Carrier Family 6 Members 14 and 15 as well as downregulation of the catabolic enzyme BCAA transaminase 1 during onset of cellular senescence, leading to highly elevated intracellular BCAA levels in senescent cells. This, in turn, activates the mammalian target of rapamycin complex 1 (mTORC1) to establish the full SASP program. Transgenic Drosophila models further indicate that orthologous BCAA regulators are involved in the induction of cellular senescence and age-related phenotypes in flies, suggesting evolutionary conservation of this metabolic pathway during aging. Finally, experimentally blocking BCAA accumulation attenuates the inflammatory response in a mouse senescence model, highlighting the therapeutic potential of modulating BCAA metabolism for the treatment of age-related and inflammatory diseases.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.(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 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 Intravital imaging of mouse embryos(Science, 2020-04-10) Huang, Qiang; Cohen, Malkiel A; Alsina, Fernando C; Devlin, Garth; Garrett, Aliesha; McKey, Jennifer; Havlik, Patrick; Rakhilin, Nikolai; Wang, Ergang; Xiang, Kun; Mathews, Parker; Wang, Lihua; Bock, Cheryl; Ruthig, Victor; Wang, Yi; Negrete, Marcos; Wong, Chi Wut; Murthy, Preetish KL; Zhang, Shupei; Daniel, Andrea R; Kirsch, David G; Kang, Yubin; Capel, Blanche; Asokan, Aravind; Silver, Debra L; Jaenisch, Rudolf; Shen, XilingEmbryonic development is a complex process that is unamenable to direct observation. In this study, we implanted a window to the mouse uterus to visualize the developing embryo from embryonic day 9.5 to birth. This removable intravital window allowed manipulation and high-resolution imaging. In live mouse embryos, we observed transient neurotransmission and early vascularization of neural crest cell (NCC)–derived perivascular cells in the brain, autophagy in the retina, viral gene delivery, and chemical diffusion through the placenta. We combined the imaging window with in utero electroporation to label and track cell division and movement within embryos and observed that clusters of mouse NCC-derived cells expanded in interspecies chimeras, whereas adjacent human donor NCC-derived cells shrank. This technique can be combined with various tissue manipulation and microscopy methods to study the processes of development at unprecedented spatiotemporal resolution.Item Open Access Longitudinal intravital imaging of mouse placenta.(Science advances, 2024-03) Zhu, Xiaoyi; Huang, Qiang; Jiang, Laiming; Nguyen, Van-Tu; Vu, Tri; Devlin, Garth; Shaima, Jabbar; Wang, Xiaobei; Chen, Yong; Ma, Lijun; Xiang, Kun; Wang, Ergang; Rong, Qiangzhou; Zhou, Qifa; Kang, Yubin; Asokan, Aravind; Feng, Liping; Hsu, Shiao-Wen D; Shen, Xiling; Yao, JunjieStudying placental functions is crucial for understanding pregnancy complications. However, imaging placenta is challenging due to its depth, volume, and motion distortions. In this study, we have developed an implantable placenta window in mice that enables high-resolution photoacoustic and fluorescence imaging of placental development throughout the pregnancy. The placenta window exhibits excellent transparency for light and sound. By combining the placenta window with ultrafast functional photoacoustic microscopy, we were able to investigate the placental development during the entire mouse pregnancy, providing unprecedented spatiotemporal details. Consequently, we examined the acute responses of the placenta to alcohol consumption and cardiac arrest, as well as chronic abnormalities in an inflammation model. We have also observed viral gene delivery at the single-cell level and chemical diffusion through the placenta by using fluorescence imaging. Our results demonstrate that intravital imaging through the placenta window can be a powerful tool for studying placenta functions and understanding the placental origins of adverse pregnancy outcomes.Item Open Access Non-genetic Alterations in Colorectal Cancer Liver Metastasis and Patient-derived Models(2022) Wang, ErgangColorectal cancer (CRC) is the third most diagnosed type of cancer, and the 5-year survival rate drops significantly once the patient develops liver metastases. Notably, over the past decade, multiple patient-derived models of cancer (PDMC) have been developed and are widely accepted as preclinical models. Current chemotherapy does not distinguish the primary and metastatic loci, and there lack a direct comparison between different PDMC (e.g., patient-derived organoids (PDO), patient-derived xenografts (PDX) and PDO-derived xenografts (PDOX)) and the patient tumor (PT). Therefore, understanding the differences between the cells from metastasized CRC and the primary site, as well as the differences between the PDMC and the original patient specimen is of critical importance.In CRC, many conventional studies have focused on associating genetic mutations with clinical phenotypes. However, non-genetic alterations including changes in chromatin accessibility, transcriptome and histone modification markers provide an alternative and even faster way for the tumor cells to adapt to their microenvironment. In this dissertation, we first focused on how the liver microenvironment can affect the epigenetic transformations of the metastasized CRC. Using high-throughput sequencing such as ATAC-seq, RNA-seq and Mint-ChIP, we identified an HGF-PU.1-DPP4 epigenetic reprogramming axis that facilitates the metastatic tumor cells to adapt to the liver microenvironment. The results were validated by extensive numbers of patient samples and the precision epigenetic modification tools CRISPR/dCas9KRAB/HDAC. We identified several FDA approved drugs including Sitagliptin and Norleual, which can be repurposed to treat CRC liver metastases. Furthermore, using the similar set of tools, we revealed that each PDMC undergo distinctive epigenetic reprogramming following two modeling axes. The first axis delineates PDX and PDO from patient, while the second axis distinguishes PDX and PDO. We further identified that the transcription factors KLF14 and EGR2 are collectively more active in the PDOX than in PDO. Moreover, we demonstrated that the varied expression level of their common downstream targets EPHA4 led to distinct drug responses in PDO to 147 FDA approved compounds. We concluded that there are differences in growth and drug sensitivity between PDOX and PDO, which should be taken into consideration when using PDMC to predict clinical outcomes.