Browsing by Author "Xuan, Zhenyu"
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Item Anaerobic Cysteine Degradation and Potential Metabolic Coordination in Salmonella Enterica and Escherichia Coli(2018-08-24) Loddeke, Melissa; Schneider, Barbara; Oguri, Tamiko; Mehta, Iti; Xuan, Zhenyu; Reitzer, Lawrence J.; Loddeke, Melissa; Schneider, Barbara; Oguri, Tamiko; Mehta, Iti; Xuan, Zhenyu; Reitzer, Lawrence J.Salmonella enterica has two CyuR-activated enzymes that degrade cysteine, i.e., the aerobic CdsH and an unidentified anaerobic enzyme; Escherichia coli has only the latter. To identify the anaerobic enzyme, transcript profiling was performed for E. coli without cyuR and with overexpressed cyuR. Thirty-seven genes showed at least 5-fold changes in expression, and the cyuPA (formerly yhaOM) operon showed the greatest difference. Homology suggested that CyuP and CyuA represent a cysteine transporter and an iron-sulfur-containing cysteine desulfidase, respectively. E. coli and S. enterica Delta cyuA mutants grown with cysteine generated substantially less sulfide and had lower growth yields. Oxygen affected the CyuR-dependent genes reciprocally; cyuP-lacZ expression was greater anaerobically, whereas cdsH-lacZ expression was greater aerobically. In E. coli and S. enterica, anaerobic cyuP expression required cyuR and cysteine and was induced by L-cysteine, D-cysteine, and a few sulfur-containing compounds. Loss of either CyuA or RidA, both of which contribute to cysteine degradation to pyruvate, increased cyuP-lacZ expression, which suggests that CyuA modulates intracellular cysteine concentrations. Phylogenetic analysis showed that CyuA homologs are present in obligate and facultative anaerobes, confirming an anaerobic function, and in archaeal methanogens and bacterial acetogens, suggesting an ancient origin. Our results show that CyuA is the major anaerobic cysteine-catabolizing enzyme in both E. coli and S. enterica, and it is proposed that anaerobic cysteine catabolism can contribute to coordination of sulfur assimilation and amino acid synthesis. IMPORTANCE Sulfur-containing compounds such as cysteine and sulfide are essential and reactive metabolites. Exogenous sulfur-containing compounds can alter the thiol landscape and intracellular redox reactions and are known to affect several cellular processes, including swarming motility, antibiotic sensitivity, and biofilm formation. Cysteine inhibits several enzymes of amino acid synthesis; therefore, increasing cysteine concentrations could increase the levels of the inhibited enzymes. This inhibition implies that control of intracellular cysteine levels, which is the immediate product of sulfide assimilation, can affect several pathways and coordinate metabolism. For these and other reasons, cysteine and sulfide concentrations must be controlled, and this work shows that cysteine catabolism contributes to this control.Item Basal Suppression of the Sonic Hedgehog Pathway by the G-Protein-Coupled Receptor Gpr161 Restricts Medulloblastoma Pathogenesis(Cell Press, 2018-11-05) Shimada, Issei S.; Hwang, Sun-Hee; Somatilaka, Bandarigoda N.; Wang, Xin; Skowron, Patryk; Kim, Jiwoong; Kim, Min; Shelton, John M.; Rajaram, Veena; Xuan, Zhenyu; Taylor, Michael D.; Mukhopadhyay, Saikat; Xuan, ZhenyuSonic hedgehog (Shh) determines cerebellar granule cell (GC) progenitor proliferation and medulloblastoma pathogenesis. However, the pathways regulating GC progenitors during embryogenesis before Shh production by Purkinje neurons and their roles in tumorigenesis remain unclear. The cilium-localized G-protein-coupled receptor Gpr161 suppresses Shh-mediated signaling in the neural tube. Here, by deleting Gpr161 in mouse neural stem cells or GC progenitors, we establish Gpr161 as a tumor suppressor in Shh subtype medulloblastoma. Irrespective of Shh production in the cerebellum, Gpr161 deletion increased downstream activity of the Shh pathway by restricting Gli3-mediated repression, causing more extensive generation and proliferation of GC