Browsing by Author "Liu, Jing"

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    ARF6 is a Novel Target for Immunotherapy in Triple Negative Breast Cancer
    (2024-07) Moulana, Fathima Ishara; Lu, Xiongbin; Pollok, Karen; Hopewell, Emily; Liu, Jing
    Triple negative breast cancer (TNBC) is one of the most aggressive breast cancer subtypes with poor clinical outcomes due to lack of effective treatments owing to its hormone receptor negative status. Immune checkpoint blockade (ICB) therapy, which prevents the exhaustion of CD8+ T cells, has shown promise in treating these patients. However, only a small proportion respond, possibly due to resistance and immune evasion mechanisms by the tumor cells. A primary mechanism by which tumor cells evade immune surveillance is by reduced tumor antigen presentation, as indicated by a decreased level of antigen-MHC-I (major histocompatibility complex-I) on the surface of tumor cells. The dynamics of tumor antigens on the cell surface and how cell endocytosis contributes to antigen presentation and their recycling is little known. Here we sought to study the roles of two proteins: clathrin and ADP-Ribosylation Factor 6 (ARF6) which are essential for clathrin-mediated endocytosis and clathrin-independent endocytosis respectively, on the surface turnover of fluorophore-conjugated antigenic peptide bound to MHC-I. We employed Total Internal Reflection Fluorescence Microscopy (TIRFM) and Single Molecule Tracking (SMT) to determine the dynamics of tumor antigen endocytosis on the surface of EO771 murine TNBC cells. We found that the inhibition of ARF6 remarkably impaired the endocytosis of the antigen-MHC-I foci, leading to extended stay of the foci on the cell membrane, while inhibition of clathrin did not, suggesting that clathrin-independent endocytosis is the primary route for MHC-I-mediated antigen endocytosis. Consistent with this finding, reduced ARF6 levels promoted in vitro tumor cell killing by CD8+ T cells and suppressed tumor growth in mice when combined with ICB therapy. We further investigated the effect of pharmacological inhibition of ARF6 in murine TNBC cells and splenic CD8+ T cells using a commercially available ARF6 inhibitor NAV-2729. Treatment with NAV-2729 increased surface MHC-I levels and enhanced the secretion of T cell functional markers such as IFN-, TNF- and IL-2, suggesting the possibility of in vivo administration of ARF6 inhibitors in combination with ICB therapy. Collectively, these data suggest that ARF6 is a novel target for the combined treatment with ICB therapy to improve its efficacy in TNBC patients.
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    DNA damage reduces heterogeneity and coherence of chromatin motions
    (National Academy of Science, 2022) Locatelli, Maëlle; Lawrimore, Josh; Lin, Hua; Sanaullah, Sarvath; Seitz, Clayton; Segall, Dave; Kefer, Paul; Moreno, Naike Salvador; Lietz, Benton; Anderson, Rebecca; Holmes, Julia; Yuan, Chongli; Holzwarth, George; Bloom, Kerry S.; Liu, Jing; Bonin, Keith; Vidi, Pierre-Alexandre; Physics, School of Science
    Chromatin motions depend on and may regulate genome functions, in particular the DNA damage response. In yeast, DNA double-strand breaks (DSBs) globally increase chromatin diffusion, whereas in higher eukaryotes the impact of DSBs on chromatin dynamics is more nuanced. We mapped the motions of chromatin microdomains in mammalian cells using diffractive optics and photoactivatable chromatin probes and found a high level of spatial heterogeneity. DNA damage reduces heterogeneity and imposes spatially defined shifts in motions: Distal to DNA breaks, chromatin motions are globally reduced, whereas chromatin retains higher mobility at break sites. These effects are driven by context-dependent changes in chromatin compaction. Photoactivated lattices of chromatin microdomains are ideal to quantify microscale coupling of chromatin motion. We measured correlation distances up to 2 µm in the cell nucleus, spanning chromosome territories, and speculate that this correlation distance between chromatin microdomains corresponds to the physical separation of A and B compartments identified in chromosome conformation capture experiments. After DNA damage, chromatin motions become less correlated, a phenomenon driven by phase separation at DSBs. Our data indicate tight spatial control of chromatin motions after genomic insults, which may facilitate repair at the break sites and prevent deleterious contacts of DSBs, thereby reducing the risk of genomic rearrangements.
