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Sohr A, Du L, Roy S. Ex vivo Drosophila Wing Imaginal Disc Culture and Furin Inhibitor Assay. Bio Protoc 2019; 9:e3336. [PMID: 33654841 PMCID: PMC7854222 DOI: 10.21769/bioprotoc.3336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/22/2019] [Accepted: 07/22/2019] [Indexed: 11/02/2022] Open
Abstract
Furin is an evolutionarily conserved proprotein convertase (PC) family enzyme with a broad range of substrates that are essential for developmental, homeostatic, and disease pathways. Classical genetic approaches and in vitro biochemical or cell biological assays identified that precursor forms of most growth factor family proteins are processed by Furin. To quantitatively assess the potential role of Furin in cleaving and modulating intercellular dispersion of a Drosophila signaling protein, we developed a simple assay by combining genetics, ex vivo organ culture, pharmacological treatment, and imaging analyses. The protocol herein describes how to ex vivo culture Drosophila wing imaginal discs expressing a fluorescently tagged Drosophila Fibroblast Growth Factor (FGF, Branchless/Bnl) over a long period of time in the presence of Furin inhibitors and monitor the cleavage and intercellular dispersion of the truncated Bnl parts using microscopy. Although the assay described here is for assessing the effect of Furin inhibition on Bnl cleavage in the Drosophila larval wing imaginal disc, the principle and methodology can easily be adopted for any other signals, tissue systems, or organisms. This strategy and protocol provide an assay for examining Furin activity on a specific substrate by directly visualizing the spatiotemporal distribution of its truncated parts in an ex vivo-cultured organ.
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Li K, Bai J, Du L, Wang X, Ke C, Yan W, Li C, Ren L, Han H, Zhao Y. Generation of porcine monoclonal antibodies based on single cell technologies. Vet Immunol Immunopathol 2019; 215:109913. [PMID: 31420069 DOI: 10.1016/j.vetimm.2019.109913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/17/2019] [Accepted: 07/30/2019] [Indexed: 01/03/2023]
Abstract
The development of a rapid and efficient system to generate porcine monoclonal antibodies (mAbs) is an important step toward the discovery of critical neutralizing targets for designing rational vaccines against porcine viruses. In this study, we established a platform for producing porcine mAbs based on single cell technologies. First, we singled out an optimal donor from 507 pigs based on serum antibody neutralizing activity against porcine reproductive and respiratory syndrome virus (PRRSV). After identifying the contribution of IgG to the neutralizing activity, single CD45R+IgG+Ag+ B cells were sorted from peripheral blood mononuclear cells (PBMCs). Single B cell RT-PCR was performed using primers designed to cover the germline repertoire of the porcine VH/VL gene segments. Paired VH/VLs were cloned into a eukaryotic expression vector and transfected into 293T cells. We demonstrate that full-length porcine mAbs were produced, and antigen-specific mAbs were obtained after further validation. The approach reported in this study can be applied to generate porcine mAbs against any given antigen and may help with the screening of neutralizing antibodies against porcine pathogens.
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Li B, Brady SW, Ma X, Shen S, Zhang Y, Li Y, Liu Y, Wang N, Flasch D, Myers M, Mulder H, Ding L, Lu Y, Tian L, Hagiwara K, Xu K, Sioson E, Wang T, Yang L, Zhao J, Zhang H, Shao Y, Sun H, Sun L, Cai J, Lin TN, Du L, Yang F, Rusch M, Edmonson M, Easton J, Zhu X, Zhang J, Cheng C, Raphael B, Tang J, Downing J, Zhou BB, Pui CH, Yang J, Zhang J. Abstract 2872: Acquisition of drug resistance mutations during chemotherapy treatment in pediatric acute lymphoblastic leukemia. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Acute lymphoblastic leukemia (ALL) is a leading cause of cancer-associated death in children. To study the mechanisms of drug resistance in ALL, we performed whole-genome sequencing of diagnosis-relapse-germline trios from 103 Chinese patients and ultra-deep sequencing of 208 serial bone marrow samples from 17 of them. Relapse-specific somatic alterations were enriched in 12 genes (NR3C1, NR3C2, TP53, NT5C2, FPGS, CREBBP, MSH2, MSH6, PMS2, WHSC1, PRPS1, and PRPS2), which were predominantly involved in response to thiopurines, glucocorticoids, methotrexate, and other drugs. Four lines of evidence indicate that these resistance mutations frequently developed during treatment, rather than pre-existing at diagnosis. First, two novel, relapse-specific mutational signatures (novel signatures 1 and 2), most likely caused by chemotherapeutic regimens, were detected in 15% and 14% of relapsed cases, respectively. Drug resistance mutations frequently appeared at novel signature-associated trinucleotide contexts, indicating that chemotherapy may directly cause drug resistance mutations in ALL. The signatures were validated in NCI TARGET relapsed ALL samples, 2% and 23% of which harbored novel signatures 1 and 2, respectively. The varying signature prevalence between cohorts may reflect treatment differences. The novel signatures were not detected in >2,000 adult cancers from the PCAWG study. Novel signature 1 induced C>G transversions, particularly at GCC and TCT trinucleotides, and showed transcription-strand bias indicating guanine adducts. Novel signature 2 favored C>T and C>G mutations at CCG, and correlated with relapse-specific dinucleotide variants and structural variants, indicating an agent causing multiple mutation types. The drugs inducing these novel signatures are being explored in vitro. Second, mathematical modeling using growth curves of drug-resistant ALL indicated that drug resistance mutations occur, in some cases, long after diagnosis, during active treatment. Third, some patients acquired multiple drug resistance mutations sequentially through successive relapses, a finding inconsistent with their pre-existence at diagnosis. Indeed, 20% of relapses had multiple drug resistance mutations targeting different drug classes. Fourth, most relapsed ALLs derived from a subclone detected at diagnosis, which then evolved additional mutations, including drug resistance mutations, not detectable at diagnosis using 2000X targeted sequencing. Drug resistance mutations were often subclonal at relapse, suggesting later appearance. Together these data indicate that fully drug-resistant clones may not necessarily pre-exist at diagnosis in ALL, but may be acquired later during treatment. Thus, early intensive or targeted treatment strategies in slow responders may forestall the subsequent development of drug resistance mutations.
