Browsing by Author "Xu, Jie"
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Item AZI23'UTR Is a New SLC6A3 Downregulator Associated with an Epistatic Protection Against Substance Use Disorders(Springer Nature, 2018-07) Liu, Kefu; Yu, Jinlong; Zhao, Juan; Zhou, Yanhong; Xiong, Nian; Xu, Jie; Wang, Tao; Bell, Richard L.; Qing, Hong; Lin, Zhicheng; Psychiatry, School of MedicineRegulated activity of SLC6A3, which encodes the human dopamine transporter (DAT), contributes to diseases such as substance abuse disorders (SUDs); however, the exact transcription mechanism remains poorly understood. Here, we used a common genetic variant of the gene, intron 1 DNP1B sequence, as bait to screen and clone a new transcriptional activity, AZI23'UTR, for SLC6A3. AZI23'UTR is a 3' untranslated region (3'UTR) of the human 5-Azacytidine Induced 2 gene (AZI2) but appeared to be transcribed independently of AZI2. Found to be present in both human cell nuclei and dopamine neurons, this RNA was shown to downregulate promoter activity through a variant-dependent mechanism in vitro. Both reduced RNA density ratio of AZI23'UTR/AZI2 and increased DAT mRNA levels were found in ethanol-naive alcohol-preferring rats. Secondary analysis of dbGaP GWAS datasets (Genome-Wide Association Studies based on the database of Genotypes and Phenotypes) revealed significant interactions between regions upstream of AZI23'UTR and SLC6A3 in SUDs. Jointly, our data suggest that AZI23'UTR confers variant-dependent transcriptional regulation of SLC6A3, a potential risk factor for SUDs.Item CD23 expression in mantle cell lymphoma is associated with CD200 expression, leukemic non-nodal form, and a better prognosis(Elsevier, 2019) Saksena, Annapurna; Yin, C. Cameron; Xu, Jie; Li, Jingyi; Zhou, Jiehao; Wang, Sa A.; Lin, Pei; Tang, Guilin; Wang, Lifu; Wang, MIchael; Miranda, Roberto N.; Medeiros, L. Jeffrey; Li, Shaoying; Pathology and Laboratory Medicine, School of MedicineMantle cell lymphoma (MCL) is usually CD23 negative, a feature helpful in distinguishing MCL from chronic lymphocytic leukemia/small lymphocytic lymphoma. However, a subset of MCL cases can be CD23+. Limited data are available regarding the clinicopathological features and prognosis of patients with CD23+ MCL. In this study, we reviewed 798 cases of MCL and identified 103 (13%) that were CD23+ by flow cytometry, all of which were positive for cyclin D1 and/or associated with CCND1/IGH. In all cases of CD23+ MCL, CD23 expression was dim partial or dim, unlike moderate to bright CD23 expression observed in chronic lymphocytic leukemia/small lymphocytic lymphoma. The clinicopathological features and outcome of patients with CD23+ MCL were compared with 240 patients with typical MCL negative for CD23. Patients with CD23+ MCL more often had an elevated leukocyte count (33% versus 18%, P = .009), bone marrow involvement (89% versus 78%, P = .02), stage 4 disease (87% versus 77%, P = .03), and a leukemic presentation (42% versus 11%, P = .0001). CD23+ MCL was also more often positive for CD200 (17% versus. 4.6%, P = .0005) and less commonly positive for SOX11 (55% versus. 74%, P = .027). All other clinicopathological features were similar. With similar treatment regimens and observation times, patients with CD23+ MCL had a significant better overall survival (P = .02) and progression-free survival (P = .029). In conclusion, CD23 expression was observed in 13% of MCL cases and is associated with a better prognosis in patients with MCL. CD23 is associated with leukocytosis, a leukemic presentation, bone marrow involvement, CD200 expression, and a lower frequency of SOX11 positivity.Item Diversity and Complexity of the Large Surface Protein Family in the Compacted Genomes of Multiple Pneumocystis Species(American Society for Microbiology, 2020-03-03) Ma, Liang; Chen, Zehua; Huang, Da Wei; Cissé, Ousmane H.; Rothenburger, Jamie L.; Latinne, Alice; Bishop, Lisa; Blair, Robert; Brenchley, Jason M.; Chabé, Magali; Deng, Xilong; Hirsch, Vanessa; Keesler, Rebekah; Kutty, Geetha; Liu, Yueqin; Margolis, Daniel; Morand, Serge; Pahar, Bapi; Peng, Li; Van Rompay, Koen K.A.; Song, Xiaohong; Song, Jun; Sukura, Antti; Thapar, Sabrina; Wang, Honghui; Weissenbacher-Lang, Christiane; Xu, Jie; Lee, Chao-Hung; Jardine, Claire; Lempicki, Richard A.; Cushion, Melanie T.; Cuomo, Christina A.; Kovacs, Joseph A.; Pathology and Laboratory Medicine, School of MedicinePneumocystis, a major opportunistic pathogen