progenitors. Moreover, earlier deletion of Gpr161 during embryogenesis increased tumor incidence and severity. GC progenitor overproduction during embryogenesis from Gpr161 deletion was cilium dependent, unlike normal development. Low GPR161 expression correlated with poor survival of SHH subtype medulloblastoma patients. Gpr161 restricts GC progenitor production by preventing premature and Shh-dependent pathway activity, highlighting the importance of basal pathway suppression in tumorigenesis.Item Complete Genome Analysis of Three Acinetobacter Baumannii Clinical Isolates in China for Insight into the Diversification of Drug Resistance Elements(2013-06-24) Zhu, Lingxiang; Yan, Zhongqiang; Zhang, Zhaojun; Zhou, Qiming; Zhou, Jinchun; Wakeland, Edward K.; Fang, Xiangdong; Xuan, Zhenyu; Shen, Dingxia; Li, Quan-Zhen; Xuan, ZhenyuBackground: The emergence and rapid spreading of multidrug-resistant Acinetobacter baumannii strains has become a major health threat worldwide. To better understand the genetic recombination related with the acquisition of drug-resistant elements during bacterial infection, we performed complete genome analysis on three newly isolated multidrug-resistant A. baumannii strains from Beijing using next-generation sequencing technology. Methodologies/Principal Findings: Whole genome comparison revealed that all 3 strains share some common drug resistant elements including carbapenem-resistant blaOXA₂₃ and tetracycline (tet) resistance islands, but the genome structures are diversified among strains. Various genomic islands intersperse on the genome with transposons and insertions, reflecting the recombination flexibility during the acquisition of the resistant elements. The blood-isolated BJAB07104 and ascites-isolated BJAB0868 exhibit high similarity on their genome structure with most of the global clone II strains, suggesting these two strains belong to the dominant outbreak strains prevalent worldwide. A large resistance island (RI) of about 121-kb, carrying a cluster of resistance-related genes, was inserted into the ATPase gene on BJAB07104 and BJAB0868 genomes. A 78-kb insertion element carrying tra-locus and blaOXA₂₃ island, can be either inserted into one of the tniB gene in the 121-kb RI on the chromosome, or transformed to conjugative plasmid in the two BJAB strains. The third strains of this study, BJAB0715, which was isolated from spinal fluid, exhibit much more divergence compared with above two strains. It harbors multiple drug-resistance elements including a truncated AbaR-22-like RI on its genome. One of the unique features of this strain is that it carries both blaOXA-23 and blaOXA-58 genes on its genome. Besides, an Acinetobacter lwoffii adeABC efflux element was found inserted into the ATPase position in BJAB0715. Conclusions: Our comparative analysis on currently completed Acinetobacter baumannii genomes revealed extensive and dynamic genome organizations, which may facilitate the bacteria to acquire drug-resistance elements into their genomes.Item Computational Modeling of Long Noncoding RNA Transcriptional Regulation(2018-12) Wang, Haozhe; Xuan, ZhenyuWith work from the past decade and rapid development of high throughput transcriptome sequencing techniques, our knowledge of noncoding RNAs has broadened. The human genome is pervasively transcribed; however, a significant fraction of the transcripts generated from the human genome does not code for proteins. Among noncoding RNAs, long non-coding RNAs (lncRNAs) play a variety of roles, ranging from transcription regulation, controlling chromatin epigenetic state, participating alternative splicing to subnuclear compartment formation. Most lncRNAs exert their functions through the interaction of protein partners. Elucidation of RNAprotein interactions is essential for understanding many critical biological processes. In particular, lncRNAs interact with ribonucleoprotein complexes and numerous chromatin regulators to target appropriate locations in the genome. Based on the support vector