Citation Format: Benshang Li, Samuel W. Brady, Xiaotu Ma, Shuhong Shen, Yingchi Zhang, Yongjin Li, Yu Liu, Ningling Wang, Diane Flasch, Matthew Myers, Heather Mulder, Lixia Ding, Yanling Lu, Liqing Tian, Kohei Hagiwara, Ke Xu, Edgar Sioson, Tianyi Wang, Liu Yang, Jie Zhao, Hui Zhang, Ying Shao, Hongye Sun, Lele Sun, Jiaoyang Cai, Ting-Nien Lin, Lijuan Du, Fan Yang, Michael Rusch, Michael Edmonson, John Easton, Xiaofan Zhu, Jingliao Zhang, Cheng Cheng, Benjamin Raphael, Jingyan Tang, James Downing, Bin-Bing Zhou, Ching-Hon Pui, Jun Yang, Jinghui Zhang. Acquisition of drug resistance mutations during chemotherapy treatment in pediatric acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2872.
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Xu C, Zeng R, Chen Q, Du L, Tong J, He Y, Xu H, Li M. Curcumin suppresses interleukin-6 production in THP-1 monocytes induced by Propionibacterium acnes extracts via downregulation of Toll-like receptor 2 expression and the nuclear factor kappa B pathway. Br J Dermatol 2019; 181:1320-1322. [PMID: 31209872 DOI: 10.1111/bjd.18228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Yang P, Du L, Ye Z. How To Deal With Uveitis Patients? Curr Mol Med 2019; 17:468-470. [PMID: 29424311 DOI: 10.2174/1566524018666180207153342] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/15/2017] [Accepted: 02/02/2018] [Indexed: 11/22/2022]
Abstract
During the past nine years, our center has grown into the largest uveitis referral center in China. To deal with this increasing stream of patients we have developed a management system to coordinate communication with our patients, their referring ophthalmologists, consultations with other medical specialties and worldrenowned foreign uveitis specialists. We have established the biggest database of uveitis patients records allowing continuous analysis of clinical features and response to treatment of patients with various uveitis entities as well as the evaluation of the relevance of various ancillary tests performed in this patient group. The establishment of a specimen biobank has been shown to be instrumental in the research on the complex immunopathological mechanisms involved in this disease. The close interaction between patient care and clinical research under one roof has led to a novel understanding of disease mechanisms and will undoubtedly lead to a tailored treatment for this disease.