in patients with a broad range of immunodeficiencies, contains abundant surface proteins encoded by a multicopy gene family, termed the major surface glycoprotein (Msg) gene superfamily. This superfamily has been identified in all Pneumocystis species characterized to date, highlighting its important role in Pneumocystis biology. In this report, through a comprehensive and in-depth characterization of 459 msg genes from 7 Pneumocystis species, we demonstrate, for the first time, the phylogeny and evolution of conserved domains in Msg proteins and provide a detailed description of the classification, unique characteristics, and phylogenetic relatedness of five Msg families. We further describe, for the first time, the relative expression levels of individual msg families in two rodent Pneumocystis species, the substantial variability of the msg repertoires in P. carinii from laboratory and wild rats, and the distinct features of the expression site for the classic msg genes in Pneumocystis from 8 mammalian host species. Our analysis suggests multiple functions for this superfamily rather than just conferring antigenic variation to allow immune evasion as previously believed. This study provides a rich source of information that lays the foundation for the continued experimental exploration of the functions of the Msg superfamily in Pneumocystis biology.Item Epistatic evidence for gender-dependant slow neurotransmission signalling in substance use disorders: PPP1R12B versus PPP1R1B(Elsevier, 2020-10-21) Liu, Kefu; Zhao, Juan; Chen, Chunnuan; Xu, Jie; Bell, Richard L.; Hall, Frank S.; Koob, George F.; Volkow, Nora D.; Qing, Hong; Lin, Zhicheng; Psychiatry, School of MedicineBackground Slow neurotransmission including DARPP-32 signalling is implicated in substance use disorders (SUDs) by experimental systems but not yet in the human aetiology. PPP1R12B, encoding another protein in the DARPP-32 family, hasn't been studied in the brain. Methods Brain-regional gene activity was assessed in three different animal models of SUDs for mRNA level alterations. Genetic associations were assessed by meta-analysis of pre-existing dbGaP GWAS datasets for main effects and epistasis with known genetic risks, followed by cell type-specific pathway delineation. Parkinson's disease (PD) was included as a dopamine-related disease control for SUDs. Findings In animal models of SUDs, environmentally-altered PPP1R12B expression sex-dependently involves motivation-related brain regions. In humans with polysubstance abuse, meta-analysis of pre-existing datasets revealed that PPP1R12B and PPP1R1B, although expressed in dopamine vs. dopamine-recipient neurons, exerted similar interactions with known genetic risks such as ACTR1B and DRD2 in men but with ADH1B, HGFAC and DRD3 in women. These interactions reached genome-wide significances (Pmeta<10−20) for SUDs but not for PD (disease selectivity: P = 4.8 × 10−142, OR = 6.7 for PPP1R12B; P = 8.0 × 10−8, OR = 2.1 for PPP1R1B). CADM2 was the common risk in the molecular signalling regardless of gender and cell type. Interpretation Gender-dependant slow neurotransmission may convey both genetic and environmental vulnerabilities selectively to SUDs. Funding Grants from National Institute on Drug Abuse (NIDA) and National Institute on Alcohol Abuse and Alcoholism (NIAAA) of U.S.A. and National Natural Science Foundation of China (NSFC).Item GPR68 Senses Flow and Is Essential for Vascular Physiology(Elsevier, 2018-04-19) Xu, Jie; Mathur, Jayanti; Vessières, Emilie; Hammack, Scott; Nonomura, Keiko; Favre, Julie; Grimaud, Linda; Petrus, Matt; Francisco, Allain; Li, Jingyuan; Lee, Van; Xiang, Fu-Li; Mainquist, James K.; Cahalan, Stuart M.; Orth, Anthony P.; Walker, John R.; Ma, Shang; Lukacs, Viktor; Bordone, Laura; Bandell, Michael; Laffitte, Bryan; Xu, Yan; Chien, Shu; Henrion, Daniel; Patapoutian, Ardem; Obstetrics and Gynecology, School of MedicineMechanotransduction plays a crucial role in vascular biology. One example of this is the local regulation of vascular resistance via flow-mediated dilation (FMD). Impairment of this process is a hallmark of endothelial dysfunction and a precursor to a wide array of vascular diseases, such as hypertension and atherosclerosis. Yet the molecules responsible for sensing flow (shear stress) within endothelial cells remain largely unknown. We designed a 384-well screening system that applies shear stress on cultured cells. We identified a