machine method, we present LncLink, a computational method used to infer the set of the most probable proteins involved in lncRNA and the genomic regions that they control. We modeled LncLink using data obtained by capture hybridization analysis of RNA targets. The inferences derived from this method are obtained by integrating transcription factor binding sites and genome-wide chromatin interactions as predictive features. To validate the method, we applied LncLink to CHART-seq data obtained from MCF-7 cells to identify putative protein binding partners of lncRNA NEAT1. Our method generated a signature of 27 proteins highly predicted to be involved in NEAT1 interaction and mediating NEAT1 chromatin targeting. Furthermore, several of these proteins have been implicated in NEAT1 binding and NEAT1-mediated transcription in the literature, confirming the reliability of our results. The findings revealed by our work provide novel insights into our understanding of key players targeted by lncRNA.Item The Distinct Metabolic Phenotype of Lung Squamous Cell Carcinoma Defines Selective Vulnerability to Glycolytic Inhibition(Springer Nature, 2018-08-20) Goodwin, Justin; Neugent, Michael L.; Lee, Shin Yup; Choe, Joshua H.; Choi, Hyunsung; Jenkins, Dana M. R.; Ruthenborg, Robin J.; Robinson, Maddox W.; Jeong, Ji Yun; Wake, Masaki; Abe, Hajime; Takeda, Norihiko; Endo, Hiroko; Inoue, Masahiro; Xuan, Zhenyu; Yoo, Hyuntae; Chen, Min; Ahn, Jung-Mo; Xuan, Zhenyu; Yoo, Hyuntae; Chen, Min; Ahn, Jung-Mo; Minna, John D.; Helke, Kristi L.; Singh, Pankaj K.; Shackelford, David B.; Kim, Jung-whan; Goodwin, Justin; Neugent, Michael L.; Lee, Shin Yup; Choe, Joshua H.; Choi, Hyunsung; Jenkins, Dana M. R.; Ruthenborg, Robin J.; Robinson, Maddox W.; Xuan, Zhenyu; Yoo, Hyuntae; Kim, Jung-whanAdenocarcinoma (ADC) and squamous cell carcinoma (SqCC) are the two predominant subtypes of non-small cell lung cancer (NSCLC) and are distinct in their histological, molecular and clinical presentation. However, metabolic signatures specific to individual NSCLC subtypes remain unknown. Here, we perform an integrative analysis of human NSCLC tumour samples, patient-derived xenografts, murine model of NSCLC, NSCLC cell lines and The Cancer Genome Atlas (TCGA) and reveal a markedly elevated expression of the GLUT1 glucose transporter in lung SqCC, which augments glucose uptake and glycolytic flux. We show that a critical reliance on glycolysis renders lung SqCC vulnerable to glycolytic inhibition, while lung ADC exhibits significant glucose independence. Clinically, elevated GLUT1-mediated glycolysis in lung SqCC strongly correlates with high F-18-FDG uptake and poor prognosis. This previously undescribed metabolic heterogeneity of NSCLC subtypes implicates significant potential for the development of diagnostic, prognostic and targeted therapeutic strategies for lung SqCC, a cancer for which existing therapeutic options are clinically insufficient.Item Heme Sequestration as an Effective Strategy for the Suppression of Tumor Growth(2021-08-01T05:00:00.000Z) Wang, Tianyuan; Zhang, Li; Lumata, Lloyd; Kim, Tae Hoon; Spiro, Stephen; Xuan, ZhenyuHeme is an essential prosthetic group in proteins and enzymes involved in oxygen utilization and metabolism. Heme also plays versatile and fascinating roles in regulating fundamental biological processes ranging from aerobic respiration to drug metabolism. Increasing experimental and epidemiological data have also shown that altered heme homeostasis accelerates the development and progression of common diseases, including various cancers, diabetes, vascular diseases, and Alzheimer's disease. The effects of heme on the pathogenesis of these diseases may be mediated via its action on various cellular signaling and regulatory proteins, as well as its function in cellular bioenergetics, specifically, oxidative phosphorylation (OXPHOS). Elevated heme levels in cancer cells intensify OXPHOS, leading to higher ATP generation and fueling tumorigenic functions. In contrast, lowered heme levels in