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Wang Y, Dai S, Cheng X, Prado E, Yan L, Hu J, He Q, Lv Y, Lv Y, Du L. Notch3 signaling activation in smooth muscle cells promotes extrauterine growth restriction-induced pulmonary hypertension. Nutr Metab Cardiovasc Dis 2019; 29:639-651. [PMID: 30954415 DOI: 10.1016/j.numecd.2019.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND AIMS Early postnatal life is a critical developmental period that affects health of the whole life. Extrauterine growth restriction (EUGR) causes cardiovascular development problems and diseases, including pulmonary arterial hypertension (PAH). PAH is characterized by proliferation, migration, and anti-apoptosis of pulmonary artery smooth muscle cells (PASMCs). However, the role of PASMCs in EUGR has not been studied. Thus, we hypothesized that PASMCs dysfunction played a role in EUGR-induced pulmonary hypertension. METHODS AND RESULTS Here we identified that postnatal nutritional restriction-induced EUGR rats exhibited an elevated mean pulmonary arterial pressure and vascular remodeling at 12 weeks old. PASMCs of EUGR rats showed increased cell proliferation and migration features. In EUGR-induced PAH rats, Notch3 signaling was activated. Relative mRNA and protein expression levels of Notch3 intracellular domain (Notch3 ICD), and Notch target gene Hey1 in PASMCs were upregulated. We further demonstrated that pharmacological inhibition of Notch3 activity by using a γ-secretase inhibitor DAPT, which blocked the cleavage of Notch proteins to ICD peptides, could effectively inhibit PASMC proliferation. Specifically knocked down of Notch3 in rat PASMCs by shRNA restored the abnormal PASMC phenotype in vitro. We found that administration of Notch signaling inhibitor DAPT could successfully reduce mean pulmonary arterial pressure in EUGR rats. CONCLUSIONS The present study demonstrated that upregulation of Notch3 signaling in PASMCs was crucial for the development of EUGR-induced PAH. Blocking Notch3-Hey1 signaling pathway in PASMCs provides a potential therapeutic target for PAH.
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MESH Headings
- Animals
- Animals, Newborn
- Arterial Pressure
- Basic Helix-Loop-Helix Transcription Factors/genetics
- Basic Helix-Loop-Helix Transcription Factors/metabolism
- Caloric Restriction
- Cell Movement
- Cell Proliferation
- Disease Models, Animal
- Growth Disorders/complications
- Growth Disorders/metabolism
- Hypertension, Pulmonary/etiology
- Hypertension, Pulmonary/metabolism
- Hypertension, Pulmonary/pathology
- Hypertension, Pulmonary/physiopathology
- Male
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Pulmonary Artery/metabolism
- Pulmonary Artery/pathology
- Pulmonary Artery/physiopathology
- Rats, Sprague-Dawley
- Receptor, Notch3/genetics
- Receptor, Notch3/metabolism
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Signal Transduction
- Vascular Remodeling
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Li F, Ma X, Du L, Shi L, Cao Q, Li N, Pang T, Liu Y, Kijlstra A, Yang P. Identification of susceptibility SNPs in CTLA-4 and PTPN22 for scleritis in Han Chinese. Clin Exp Immunol 2019; 197:230-236. [PMID: 30921471 DOI: 10.1111/cei.13298] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2019] [Indexed: 12/12/2022] Open
Abstract
The aim of this study was to determine the association between 13 single nucleotide polymorphisms (SNPs) in the cytotoxic T lymphocyte-associated antigen-4 (CTLA4) and protein tyrosine phosphatase non-receptor type 22 (PTPN22) genes with scleritis in a Chinese Han population. We recruited 432 scleritis patients and 710 healthy controls. Four tag SNPs of CTLA4 and nine tag SNPs of PTPN22 were selected using Haploview. Genotyping was performed with the Sequenom MassArray® iPLEX GOLD Assay. Genotype and allele frequency differences were analyzed by χ2 test and Bonferroni correction. Haplotype analysis was performed to further evaluate the association of these two genes with scleritis. In this study, CTLA4/rs3087243 G allele frequency and GG genotype frequency were significantly increased in scleritis patients compared to healthy controls [corrected P-value (Pc) = 0·02, odds ratio (OR) = 1·475, 95% confidence interval (CI) = 1·175-1·851; Pc = 0·04, OR = 1·546, 95% CI = 1·190-2·008, respectively]. None of the tested SNPs in the PTPN22 gene showed an association with scleritis. Haplotype analysis revealed a lower frequency of a CTLA4 TCAA haplotype (order of SNPs: rs733618, rs5742909, rs231775, rs3087243) (Pc = 4·26 × 10-3 , OR = 0·618, 95% CI = 0·540-0·858) and a higher frequency of a PTPN22 TTATACGCG haplotype (order of SNPs: rs3789604, rs150426536, rs1746853, rs1217403, rs1217406, rs3789609, rs1217414, rs3789612, rs2488457) (Pc = 2·83 × 10-4 , OR = 1·457, 95% CI = 1·210-1·754) in scleritis patients when compared to healthy controls. In conclusion, our findings indicate that CTLA4 and PTPN22 might confer genetic susceptibility to scleritis in a Chinese Han population.