mechanosensitive cell line that exhibits shear stress-activated calcium transients, screened a focused RNAi library, and identified GPR68 as necessary and sufficient for shear stress responses. GPR68 is expressed in endothelial cells of small-diameter (resistance) arteries. Importantly, Gpr68-deficient mice display markedly impaired acute FMD and chronic flow-mediated outward remodeling in mesenteric arterioles. Therefore, GPR68 is an essential flow sensor in arteriolar endothelium and is a critical signaling component in cardiovascular pathophysiology.Item Liver-specific in vivo base editing of Angptl3 via AAV delivery efficiently lowers blood lipid levels in mice(BMC, 2023-06-15) Zuo, Yuanbojiao; Zhang, Chen; Zhou, Yuan; Li, Haiwen; Xiao, Weidong; Herzog, Roland W.; Xu, Jie; Zhang, Jifeng; Chen, Y. Eugene; Han, Renzhi; Pediatrics, School of MedicineBackground: Gene editing has emerged as an exciting therapeutic development platform for numerous genetic and nongenetic diseases. Targeting lipid-modulating genes such as angiopoietin-related protein 3 (ANGPTL3) with gene editing offers hope for a permanent solution to lower cardiovascular disease risks associated with hypercholesterolemia. Results: In this study, we developed a hepatocyte-specific base editing therapeutic approach delivered by dual adeno-associated virus (AAV) to enable hepatocyte-specific targeting of Angptl3 to lower blood lipid levels. Systemic AAV9-mediated delivery of AncBE4max, a cytosine base editor (CBE), targeting mouse Angptl3 resulted in the installation of a premature stop codon in Angptl3 with an average efficiency of 63.3 ± 2.3% in the bulk liver tissue. A near-complete knockout of the ANGPTL3 protein in the circulation were observed within 2-4 weeks following AAV administration. Furthermore, the serum levels of triglyceride (TG) and total cholesterol (TC) were decreased by approximately 58% and 61%, respectively, at 4 weeks after treatment. Conclusions: These results highlight the promise of liver-targeted Angptl3 base editing for blood lipid control.Item Potential therapies targeting nuclearmetabolic regulation in cancer(Wiley, 2023-11-29) Chen, Yanjie; Xu, Jie; Liu, Xiaoyi; Guo, Linlin; Yi, Ping; Cheng, Chunming; Microbiology and Immunology, School of MedicineThe interplay between genetic alterations and metabolic dysregulation is increasingly recognized as a pivotal axis in cancer pathogenesis. Both elements are mutually reinforcing, thereby expediting the ontogeny and progression of malignant neoplasms. Intriguingly, recent findings have highlighted the translocation of metabolites and metabolic enzymes from the cytoplasm into the nuclear compartment, where they appear to be intimately associated with tumor cell proliferation. Despite these advancements, significant gaps persist in our understanding of their specific roles within the nuclear milieu, their modulatory effects on gene transcription and cellular proliferation, and the intricacies of their coordination with the genomic landscape. In this comprehensive review, we endeavor to elucidate the regulatory landscape of metabolic signaling within the nuclear domain, namely nuclear metabolic signaling involving metabolites and metabolic enzymes. We explore the roles and molecular mechanisms through which metabolic flux and enzymatic activity impact critical nuclear processes, including epigenetic modulation, DNA damage repair, and gene expression regulation. In conclusion, we underscore the paramount significance of nuclear metabolic signaling in cancer biology and enumerate potential therapeutic targets, associated pharmacological interventions, and implications for clinical applications. Importantly, these emergent findings not only augment our conceptual understanding of tumoral metabolism but also herald the potential for innovative therapeutic paradigms targeting the metabolism–genome transcriptional axis.Item Real-world Effectiveness of BNT162b2 Against Infection and Severe Diseases in Children and Adolescent(medRxiv, 2023-11-13) Wu, Qiong; Tong, Jiayi; Zhang, Bingyu; Zhang, Dazheng; Chen, Jiajie; Lei, Yuqing; Lu, Yiwen; Wang, Yudong; Li, Lu; Shen, Yishan; Xu, Jie; Bailey, L. Charles; Bian, Jiang; Christakis, Dimitri A.; Fitzgerald, Megan L.; Hirabayashi, Kathryn; Jhaveri, Ravi; Khaitan, Alka; Lyu, Tianchen; Rao, Suchitra; Razzaghi, Hanieh; Schwenk, Hayden T.; Wang, Fei; Witvliet, Margot I.; Tchetgen Tchetgen, Eric J.; Morris, Jeffrey S.; Forrest, Christopher