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    Enhancing anti-tumor potential: low-intensity vibration suppresses osteosarcoma progression and augments MSCs' tumor-suppressive abilities
    (Ivyspring, 2024-01-27) Xiong, Xue; Huo, Qingji; Li, Kexin; Cui, Changpeng; Chang, Chunyi; Park, Charles; Ku, BonHeon; Hong, Chin-Suk; Lim, HeeChang; Pandya, Pankita H.; Saadatzadeh, M. Reza; Bijangi-Vishehsaraei, Khadijeh; Lin, Chien-Chi; Kacena, Melissa A.; Pollok, Karen E.; Chen, Andy; Liu, Jing; Thompson, William R.; Li, Xue-Lian; Li, Bai-Yan; Yokota, Hiroki; Anatomy, Cell Biology and Physiology, School of Medicine
    Rationale: Osteosarcoma (OS), a common malignant bone tumor, calls for the investigation of novel treatment strategies. Low-intensity vibration (LIV) presents itself as a promising option, given its potential to enhance bone health and decrease cancer susceptibility. This research delves into the effects of LIV on OS cells and mesenchymal stem cells (MSCs), with a primary focus on generating induced tumor-suppressing cells (iTSCs) and tumor-suppressive conditioned medium (CM). Methods: To ascertain the influence of vibration frequency, we employed numerical simulations and conducted experiments to determine the most effective LIV conditions. Subsequently, we generated iTSCs and CM through LIV exposure and assessed the impact of CM on OS cells. We also explored the underlying mechanisms of the tumor-suppressive effects of LIV-treated MSC CM, with a specific focus on vinculin (VCL). We employed cytokine array, RNA sequencing, and Western blot techniques to investigate alterations in cytokine profiles, transcriptomes, and tumor suppressor proteins. Results: Numerical simulations validated LIV frequencies within the 10-100 Hz range. LIV induced notable morphological changes in OS cells and MSCs, confirming its dual role in inhibiting OS cell progression and promoting MSC conversion into iTSCs. Upregulated VCL expression enhanced MSC responsiveness to LIV, significantly bolstering CM's efficacy. Notably, we identified tumor suppressor proteins in LIV-treated CM, including procollagen C endopeptidase enhancer (PCOLCE), histone H4 (H4), peptidylprolyl isomerase B (PPIB), and aldolase A (ALDOA). Consistently, cytokine levels decreased significantly in LIV-treated mouse femurs, and oncogenic transcript levels were downregulated in LIV-treated OS cells. Moreover, our study demonstrated that combining LIV-treated MSC CM with chemotherapy drugs yielded additive anti-tumor effects. Conclusions: LIV effectively impeded the progression of OS cells and facilitated the transformation of MSCs into iTSCs. Notably, iTSC-derived CM demonstrated robust anti-tumor properties and the augmentation of MSC responsiveness to LIV via VCL. Furthermore, the enrichment of tumor suppressor proteins within LIV-treated MSC CM and the reduction of cytokines within LIV-treated isolated bone underscore the pivotal tumor-suppressive role of LIV within the bone tumor microenvironment.
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    A guide for single-particle chromatin tracking in live cell nuclei
    (Wiley, 2022) Zhang, Mengdi; Seitz, Clayton; Chang, Garrick; Iqbal, Fadil; Lin, Hua; Liu, Jing; Physics, School of Science
    The emergence of labeling strategies and live cell imaging methods enables the imaging of chromatin in living cells at single digit nanometer resolution as well as milliseconds temporal resolution. These technical breakthroughs revolutionize our understanding of chromatin structure, dynamics and functions. Single molecule tracking algorithms are usually preferred to quantify the movement of these intranucleus elements to interpret the spatiotemporal evolution of the chromatin. In this review, we will first summarize the fluorescent labeling strategy of chromatin in live cells which will be followed by a systematic comparison of live cell imaging instrumentation. With the proper microscope, we will discuss the image analysis pipelines to extract the biophysical properties of the chromatin. Finally, we expect to give practical suggestions to broad biologists on how to select methods and link to the model properly according to different investigation purposes. This article is protected by copyright. All rights reserved.
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    Histone Deacetylase Inhibitors Prevent Cytokine-Induced β Cell Dysfunction Through Restoration of Stromal Interaction Molecule 1 Expression and Activation of Store-Operated Calcium Entry
    (bioRxiv, 2023-12-08) Lee, Chih-Chun; Kono, Tatsuyoshi; Syed, Farooq; Weaver, Staci A.; Sohn, Paul; Wu, Wenting; Chang, Garrick; Liu, Jing; Slak Rupnik, Marjan; Evans-Molina, Carmella; Pediatrics, School of Medicine
    Histone deacetylase inhibitors (HDIs) modulate β cell function in preclinical models of diabetes; however, the mechanisms underlying these beneficial effects have not been determined. In this study, we investigated the impact of the HDI sodium butyrate (NaB) on β cell function and calcium (Ca2+) signaling using ex vivo and in vitro models of diabetes. Our results show that NaB significantly improved glucose-stimulated insulin secretion in islets from human organ donors with type 2 diabetes and in cytokine-treated INS-1 β cells. Consistently, NaB partially rescued glucose-stimulated Ca2+ oscillations in mouse islets treated with proinflammatory cytokines. Because the oscillatory phenotype of Ca2+ in the β cell is governed by changes in endoplasmic reticulum (ER) Ca2+ levels, next we explored the relationship between NaB and store-operated calcium entry (SOCE), a rescue mechanism that acts to refill ER Ca2+ levels through STIM1-mediated gating of plasmalemmal Orai channels. We found that NaB treatment preserved basal ER Ca2+ levels and restored SOCE in IL-1β-treated INS-1 cells. Furthermore, we linked these changes with the restoration of STIM1 levels in cytokine-treated INS-1 cells and mouse islets, and we found that NaB treatment was sufficient to prevent β cell death in response to IL-1β treatment. Mechanistically, NaB counteracted cytokine-mediated reductions in phosphorylation levels of key signaling molecules, including AKT, ERK1/2, glycogen synthase kinase-3α (GSK-3α), and GSK-3β. Taken together, these data support a model whereby HDI treatment promotes β cell function and Ca2+ homeostasis under proinflammatory conditions through STIM1-mediated control of SOCE and AKT-mediated inhibition of GSK-3.