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Peng Z, Sun YH, Zhu HM, Gui M, Du L, Zhang DZ, Ren H. [Dynamic analysis of the academic influence in Chinese Journal of Hepatology from 2010 to 2016]. ZHONGHUA GAN ZANG BING ZA ZHI = ZHONGHUA GANZANGBING ZAZHI = CHINESE JOURNAL OF HEPATOLOGY 2019; 26:457-459. [PMID: 30317761 DOI: 10.3760/cma.j.issn.1007-3418.2018.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To dynamically analyze the discipline status, influence factors and key issues of Chinese Journal of Hepatology from 2010 to 2016 and explore the development rules of citation indexes. Methods: We collected information published by the China Institute of Scientific and Technological Information [China Science and Technology Journal Citation Report (Core Edition)] and Wanfang Database Periodicals statistical analysis platform from 2010 to 2016. A bibliometric analyses on article volume, citation frequency, citation rate, h-index, ratio of fund-aided papers, periodical influence, key number published period, number of relevant articles, and so on were analyzed for annual's impact factor. Results: According to the data released by the China Institute of Science and Technology Information, from 2010 to 2011, the impact factor of Chinese Journal of Hepatology was at leading level in the field of internal medicine and ranked sixth in the Journal of Internal Medicine. From 2012 to 2016, the overall comprehensive assessment score and citation frequency score of Chinese Journal of Hepatology were ranked first in the Journal of Gastroenterology. Core impact factors kept the discipline ahead. Indexes such as immediacy index, h- index, cited half-life and all other indicators were increased. Citation rate was >90% and cited issue number had greatly increased. Conclusion: Chinese Journal of Hepatology has a leading position in the Journal of Gastroenterology and credited by inland readers and authors of digestive and infectious fields. It has played a positive role in promoting the development of the discipline.
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Horn L, Whisenant J, Wakelee H, Reckamp K, Qiao H, Du L, Hernandez J, Huang V, Waqar S, Patel S, Sanborn R, Shaffer T, Garg K, Holzhausen A, Harrow K, Liang C, Lim L, Li M, Lovly C. Circulating tumor (ct) DNA analysis to monitor response and resistance to ensartinib in patients (pts) with ALK+ non-small cell lung cancer (NSCLC). Ann Oncol 2019. [DOI: 10.1093/annonc/mdz063.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Chen Z, Zou J, Chen B, Du L, Wang M. Protecting books from mould damage by decreasing paper bioreceptivity to fungal attack using decoloured cell-free supernatant of Lysobacter enzymogenes C3. J Appl Microbiol 2019; 126:1772-1784. [PMID: 30920096 DOI: 10.1111/jam.14265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/27/2019] [Accepted: 03/21/2019] [Indexed: 11/28/2022]
Abstract
AIMS To evaluate whether decoloured cell-free supernatant of Lysobacter enzymogenes C3 can decrease paper bioreceptivity to fungal attack. METHODS AND RESULTS To prepare colourless C3 supernatant, single-factor design and uniform design were applied. The optimum conditions with high decolouration degree and low antifungal activity loss were achieved as follows: carbon granule content 1·6% (M/V), temperature 27°C, decolouring time 1·2 h and pH 8·0. An agar plate bioassay was used to assess the antifungal activity of the decoloured supernatant against the fungal isolates obtained from contaminated books, and strong suppression was observed. Small-sacle laboratory test was further introduced, in which common book papers were artificially inoculated with the fungal isolates, and then sprayed uniformly with decoloured supernatant or water. The results showed that, after treatment, the paper showed a significantly low extent of fungal colonization and high tensile strength, and maintained the same colour before and after treatment. CONCLUSION These results suggest that the decoloured C3 supernatant inhibits fungal growth on types of paper commonly used in books. SIGNIFICANCE AND IMPACT OF THE STUDY Decoloured C3 supernatant could be used as a preventive agent to protect books and other paper-based items against fungal growth.
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Du L, Gallinger Z. A250 POTENTIAL OF ADAPTIVE DESIGNS TO ADDRESS CURRENT CHALLENGES IN TRIAL EVALUATION OF TREATMENTS FOR CROHN’S DISEASE. J Can Assoc Gastroenterol 2019. [DOI: 10.1093/jcag/gwz006.249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Du L, Jackson TD, Chong RY, Nguyen GC. A72 NUTRITIONAL INDICATORS AND POSTOPERATIVE OUTCOMES IN INFLAMMATORY BOWEL DISEASE: THE NSQIP SURGICAL COHORT. J Can Assoc Gastroenterol 2019. [DOI: 10.1093/jcag/gwz006.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Sohr A, Du L, Wang R, Lin L, Roy S. Drosophila FGF cleavage is required for efficient intracellular sorting and intercellular dispersal. J Cell Biol 2019; 218:1653-1669. [PMID: 30808704 PMCID: PMC6504889 DOI: 10.1083/jcb.201810138] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/30/2019] [Accepted: 02/05/2019] [Indexed: 01/15/2023] Open
Abstract
Bnl controls tracheal development in Drosophila, but it is unclear how this fibroblast growth factor is prepared for tissue-specific dispersal. Sohr et al. find that Furin1 cleaves Bnl in the Golgi, which polarizes its sorting to the basal surface of the source cells and determines its range of cytoneme-mediated intercellular dispersion, signaling, and branching morphogenesis. How morphogenetic signals are prepared for intercellular dispersal and signaling is fundamental to the understanding of tissue morphogenesis. We discovered an intracellular mechanism that prepares Drosophila melanogaster FGF Branchless (Bnl) for cytoneme-mediated intercellular dispersal during the development of the larval Air-Sac-Primordium (ASP). Wing-disc cells express Bnl as a proprotein that is cleaved by Furin1 in the Golgi. Truncated Bnl sorts asymmetrically to the basal surface, where it is received by cytonemes that extend from the recipient ASP cells. Uncleavable mutant Bnl has signaling activity but is mistargeted to the apical side, reducing its bioavailability. Since Bnl signaling levels feedback control cytoneme production in the ASP, the reduced availability of mutant Bnl on the source basal surface decreases ASP cytoneme numbers, leading to a reduced range of signal/signaling gradient and impaired ASP growth. Thus, enzymatic cleavage ensures polarized intracellular sorting and availability of Bnl to its signaling site, thereby determining its tissue-specific intercellular dispersal and signaling range.