neurons may reduce OXPHOS, leading to defects in bioenergetics and causing neurological deficits. Additionally, heme has been shown to modulate the activities of diverse cellular proteins influencing disease pathogenesis. These include tumor suppressor P53 protein, progesterone receptor membrane component 1 protein PGRMC1, cystathionine-βsynthase CBS, and the nuclear receptor subfamily member Rev-Erbα. Here, we generated small heme-sequestering proteins (HeSPs) based on bacterial hemophores. These HeSPs contain neutral mutations in the heme-binding pocket of hemophores and hybrid sequences from hemophores of different bacteria. We showed that HeSPs bound to heme and effectively extracted heme from hemoglobin. They strongly inhibited heme uptake and cell proliferation and induced apoptosis in non-small lung cancer (NSCLC) cells, while their effects on non-tumorigenic cell lines representing normal lung cells were not significant. HeSPs strongly suppressed the growth of human NSCLC tumor xenografts in mice. HeSPs decreased oxygen consumption rates and ATP levels in tumor cells isolated from treated mice, while they did not affect liver and blood cell functions. Immunohistochemistry revealed that HeSPs reduced the levels of key enzymes and transporters involved in heme synthesis and uptake, as well as the uptake and metabolism of the main fuels for cancer cells, glucose and glutamine. Further, we found that HeSPs reduced the levels of angiogenic and vascular markers, as well as vessel density in tumor tissues. Together, these results demonstrate that HeSPs act via multiple mechanisms, including the inhibition of oxidative phosphorylation, to suppress tumor growth and progression. Evidently, heme sequestration can be a powerful strategy for suppressing lung tumors and likely drug-resistant tumors that rely on oxidative phosphorylation for survival.Item De Novo Deciphering Three-Dimensional Chromatin Interaction and Topological Domains by Wavelet Transformation of Epigenetic Profiles(Oxford University Press, 2016-04-07) Chen, Yong; Wang, Yunfei; Xuan, Zhenyu; Chen, Min; Zhang, Michael Q.; 0000 0001 1707 1372 (Zhang, MQ); 0000-0002-4029-8716 (Chen, M); Chen, Yong; Wang, Yunfei; Xuan, Zhenyu; Chen, Min; Zhang, Michael Q.Defining chromatin interaction frequencies and topological domains is a great challenge for the annotations of genome structures. Although the chromosome conformation capture (3C) and its derivative methods have been developed for exploring the global interactome, they are limited by high experimental complexity and costs. Here we describe a novel computational method, called CITD, for de novo prediction of the chromatin interaction map by integrating histone modification data. We used the public epigenomic data from human fibroblast IMR90 cell and embryonic stem cell (H1) to develop and test CITD, which can not only successfully reconstruct the chromatin interaction frequencies discovered by the Hi-C technology, but also provide additional novel details of chromosomal organizations. We predicted the chromatin interaction frequencies, topological domains and their states (e.g. active or repressive) for 98 additional cell types from Roadmap Epigenomics and ENCODE projects. A total of 131 protein-coding genes located near 78 preserved boundaries among 100 cell types are found to be significantly enriched in functional categories of the nucleosome organization and chromatin assembly. CITD and its predicted results can be used for complementing the topological domains derived from limited Hi-C data and facilitating the understanding of spatial principles underlying the chromosomal organization.Item Prioritization of Cancer-Related Genomic Variants by SNP Association Network(Libertas Academica, 2015-04-01) Liu, Changning; Xuan, Zhenyu; 0000-0001-9344-8493 (Xuan, Z); Xuan, ZhenyuWe have developed a general framework to construct an association network of single nucleotide polymorphisms (SNPs) (SNP association network, SAN) based on the functional interactions of genes located