B.; Chen, Yong; Pediatrics, School of MedicineBackground: The efficacy of the BNT162b2 vaccine in pediatrics was assessed by randomized trials before the Omicron variant's emergence. The long-term durability of vaccine protection in this population during the Omicron period remains limited. Objective: To assess the effectiveness of BNT162b2 in preventing infection and severe diseases with various strains of the SARS-CoV-2 virus in previously uninfected children and adolescents. Design: Comparative effectiveness research accounting for underreported vaccination in three study cohorts: adolescents (12 to 20 years) during the Delta phase, children (5 to 11 years) and adolescents (12 to 20 years) during the Omicron phase. Setting: A national collaboration of pediatric health systems (PEDSnet). Participants: 77,392 adolescents (45,007 vaccinated) in the Delta phase, 111,539 children (50,398 vaccinated) and 56,080 adolescents (21,180 vaccinated) in the Omicron period. Exposures: First dose of the BNT162b2 vaccine vs. no receipt of COVID-19 vaccine. Measurements: Outcomes of interest include documented infection, COVID-19 illness severity, admission to an intensive care unit (ICU), and cardiac complications. The effectiveness was reported as (1-relative risk)*100% with confounders balanced via propensity score stratification. Results: During the Delta period, the estimated effectiveness of BNT162b2 vaccine was 98.4% (95% CI, 98.1 to 98.7) against documented infection among adolescents, with no significant waning after receipt of the first dose. An analysis of cardiac complications did not find an increased risk after vaccination. During the Omicron period, the effectiveness against documented infection among children was estimated to be 74.3% (95% CI, 72.2 to 76.2). Higher levels of effectiveness were observed against moderate or severe COVID-19 (75.5%, 95% CI, 69.0 to 81.0) and ICU admission with COVID-19 (84.9%, 95% CI, 64.8 to 93.5). Among adolescents, the effectiveness against documented Omicron infection was 85.5% (95% CI, 83.8 to 87.1), with 84.8% (95% CI, 77.3 to 89.9) against moderate or severe COVID-19, and 91.5% (95% CI, 69.5 to 97.6)) against ICU admission with COVID-19. The effectiveness of the BNT162b2 vaccine against the Omicron variant declined after 4 months following the first dose and then stabilized. The analysis revealed a lower risk of cardiac complications in the vaccinated group during the Omicron variant period. Limitations: Observational study design and potentially undocumented infection. Conclusions: Our study suggests that BNT162b2 was effective for various COVID-19-related outcomes in children and adolescents during the Delta and Omicron periods, and there is some evidence of waning effectiveness over time.Item A semi-analytical algorithm for deriving the particle size distribution slope of turbid inland water based on OLCI data: A case study in Lake Hongze(Elsevier, 2021-02) Lei, Shaohua; Xu, Jie; Li, Yunmei; Li, Lin; Lyu, Heng; Liu, Ge; Chen, Yu; Lu, Chunyan; Tian, Chao; Jiao, Wenzhe; Earth Sciences, School of ScienceThe particle size distribution (PSD) slope (ξ) can indicate the predominant particle size, material composition, and inherent optical properties (IOPs) of inland waters. However, few semi-analytical methods have been proposed for deriving ξ from the surface remote sensing reflectance due to the variable optical state of inland waters. A semi-analytical algorithm was developed for inland waters having a wide range of turbidity and ξ in this study. Application of the proposed model to Ocean and Land Color Instrument (OLCI) imagery of the water body resulted in several important observations: (1) the proposed algorithm (754 nm and 779 nm combination) was capable of retrieving ξ with R2 being 0.72 (p < 0.01, n = 60), and MAPE and RMSE being 4.37% and 0.22 (n = 30) respectively; (2) the ξ in HZL was lower in summer than other seasons during the period considered, this variation was driven by the phenological cycle of algae and the runoff caused by rainfall; (3) the band optimization proposed in this study is important for calculating the particle backscattering slope (η) and deriving ξ because it is feasible for both algae dominant and sediment governed turbid inland lakes. These observations help improve our understanding of the relationship between IOPs and ξ, which are affected by different bio-optic processes and algal phenology in the lake environment.