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Marczyk M, Fu C, Lau R, Du L, Trevarton AJ, Sinn BV, Gould RE, Symmans WF, Hatzis C. Abstract P4-08-20: Pre-analytical effects of FFPE extraction methods on targeted and whole transcriptome sequencing assays for endocrine sensitivity in metastatic breast cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p4-08-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The clinical management of patients with metastatic HR-positive breast cancer is often uncertain due to decreased sensitivity to anti-estrogen therapy over time. Recently, we developed a targeted RNAseq based 18-transcript SET ER/PR assay of endocrine sensitivity from biopsies of metastatic cancer. In this work we assess the effect of pre-analytical factors, specifically RNA extraction methods for FFPE tissue samples, on the reliability of the targeted RNAseq assay.
Methods: FFPE blocks and matched fresh frozen (FF) sections from 12 tumors were collected at MD Anderson Cancer Center. RNA from FFPE slides was extracted in duplicate using three kits (Norgen, Qiagen, Roche), and RNAseq libraries from all samples were prepared using Kapa Total RNAseq kit. Targeted RNA libraries were prepared using droplet-based PCR (RainDance), and also by transcriptome-wide RNAseq for comparison. Reads were mapped to genomic sequence using STAR and expression was quantified using RSEM. Expression data were normalized based on expression of 10 reference genes. The effect of FFPE RNA extraction kit on the reliability of the SET index was assessed using linear mixed effects model (LME) analysis, and agreement with FF was assessed using the concordance correlation coefficient (CCC).
Results: Analysis of the whole transcriptome RNAseq data confirmed minimal 3'-end transcript bias from FFPE samples, irrespective of transcript size or FFPE kit. All 18 genes included in the SET index had high overall concordance between FFPE and FF (median CCC percentile=98.8, range 57.2-99.9 for Norgen; similar for the other two kits) and relatively consistent bias across genes, as estimated by the random effects of the LME model. Furthermore, compared to random 18-gene indices, concordance in the SET index values between FF and FFPE was higher than 99.8% of the random samples, verifying the analytical reliability of the selected genes. For the targeted RNAseq assay, RNA from FFPE extracted with the Norgen kit showed the highest concordance compared to FF (CCC=0.956, 95%CI 0.871-0.985). In general, the analytical variation of SET from FFPE samples was greater than that from FF (1.71-2.71 fold greater), with the lowest variation associated with the Norgen kit. The SET index values from targeted RNAseq for both FF and FFPE samples were consistently lower compared to transcriptome-wide RNAseq but were highly correlated, with the Norgen kit having the highest correlation between targeted and transcriptome-wide RNAseq (rho=0.915).
Conclusions: All three FFPE RNA extraction kits have excellent analytical performance compared to FF samples. The Norgen kit may be marginally better yielding higher concordance with FF and lower analytical variation between replicates. All genes in the SET ER/PR showed very good analytical performance in comparison to random indices and individual genes. Targeted gene RNA sequencing appears very promising as a platform for clinical deployment of quantitative assays, showing only a small (fixable) bias compared to RNAseq.
Citation Format: Marczyk M, Fu C, Lau R, Du L, Trevarton AJ, Sinn BV, Gould RE, Symmans WF, Hatzis C. Pre-analytical effects of FFPE extraction methods on targeted and whole transcriptome sequencing assays for endocrine sensitivity in metastatic breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-08-20.
