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Zhu Y, Gan X, Qin R, Lin Z. Identification of Six Diagnostic Biomarkers for Chronic Lymphocytic Leukemia Based on Machine Learning Algorithms. JOURNAL OF ONCOLOGY 2022; 2022:3652107. [PMID: 36467501 PMCID: PMC9715328 DOI: 10.1155/2022/3652107] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/13/2022] [Accepted: 09/30/2022] [Indexed: 09/19/2023]
Abstract
BACKGROUND Chronic lymphocytic leukemia (CLL) is the most common type of leukemia in adults. Thus, novel reliable biomarkers need to be further explored to increase diagnostic, therapeutic, and prognostic effectiveness. METHODS Six datasets containing CLL and control samples were downloaded from the Gene Expression Omnibus database. Differential gene expression analysis, weighted gene coexpression network analysis (WGCNA), and the least absolute shrinkage and selection operator (LASSO) regression were applied to identify potential diagnostic biomarkers for CLL using R software. The diagnostic performance of the hub genes was then measured by the receiver operating characteristic (ROC) curve analysis. Functional analysis was implemented to uncover the underlying mechanisms. Additionally, correlation analysis was performed to assess the relationship between the hub genes and immunity characteristics. RESULTS A total number of 47 differentially expressed genes (DEGs) and 25 candidate hub genes were extracted through differential gene expression analysis and WGCNA, respectively. Based on the 14 overlapped genes between the DEGs and the candidate hub genes, LASSO regression analysis was used, which identified a final number of six hub genes as potential biomarkers for CLL: ABCA6, CCDC88A, PMEPA1, EBF1, FILIP1L, and TEAD2. The ROC curves of the six genes showed reliable predictive ability in the training and validation cohorts, with all area under the curve (AUC) values over 0.80. Functional analysis revealed an abnormal immune status in the CLL patients. A significant correlation was found between the hub genes and the immune-related pathways, indicating a possible tight connection between the hub genes and tumor immunity in CLL. CONCLUSION This study was based on machine learning algorithms, and we identified six genes that could be possible CLL markers, which may be involved in CLL pathogenesis and progression through immune-related signal pathways.
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Affiliation(s)
- Yidong Zhu
- Department of Traditional Chinese Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Xinjin Gan
- Department of Hematology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Ruoyan Qin
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Zhikang Lin
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
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Hypermethylation-Mediated Silencing of CIDEA, MAL and PCDH17 Tumour Suppressor Genes in Canine DLBCL: From Multi-Omics Analyses to Mechanistic Studies. Int J Mol Sci 2022; 23:ijms23074021. [PMID: 35409379 PMCID: PMC9000013 DOI: 10.3390/ijms23074021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 11/23/2022] Open
Abstract
Gene expression is controlled by epigenetic deregulation, a hallmark of cancer. The DNA methylome of canine diffuse large B-cell lymphoma (cDLBCL), the most frequent malignancy of B-lymphocytes in dog, has recently been investigated, suggesting that aberrant hypermethylation of CpG loci is associated with gene silencing. Here, we used a multi-omics approach (DNA methylome, transcriptome and copy number variations) combined with functional in vitro assays, to identify putative tumour suppressor genes subjected to DNA methylation in cDLBCL. Using four cDLBCL primary cell cultures and CLBL-1 cells, we found that CiDEA, MAL and PCDH17, which were significantly suppressed in DLBCL samples, were hypermethylated and also responsive (at the DNA, mRNA and protein level) to pharmacological unmasking with hypomethylating drugs and histone deacetylase inhibitors. The regulatory mechanism underneath the methylation-dependent inhibition of those target genes expression was then investigated through luciferase and in vitro methylation assays. In the most responsive CpG-rich regions, an in silico analysis allowed the prediction of putative transcription factor binding sites influenced by DNA methylation. Interestingly, regulatory elements for AP2, MZF1, NF-kB, PAX5 and SP1 were commonly identified in all three genes. This study provides a foundation for characterisation and experimental validation of novel epigenetically-dysregulated pathways in cDLBCL.