in the flanking regions of SNPs. SAN, which was constructed based on protein-protein interactions in the Human Protein Reference Database (HPRD), showed significantly enriched signals in both linkage disequilibrium (LD) and long-range chromatin interaction (Hi-C). We used this network to further develop two methods for predicting and prioritizing disease-associated genes from genome-wide association studies (GWASs). We found that random walk with restart (RWR) using SAN (RWR-SAN) can greatly improve the prediction of lung-cancer-associated genes by comparing RWR with the use of network in HPRD (AUC 0.81 vs 0.66). In a reanalysis of the GWAS dataset of age-related macular degeneration (AMD), SAN could identify more potential AMD-associated genes that were previously ranked lower in the GWAS study. The interactions in SAN could facilitate the study of complex diseases.Item The Protective Role of Dot1L in UV-Induced Melanomagenesis(Nature Publishing Group, 2018-11-05) Zhu, Bo; Chen, Shuyang; Wang, Hongshen; Yin, Chengqian; Han, Changpeng; Peng, Cong; Liu, Zhaoqian; Wan, Lixin; Zhang, Xiaoyang; Zhang, Jie; Lian, Christine G.; Ma, Peilin; Xu, Zhi-xiang; Prince, Sharon; Wang, Tao; Gao, Xiumei; Shi, Yujiang; Liu, Dali; Liu, Min; Wei, Wenyi; Wei, Zhi; Pan, Jingxuan; Wang, Yongjun; Xuan, Zhenyu; Hess, Jay; Hayward, Nicholas K.; Goding, Colin R.; Chen, Xiang; Zhou, Jun; Cui, Rutao; 0000-0001-9344-8493 (Xuan, Z); Xuan, ZhenyuThe DOT1L histone H3 lysine 79 (H3K79) methyltransferase plays an oncogenic role in MLL-rearranged leukemogenesis. Here, we demonstrate that, in contrast to MLL-rearranged leukemia, DOT1L plays a protective role in ultraviolet radiation (UVR)-induced melanoma development. Specifically, the DOT1L gene is located in a frequently deleted region and undergoes somatic mutation in human melanoma. Specific mutations functionally compromise DOT1L methyltransferase enzyme activity leading to reduced H3K79 methylation. Importantly, in the absence of DOT1L, UVR-induced DNA damage is inefficiently repaired, so that DOT1L loss promotes melanoma development in mice after exposure to UVR. Mechanistically, DOT1L facilitates DNA damage repair, with DOT1L-methylated H3K79 involvement in binding and recruiting XPC to the DNA damage site for nucleotide excision repair (NER). This study indicates that DOT1L plays a protective role in UVR-induced melanomagenesis.Item RNA Control in Sensory Neurons: a Functional Genomics Approach(May 2023) Chase, Rebecca Lynn 1997-; Xuan, Zhenyu; Coskunuzer, Baris; Campbell, Zachary; Sapkota, Darshan; Jia, LinThis work investigates the molecular mechanisms of pain signaling at the level of translation in sensory neurons. Pain-sensing neurons, or nociceptors, are integral to the genesis of many forms of chronic pain. Here, we apply functional genomics approaches to examine the role of translational control in pain. High-throughput sequencing experiments reveal potential molecular targets, which are confirmed using pharmacology, electrophysiology, and behavioral methods. With these methods, we examine the role of the nonsense mediated decay (NMD) pathway, eukaryotic initiation factor 5A (eIF5A), and the S6 ribosomal protein kinase 1 (S6K1) in pain. Along with these findings, we investigate the use of human induced pluripotent stem cell (hiPSC)-derived sensory neurons in pain research using high-throughput RNA sequencing. We also present one of the few datasets employing ribosome profiling on the dorsal root ganglion (DRG) in the presence of inflammatory mediators. Lastly, we show our foundational work linking NMD to pain. Overall, these findings highlight the role of translational control in pain.Item The Swi3 Protein Plays A Unique Role In Regulating Respiration In Eukaryotes(2016-06-30) Lal, Sneha; Alam, Md Maksudul; Hooda, Jagmohan; Shah, Ajit; Cao, Thai M.; Xuan, Zhenyu; Zhang, Li; Lal, Sneha; Alam, Md Maksudul; Hooda, Jagmohan; Shah, Ajit; Cao, Thai M.; Xuan, Zhenyu; Zhang, LiRecent experimental evidence increasingly shows that the dysregulation of