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Du L, Yang F, Fang H, Sun H, Chen Y, Xu Y, Li H, Zheng L, Zhou BBS. AICAr suppresses cell proliferation by inducing NTP and dNTP pool imbalances in acute lymphoblastic leukemia cells. FASEB J 2019; 33:4525-4537. [PMID: 30702927 DOI: 10.1096/fj.201801559rr] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
It has been shown that 5-amino-4-imidazolecarboxamide riboside (AICAr) can inhibit cell proliferation and induce apoptosis in childhood acute lymphoblastic leukemia (ALL) cells. Although AICAr could regulate cellular energy metabolism by activating AMPK, the cytotoxic mechanisms of AICAr are still unclear. Here, we knocked out TP53 or PRKAA1 gene (encoding AMPKα1) in NALM-6 and Reh cells by using the clustered regularly interspaced short palindromic repeats/Cas9 system and found that AICAr-induced proliferation inhibition was independent of AMPK activation but dependent on p53. Liquid chromatography-mass spectrometry analysis of nucleotide metabolites indicated that AICAr caused an increase in adenosine triphosphate, deoxyadenosine triphosphate, and deoxyguanosine triphosphate levels by up-regulating purine biosynthesis, while AICAr led to a decrease in cytidine triphosphate, uridine triphosphate, deoxycytidine triphosphate, and deoxythymidine triphosphate levels because of reduced phosphoribosyl pyrophosphate production, which consequently impaired the pyrimidine biosynthesis. Ribonucleoside triphosphate (NTP) pool imbalances suppressed the rRNA transcription efficiency. Furthermore, deoxy-ribonucleoside triphosphate (dNTP) pool imbalances induced DNA replication stress and DNA double-strand breaks, followed by cell cycle arrest and apoptosis in ALL cells. Exogenous uridine could rebalance the NTP and dNTP pools by supplementing pyrimidine and then attenuate AICAr-induced cytotoxicity. Our data indicate that RNA transcription inhibition and DNA replication stress induced by NTP and dNTP pool imbalances might play a key role in AICAr-mediated cytotoxic effects on ALL cells, suggesting a potential clinical application of AICAr in future ALL therapy.-Du, L., Yang, F., Fang, H., Sun, H., Chen, Y., Xu, Y., Li, H., Zheng, L., Zhou, B.-B. S. AICAr suppresses cell proliferation by inducing NTP and dNTP pool imbalances in acute lymphoblastic leukemia cells.
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Jia S, Li J, Sui G, Du L, Zhang Y, Zhuang Y, Li B. Synthesis of 3D flower-like structured Gd/TiO2@rGO nanocomposites via a hydrothermal method with enhanced visible-light photocatalytic activity. RSC Adv 2019; 9:31177-31185. [PMID: 35529388 PMCID: PMC9072527 DOI: 10.1039/c9ra06045f] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 09/23/2019] [Indexed: 12/03/2022] Open
Abstract
In this study, novel Gd/TiO2@rGO (GTR) nanocomposites with high photocatalytic performance were fabricated via a one-pot solvothermal approach. During the preparation step, graphene oxide (GO) was reduced to reduced graphene oxide (rGO), and subsequently, on the surfaces of which anatase TiO2 doped with Gd metal was grown in situ with a 3D petal-like structure. Gd doping into the classical TiO2@rGO system efficiently expands the absorption range of light, improves the separation of photogenerated electrons, and increases the photocatalytic reaction sites. The specific surface areas, morphological structures, and valence and conduction bands of the obtained GTR nanocomposites were analyzed and correlated with their enhanced photocatalytic performances for the degradation of an aqueous RhB solution. The experimental results indicated that the best performance was achieved with the 3% GTR composite, which exhibited the highest photoelectrocatalytic activity because of two aspects: the rapid separation of electrons and holes, and improvement in adsorption capacity. As compared with pure TiO2, the GTR composites demonstrated enhanced photoactivity due to synergetic effects between the effective photo-induced electron transfer from TiO2 to the surface of the rGO acceptor through interfacial interactions and the variation of structure and electrons under the adoption of Gd. One-pot green synthesis of 3D flower-like structured Gd/TiO2@rGO nanocomposites via a hydrothermal method with high photocatalytic activity.![]()
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Du L, Li T, Wu S, Zhu HF, Zou FY. Electrospun composite nanofibre fabrics containing green reduced Ag nanoparticles as an innovative type of antimicrobial insole. RSC Adv 2019; 9:2244-2251. [PMID: 35516127 PMCID: PMC9059877 DOI: 10.1039/c8ra08363k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 12/31/2018] [Indexed: 11/21/2022] Open
Abstract
In this study, polyvinyl alcohol (PVA) nanofibrous membranes containing silver nanoparticles (Ag NPs) were successfully fabricated by the combination of electrospinning and a green reduction approach. Through the electrospinning technique, uniform and smooth nanofibres can be obtained, and the Ag NPs with a narrow size distributions are well dispersed in PVA nanofibres. The investigation indicates that the mass ratio of reductant tea polyphenols and AgNO3 play a crucial role in controlling the size of the Ag NPs. More importantly, multi-layered fabrics with a layer of PVA/Ag NP nanofibrous membrane layered onto cotton substrates were developed and applied to shoe insoles. The fabricated shoe insoles with functionalized PVA nanofibres exhibit remarkable antimicrobial activity against both E. coli and S. aureus (i.e. antibacterial rate > 99%). The creation of such an encouraging fabric could establish a new optimization methodology for producing nanoengineered functional textiles. This study aims to develop an antimicrobial insole with an electrospun nanofibre mat which contains green reduced Ag NPs by a facile fabrication method.![]()