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Association Between SHMT1 rs1979277 Polymorphism and Risk of Acute Lymphoblastic Leukemia: A Systematic Review and Meta-analysis. J Pediatr Hematol Oncol 2022; 44:e616-e622. [PMID: 33974584 DOI: 10.1097/mph.0000000000002173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/06/2021] [Indexed: 11/26/2022]
Abstract
OBJECTIVES The aim of this study was to explore the potential association the cytosolic serine hydroxy methyltransferase (SHMT1) rs1979277 polymorphism and the risk of acute lymphoblastic leukemia (ALL). MATERIALS AND METHODS Comprehensive search of Web of Science, PubMed, Ovid, Cochrane Library, Embase, China National Knowledge Infrastructure (CNKI), and China Biomedical Literature Database electronic database, was performed to identify relevant studies published throughout April 30, 2019. The heterogeneity in the study was judged by the I2 and P-values, and then the random ratio or fixed effect was used to calculate the pooled odds ratios (OR) based on the presence or absence of heterogeneity. Sensitivity analysis is used to estimate the impact of individual studies on aggregate estimates. The publication bias of the study was tested using a funnel plot and an Egger regression. RESULTS Nine studies with a total of 6492 participants (2971 patients; 3521 controls) were included in this meta-analysis. We found that SHMT1 rs1979277 polymorphism was not significantly associated with the risk of ALL in the dominant model: CC versus CT+TT (OR=0.84, 95% confidence interval [CI]: 0.46-1.54, P=0.57), recessive model: CC+CT versus TT (OR=0.81, 95% CI: 0.44-1.49, P=0.50) and allele model: C versus T (OR=0.84, 95% CI: 0.52-1.35, P=0.48). In subgroup analysis by ethnicity, no significant association were found in dominant, recessive and allele models in both Caucasian and Asian populations. CONCLUSION Our study indicated that the SHMT1 rs1979277 polymorphism was not associated with the risk of susceptibility to ALL.
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Yan H, Tian S, Kleinstern G, Wang Z, Lee JH, Boddicker NJ, Cerhan JR, Kay NE, Braggio E, Slager SL. Chronic lymphocytic leukemia (CLL) risk is mediated by multiple enhancer variants within CLL risk loci. Hum Mol Genet 2021; 29:2761-2774. [PMID: 32744316 DOI: 10.1093/hmg/ddaa165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/02/2020] [Accepted: 07/25/2020] [Indexed: 12/12/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in Western countries. It has a strong genetic basis, showing a ~ 8-fold increased risk of CLL in first-degree relatives. Genome-wide association studies (GWAS) have identified 41 risk variants across 41 loci. However, for a majority of the loci, the functional variants and the mechanisms underlying their causal roles remain undefined. Here, we examined the genetic and epigenetic features associated with 12 index variants, along with any correlated (r2 ≥ 0.5) variants, at the CLL risk loci located outside of gene promoters. Based on publicly available ChIP-seq and chromatin accessibility data as well as our own ChIP-seq data from CLL patients, we identified six candidate functional variants at six loci and at least two candidate functional variants at each of the remaining six loci. The functional variants are predominantly located within enhancers or super-enhancers, including bi-directionally transcribed enhancers, which are often restricted to immune cell types. Furthermore, we found that, at 78% of the functional variants, the alternative alleles altered the transcription factor binding motifs or histone modifications, indicating the involvement of these variants in the change of local chromatin state. Finally, the enhancers carrying functional variants physically interacted with genes enriched in the type I interferon signaling pathway, apoptosis, or TP53 network that are known to play key roles in CLL. These results support the regulatory roles for inherited noncoding variants in the pathogenesis of CLL.
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Affiliation(s)
- Huihuang Yan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Shulan Tian
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Geffen Kleinstern
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhiquan Wang
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jeong-Heon Lee
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Neil E Kay
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Esteban Braggio
- Division of Hematology/Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
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Geographical origin identification of two salmonid species via flavor compound analysis using headspace-gas chromatography-ion mobility spectrometry combined with electronic nose and tongue. Food Res Int 2021; 145:110385. [PMID: 34112388 DOI: 10.1016/j.foodres.2021.110385] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/08/2021] [Accepted: 05/02/2021] [Indexed: 11/23/2022]
Abstract
The flavor of salmonids is affected by species and origin. Sources of salmonid fish fillets are complex and difficult to identify and label fraud occasionally occurs in the market. In this study, headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS), electronic nose, electronic tongue and amino acid detection technologies were used to analyze flavor compounds in two salmonid species from different geographical origins. Fingerprints of volatile compounds of salmonid were constructed using HS-GC-IMS technology. Free amino acid (FAA) content differed in salmonids from different geographical origins. Regarding salmonid odor, HS-GC-IMS analysis results were basically consistent with those of the electronic nose. Regarding taste, the conclusions drawn from the electronic tongue were consistent with the amino acid test results. Therefore, our results demonstrate that flavor compounds can be used to distinguish salmonids from different geographical origins, providing a new dimension to food safety and authenticity. Furthermore, HS-GC-IMS, electronic nose and tongue can be used as tools in the market to identify food fraud.