cellular bioenergetics is associated with a wide array of common human diseases, including cancer, neurological diseases and diabetes. Respiration provides a vital source of cellular energy for most eukaryotic cells, particularly high energy demanding cells. However, the understanding of how respiration is globally regulated is very limited. Interestingly, recent evidence suggests that Swi3 is an important regulator of respiration genes in yeast. In this report, we performed an array of biochemical and genetic experiments and computational analysis to directly evaluate the function of Swi3 and its human homologues in regulating respiration. First, we showed, by computational analysis and measurements of oxygen consumption and promoter activities, that Swi3, not Swi2, regulates genes encoding functions involved in respiration and oxygen consumption. Biochemical analysis showed that the levels of mitochondrial respiratory chain complexes were substantially increased in Delta swi3 cells, compared with the parent cells. Additionally, our data showed that Swi3 strongly affects haem/oxygen-dependent activation of respiration gene promoters whereas Swi2 affects only the basal, haem-independent activities of these promoters. We found that increased expression of aerobic expression genes is correlated with increased oxygen consumption and growth rates in Delta swi3 cells in air. Furthermore, using computational analysis and RNAi knockdown, we showed that the mammalian Swi3 BAF155 and BAF170 regulate respiration in HeLa cells. Together, these experimental and computational data demonstrated that Swi3 and its mammalian homologues are key regulators in regulating respiration.Item Synthetic Design of Cerium-Based Intermetallics(2021-05-01T05:00:00.000Z) Weiland, Ashley; Chan, Julia; Xuan, Zhenyu; Zheng, Jie; Nielsen, Steven O.; Walker, Amy V.Ce-based highly correlated systems are of interest due to Ce3+ (S=1/2) providing an ideal f-electron system to study the interplay of localized magnetic moments and conduction electrons. The growth of high-quality single crystals is of utmost importance to ensure the determination of intrinsic anisotropic properties. This dissertation presents the single crystal growth and d etailed characterization of Ce-containing intermetallics. Motivated by the search for new spintronic devices based on topological materials, the first study highlights the incorporation of Bi in the topological parent compound, CeSbTe. Sb net containing CeSbTe has been studied to show the interplay of magnetism and topology. Inserting Bi, a larger element, provides the opportunity to change the Fermi surface while preserving topologically relevant features. We show the band structure engineering of potential topological materials LnSb1-xBixTe (Ln = La, Ce, Pr; x ~ 0.2) and CeBiTe. Continuing our search for novel quantum materials, our elucidation of crystal growth parameters of Ce-based intermetallics, led to the identification of a new intermetallic homologous series An+1MnX3n+1 (A = rare earth; M = transition metal; X = tetrels; n = 1 – 6) built up of structural subunits such as AlB2, AuCu3, and BaNiSn3. The homologous series serves as a model system for studying the coupling between localized f-electrons and conduction electrons. Additionally, the stacking of heterostructural subunits is an exciting way to modify physical properties of related phases, highlighting the importance of structural building blocks as a new avenue to study magnetism and topology. Crystal growth, detailed single crystal structural modeling, and magnetic and transport properties of Ce5Co4+xGe13-ySny (n = 4), Ce6Co5+xGe16-ySny (n = 5), and Ce7Co6+xGe19-ySny (n = 6), are presented. The similarities between the synthetic profiles used to grow n = 4 – 6 brought about new questions which led to our work investigating phase formation. Finally, the process for designing in situ synchrotron experiments, including a new sample environment and furnace apparatus for the use with flux grown intermetallics, is presented.