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Du L, Xie HN, Zheng J, He M. [Analysis of copy number variation by CMA in fetus with increased nuchal translucency]. ZHONGHUA FU CHAN KE ZA ZHI 2018; 53:671-676. [PMID: 30369122 DOI: 10.3760/cma.j.issn.0529-567x.2018.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigated the clinical value of chromosomal microarray analysis (CMA) in fetuses with increased nuchal translucency (NT) . Methods: Totally 101 cases out of 19 261 singleton fetuses who underwent the first trimester (11-13+6 weeks) ultrasound examination from January 2015 to June 2017 at First Affiliated Hospital of Sun Yat-sen University were diagnosed with NT ≥2.5 mm and underwent invasive prenatal test for fetal karyotype and CMA. According to the combination of other ultrasound abnormalities, the cases were divided into isolated group (67.3%, 68/101) and complicated group (32.7%, 33/101) . In addition, the cases were divided into 5 groups according to the thickness of NT, 2.5-2.9 mm (borderline thickening; 16.8%, 17/101) , 3.0-3.4 mm (33.7%, 34/101) , 3.5-4.4 mm (16.8%, 17/101) , 4.5-5.4 mm (15.8%, 16/101) , and ≥5.5 mm (16.8%, 17/101) . Chi square test was used to detect the different rates of other combined ultrasound abnormalities and abnormal chromosome between 5 groups. Results: The median thickness of NT was 3.4 mm (2.5-8.5 mm) . And 32 cases (31.7%, 32/101) had abnormal karyotype. There was a significant difference in the frequency of abnormal karyotype between the isolated and the complicated group (20.6% vs 54.5%, P<0.01) . Among 69 cases (68.3%, 69/101) of normal karyotype, 3 cases (4.3%, 3/69) were detected with pathogenic copy number variation (CNV) by CMA. Thirty-five cases with chromosomal abnormalities (include abnormal karyotype and pathogenic CNV) , there was a significant difference in the frequency of chromosomal abnormalities between the isolated and the complicated group (23.5% vs 57.6%, P=0.001) . The median age of pregnant women in 5 groups was 35 years (24-39 years) , 33 years (23-46 years) , 31 years (21-46 years) , 33 years (21-41 years) and 35 years (21-43 years) . The rates of chromosomal abnormalities increased with the increase of NT thickness. There was significant difference in the incidence of associated chromosomal abnormalities among 5 groups (P<0.05) . Comparative analysis within the 5 groups, the incidence of associated chromosomal abnormalities between NT 2.5-2.9 mm and ≥5.5 mm was significantly different (P=0.005) , while the differences between the other groups were not significant (P>0.05) . Conclusions: There is a high risk of fetal chromosomal abnormalities in borderline NT thickening (2.5-2.9 mm) at advanced maternal age, but the pathogenic CNV is not detected. Chromosomal microdeletion or microduplication could be further detected in the NT thickening (≥3.0 mm) fetuses with normal karyotype by chromosome microarray analysis, while the positive rate is relatively low, and the variants of unknown significance might be detected.
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Du L, Sohr A, Yan G, Roy S. Feedback regulation of cytoneme-mediated transport shapes a tissue-specific FGF morphogen gradient. eLife 2018; 7:38137. [PMID: 30328809 PMCID: PMC6224196 DOI: 10.7554/elife.38137] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 10/16/2018] [Indexed: 12/22/2022] Open
Abstract
Gradients of signaling proteins are essential for inducing tissue morphogenesis. However, mechanisms of gradient formation remain controversial. Here we characterized the distribution of fluorescently-tagged signaling proteins, FGF and FGFR, expressed at physiological levels from the genomic knock-in alleles in Drosophila. FGF produced in the larval wing imaginal-disc moves to the air-sac-primordium (ASP) through FGFR-containing cytonemes that extend from the ASP to contact the wing-disc source. The number of FGF-receiving cytonemes extended by ASP cells decreases gradually with increasing distance from the source, generating a recipient-specific FGF gradient. Acting as a morphogen in the ASP, FGF activates concentration-dependent gene expression, inducing pointed-P1 at higher and cut at lower levels. The transcription-factors Pointed-P1 and Cut antagonize each other and differentially regulate formation of FGFR-containing cytonemes, creating regions with higher-to-lower numbers of FGF-receiving cytonemes. These results reveal a robust mechanism where morphogens self-generate precise tissue-specific gradient contours through feedback regulation of cytoneme-mediated dispersion. When an embryo develops, its cells must work together and ‘talk’ with each other so they can build the tissues and organs of the body. A cell can communicate with its neighbors by producing a signal, also known as a morphogen, which will tell the receiving cells what to do. Once outside the cell, a morphogen spreads through the surrounding tissue and forms a gradient: there is more of the molecule closer