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    Histone deacetylase inhibitors protect against cisplatin-induced acute kidney injury by activating autophagy in proximal tubular cells
    (Nature Publishing group, 2018-02-23) Liu, Jing; Livingston, Man J.; Dong, Guie; Tang, Chengyuan; Su, Yunchao; Wu, Guangyu; Yin, Xiao-Ming; Dong, Zheng; Pathology and Laboratory Medicine, School of Medicine
    Histone deacetylase inhibitors (HDACi) have therapeutic effects in models of various renal diseases including acute kidney injury (AKI); however, the underlying mechanism remains unclear. Here we demonstrate that two widely tested HDACi (suberoylanilide hydroxamic acid (SAHA) and trichostatin A (TSA)) protect the kidneys in cisplatin-induced AKI by enhancing autophagy. In cultured renal proximal tubular cells, SAHA and TSA enhanced autophagy during cisplatin treatment. We further verified the protective effect of TSA against cisplatin-induced apoptosis in these cells. Notably, inhibition of autophagy by chloroquine or by autophagy gene 7 (Atg7) ablation diminished the protective effect of TSA. In mice, TSA increased autophagy in renal proximal tubules and protected against cisplatin-induced AKI. The in vivo effect of TSA was also abolished by chloroquine and by Atg7 knockout specifically from renal proximal tubules. Mechanistically, TSA stimulated AMPK and inactivated mTOR during cisplatin treatment of proximal tubule cells and kidneys in mice. Together, these results suggest that HDACi may protect kidneys by activating autophagy in proximal tubular cells.
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    Impact of Proinflammatory Cytokines on Alternative Splicing Patterns in Human Islets
    (American Diabetes Association, 2021) Wu, Wenting; Syed, Farooq; Simpson, Edward; Lee, Chih-Chun; Liu, Jing; Chang, Garrick; Dong, Chuanpeng; Seitz, Clayton; Eizirik, Decio L.; Mirmira, Raghavendra G.; Liu, Yunlong; Evans-Molina, Carmella; Medical and Molecular Genetics, School of Medicine
    Alternative splicing (AS) within the β-cell has been proposed as one potential pathway that may exacerbate autoimmunity and unveil novel immunogenic epitopes in type 1 diabetes (T1D). We used a computational strategy to prioritize pathogenic splicing events in human islets treated with interleukin-1β plus interferon-γ as an ex vivo model of T1D and coupled this analysis with a k-mer–based approach to predict RNA-binding proteins involved in AS. In total, 969 AS events were identified in cytokine-treated islets, with a majority (44.8%) involving a skipped exon. ExonImpact identified 129 events predicted to affect protein structure. AS occurred with high frequency in MHC class II–related mRNAs, and targeted quantitative PCR validated reduced inclusion of exon 5 in the MHC class II gene HLA-DMB. Single-molecule RNA fluorescence in situ hybridization confirmed increased HLA-DMB splicing in β-cells from human donors with established T1D and autoantibody positivity. Serine/arginine-rich splicing factor 2 was implicated in 37.2% of potentially pathogenic events, including exon 5 exclusion in HLA-DMB. Together, these data suggest that dynamic control of AS plays a role in the β-cell response to inflammatory signals during T1D evolution.
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    Investigation of PT Symmetry Breaking and Exceptional Points in Delay-coupled Semiconductor Lasers
    (2021-08) Wilkey, Andrew; Vemuri, Gautam; Joglekar, Yogesh; Liu, Jing; Ou, Jeff; Petrache, Horia
    This research investigates characteristics of PT (parity-time) symmetry breaking in a system of two optically-coupled, time-delayed semiconductor lasers. A theoretical rate equation model for the lasers' electric fields is presented and then reduced to a 2x2 Hamiltonian model, which, in the absence of time-delay, is PT-symmetric. The important parameters we control are the temporal separation of the lasers, the frequency detuning, and the coupling strength. The detuning is experimentally controlled by varying the lasers' temperatures, and intensity vs. detuning behavior are examined, specifically how the PT-transition and the period and amplitude of sideband intensity oscillations change with coupling and delay. Experiments are compared to analytic predictions and numerical results, and all are found to be in good agreement. Eigenvalues, eigenvectors, and exceptional points of the reduced Hamiltonian model are numerically and analytically investigated, specifically how nonzero delay affects existing exceptional points.