to the signaling cells and less further away. The cells that receive the message respond differently depending on how much morphogen they get, and therefore on where they are placed in the embryo. How morphogens move in tissues to create gradients is still poorly understood. One hypothesis is that, once released, they spread passively through the space between cells. Instead, recent research has shown that some morphogens travel through long, thin cellular extensions known as cytonemes. These structures directly connect the cells that produce a morphogen with the ones that receive the molecule. Yet, it is still unclear how cytonemes can help to form gradients. Du et al. aimed to resolve this question by following a morphogen called Branchless as it traveled through fruit fly embryos. Branchless is important for sculpting the embryonic airway tissue into a delicate network of branched tubes which supply oxygen to the cells of an adult fly. However, no one knew how cells communicate Branchless, whether or not Branchless formed a gradient, and if it did, how this gradient was created to set up the plan to form airway tubes. It was assumed that the molecule would diffuse passively to reach airway cells – but this is not what the experiments by Du et al. showed. To directly observe how Branchless moves among cells, insects were genetically engineered to produce Branchless molecules attached to a fluorescent ‘tag’. Microscopy experiments using these flies revealed that Branchless did not diffuse passively; instead, airway cells used cytonemes to ‘reach’ towards the cells that produced the molecule, collecting the signal directly from its source. The gradient was created because the airway cells near the cells that make Branchless had more cytonemes, and therefore received more of the molecule compared to the cells that were placed further away. Genetic analysis of the airway tissue showed that Branchless acts as a morphogen to switch on different genes in the receiving cells placed in different locations. The target genes activated by the gradient instruct the receiving cells on how many cytonemes need to be extended, which helps the gradient to maintain itself over time. Du et al. demonstrate for the first time how cytonemes can relay a signal to establish a gradient in a developing tissue. Dissecting how cells exchange information to create an organism could help to understand how this communication fails and leads to disorders.
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Blayney D, Ogenstad S, Shi Y, Zhang Q, Du L, Huang L, Mohanlal R. P1.01-06 Plinabulin, a Novel Immuno-Oncology Agent Mitigates Docetaxel Chemotherapy -Induced-Neutropenia and -Thrombocytopenia in NSCLC Patients. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Du L, Qu B, Ma N, Huang X, Yu W, Xu S, Dai X. P1.17-03 Potential Associated SNPs by GWAS with Radiation Pneumonitis (RP) in Patients with Lung Cancer Treated with Radiotherapy. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.1036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Blayney D, Ogenstad S, Shi YK, Zhang Q, Du L, Huang L, Mohanlal R. Plinabulin (Plin), a novel non-G-CSF molecule for the revention of chemotherapy-induced neutropenia (CIN), has the potential to positively impact tumor micro environment. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy300.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Ying L, Zou R, Du L, Shi L, Zhang N, Jin J, Wu J, Zhang F, Chen K, Huang M, Zhang Y, Lin A, Yu H, Zhou L, Mao W, Su D. A serum miRNA biomarker panel for the detection of early stage non-small cell lung cancer. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy290.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Du L, Qu B, Ma N, He Q, Yang W, Wang Q. P1.17-19 Correlation of Dosimetric and Clinical Factors with Radiation Pneumonitis in Lung Cancer Patients Received Involved-Field IMRT. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.1052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Wang D, Chen Y, Fang H, Zheng L, Li Y, Yang F, Xu Y, Du L, Zhou BBS, Li H. Increase of PRPP enhances chemosensitivity of PRPS1 mutant acute lymphoblastic leukemia cells to 5-Fluorouracil. J Cell Mol Med 2018; 22:6202-6212. [PMID: 30255549 PMCID: PMC6237573 DOI: 10.1111/jcmm.13907] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/10/2018] [Indexed: 12/21/2022] Open
Abstract
Relapse‐specific mutations in phosphoribosyl pyrophosphate synthetase 1 (PRPS1), a rate‐limiting purine biosynthesis enzyme, confer significant drug resistances to combination chemotherapy in acute lymphoblastic leukemia (ALL). It is of particular interest to identify drugs to overcome these resistances. In this study, we found that PRPS1 mutant ALL cells specifically showed more chemosensitivity to 5‐Fluorouracil (5‐FU) than control cells, attributed to increased apoptosis of PRPS1 mutant cells by 5‐FU. Mechanistically, PRPS1 mutants increase the level of intracellular phosphoribosyl pyrophosphate (PRPP), which causes the apt conversion of 5‐FU to FUMP and FUTP in Reh cells, to promote 5‐FU‐induced DNA damage and apoptosis. Our study not only provides mechanistic rationale for re‐targeting drug resistant cells in ALL, but also implicates that ALL patients who harbor relapse‐specific mutations of PRPS1 might benefit from 5‐FU‐based chemotherapy in clinical settings.
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