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    Laser Shock Tuning Dynamic Interlayer Coupling in Graphene–Boron Nitride Moiré Superlattices
    (ACS, 2019) Kumar, Prashant; Liu, Jing; Motlag, Maithilee; Tong, Lei; Hu, Yaowu; Huang, Xinyu; Bandopadhyay, Arkamita; Pati, Swapan K.; Ye, Lei; Irudayaraj, Joseph; Cheng, Gary J.; Physics, School of Science
    In the emergence of graphene and many two-dimensional (2D) materials, the most exciting applications come from stacking them into 3D devices, promising many excellent possibilities for neoteric electronics and optoelectronics. Layers of semiconductors, insulators, and conductors can be stacked to form van der Waals heterostructures, after the weak bonds formed between the layers. However, the interlayer coupling in these heterostructures is usually hard to modulate, resulting in difficulty to realize their emerging optical or electronic properties. Especially, the relationship between interlayer distance and interlayer coupling remains to be investigated, due to the lack of effective technology. In this work, we have used laser shocking to controllably tune the interlayer distance between graphene (Gr) and boron nitride (BN) in the Gr/BN/Gr heterostructures and the strains in the 2D heterolayers, providing a simple and effective way to modify their optic and electronic properties. After lase shocking, the reduction of interlayer distance is calculated by molecular dynamics (MD) simulation. Some atoms in Gr or BN are out-of-plane as well. In Raman measurements, the G peak in the heterostructure shows a red-shifted trend after laser shocking, indicating the strong phonon coupling in the interlayer. Moreover, the larger transparency after laser shocking also verifies the stronger photon coupling in the heterostructure. To investigate the effects of the interlayer coupling of heterostructure on its out-of-plane electronic behavior, we have investigated the electronic tunneling behavior. The heterostructure after laser shock reveals a lager tunneling current and lower tunneling threshold, proving an unexpected better electrical property. From DFT calculations, laser shocking can modulate the band gap structure of graphene in Gr/BN/Gr heterostructures; therefore, the heterostructures can be implemented as a unique photonic platform to modulate the emission characters of the anchored CdSe/ZnS core–shell quantum dots. Remarkably, the effective laser shocking method is also applicable to various otherwise noninteracting 2D materials, resulting in many new phenomena, which will lead science and technology to unexplored territories.
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    Loading-induced antitumor capability of murine and human urine
    (Wiley, 2020-06) Wu, Di; Fan, Yao; Liu, Shengzhi; Woollam, Mark D.; Sun, Xun; Murao, Eiji; Zha, Rongrong; Prakash, Rahul; Park, Charles; Siegel, Amanda P.; Liu, Jing; Agarwal, Mangilal; Li, Bai-Yan; Yokota, Hiroki; Biomedical Engineering, School of Engineering and Technology
    While urine has been considered as a useful bio-fluid for health monitoring, its dynamic changes to physical activity are not well understood. We examined urine's possible antitumor capability in response to medium-level, loading-driven physical activity. Urine was collected from mice subjected to 5-minute skeletal loading and human individuals before and after 30-minute step aerobics. Six cancer cell lines (breast, prostate, and pancreas) and a mouse model of the mammary tumor were employed to evaluate the effect of urine. Compared to urine collected prior to loading, urine collected post-activity decreased the cellular viability, proliferation, migration, and invasion of tumor cells, as well as tumor weight in the mammary fat pad. Detection of urinary volatile organic compounds and ELISA assays showed that the loading-conditioned urine reduced cholesterol and elevated dopamine and melatonin. Immunohistochemical fluorescent images presented upregulation of the rate-limiting enzymes for the production of dopamine and melatonin in the brain. Molecular analysis revealed that the antitumor effect was linked to the reduction in molecular vinculin-linked molecular force as well as the downregulation of the Lrp5-CSF1-CD105 regulatory axis. Notably, the survival rate for the high expression levels of Lrp5, CSF1, and CD105 in tumor tissues was significantly lowered in the Cancer Genome Atlas database. Collectively, this study revealed that 5- or 10-minute loading-driven physical activity was sufficient to induce the striking antitumor effect by activating the neuronal signaling and repressing cholesterol synthesis. The result supported the dual role of loading-conditioned urine as a potential tumor suppressor and a source of diagnostic biomarkers.