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Potentials of miR-15/16 targeting cancer stem cell pathways: Novel implication in cancer chemotherapy. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Clinical Relevance of +936 C>T VEGFA and c.233C>T bFGF Polymorphisms in Chronic Lymphocytic Leukemia. Genes (Basel) 2020; 11:genes11060686. [PMID: 32585853 PMCID: PMC7349122 DOI: 10.3390/genes11060686] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/14/2020] [Accepted: 06/19/2020] [Indexed: 12/21/2022] Open
Abstract
Angiogenesis process contributes to the pathogenesis of B-cell chronic lymphocytic leukemia (B-CLL) being the levels of VEGFA and bFGF higher in patients than in healthy controls. Our aim was to evaluate the implication of angiogenesis factors genetic variants in the predisposition to B-CLL and their association with clinical factors and survival. We performed a population-based case-control study in 224 Spanish B-CLL patients and 476 healthy randomly selected controls to evaluate susceptibility to developing B-CLL. Six polymorphisms were evaluated: rs1109324, rs1547651, rs3025039 (+936 C>T), rs833052 of the VEGFA gene, rs1449683 (c.233C>T) of the bFGF gene and (−710 C>T) of the VEGFR1 gene. The association between clinical parameters and patient outcome was analyzed. Carriers of the CT/TT variants of rs3025039 showed a significant protective effect against developing B-CLL. The CT/TT variants of rs1449683 show a tendency towards the development of the disease and the same variants associated significantly with higher genetic risk and with reduced disease free survival. Moreover, the association persisted in the early-stage disease subgroup. Our study provides evidence of the protective effect of the T/- rs3025039 VEGFA variant against B-CLL development and the association of CT/TT variants of the rs1449683 bFGF gene with genetic risk and an adverse survival.
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Zhang Y, Kou C, Wang S, Zhang Y. Genome-wide Differential-based Analysis of the Relationship between DNA Methylation and Gene Expression in Cancer. Curr Bioinform 2019. [DOI: 10.2174/1574893614666190424160046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Background::
DNA methylation is an epigenetic modification that plays an important
role in regulating gene expression. There is evidence that the hypermethylation of promoter regions
always causes gene silencing. However, how the methylation patterns of other regions in the
genome, such as gene body and 3’UTR, affect gene expression is unknown.
Objective::
The study aimed to fully explore the relationship between DNA methylation and expression
throughout the genome-wide analysis which is important in understanding the function of
DNA methylation essentially.
Method::
In this paper, we develop a heuristic framework to analyze the relationship between the
methylated change in different regions and that of the corresponding gene expression based on differential
analysis.
Results::
To understande the methylated function of different genomic regions, a gene is divided
into seven functional regions. By applying the method in five cancer datasets from the Synapse database,
it was found that methylated regions with a significant difference between cases and controls
were almost uniformly distributed in the seven regions of the genome. Also, the effect of
DNA methylation in different regions on gene expression was different. For example, there was a
higher percentage of positive relationships in 1stExon, gene body and 3’UTR than in TSS1500 and
TSS200. The functional analysis of genes with a significant positive and negative correlation between
DNA methylation and gene expression demonstrated the epigenetic mechanism of cancerassociated
genes.
Conclusion::
Differential based analysis helps us to recognize the change in DNA methylation and
how this change affects the change in gene expression. It provides a basis for further integrating
gene expression and DNA methylation data to identify disease-associated biomarkers.
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Affiliation(s)
- Yuanyuan Zhang
- School of information and control engineering, Qingdao University of Technology, Qingdao, Shandong, China
| | - Chuanhua Kou
- School of information and control engineering, Qingdao University of Technology, Qingdao, Shandong, China
| | - Shudong Wang
- College of Computer and Communication Engineering, China University of Petroleum (East China), Qingdao, Shandong, China
| | - Yulin Zhang
- College of Mathematics and Systems Science, Shandong University of Science and Technology, Qingdao, Shandong, China
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Song Y, Han J, Cao F, Ma H, Cao B, An X. Endometrial genome-wide DNA methylation patterns of Guanzhong dairy goats at days 5 and 15 of the gestation period. Anim Reprod Sci 2019; 208:106124. [PMID: 31405455 DOI: 10.1016/j.anireprosci.2019.106124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 05/05/2019] [Accepted: 07/12/2019] [Indexed: 12/29/2022]
Abstract
Uterine receptivity for the embryo is established and maintained through a series of precise cellular and molecular events, such as DNA methylation. There have been no studies to elucidate entire genome DNA methylation changes associated with embryo receptivity development of the endometrium (RE). In the present study, there was development of a complete genome-wide DNA methylome maps of the RE using whole-genome bisulphite sequencing and bioinformatics analysis. As many as 163.06 Gb of sequencing data averaging 81.53 Gb per sample were obtained for genome bisulphite sequencing of endometrium samples. There were distinct genome-wide DNA methylation patterns in pre-receptive endometrium (PE; Day 5 of gestation) and RE (Day 15 of gestation). There were as many as 16,467 differentially methylated regions (DMRs); 21,391 DMRs were less methylated in RE samples compared with PE samples (P-values ≤ 0.05 and |log2 (fold change)| ≥ 2). Compared with PE samples, methylation ratios of IGF2BP2, ACOX2, PTGDS, VEGFB and PTGDR2 genes were markedly less in RE samples (P-value ≤ 0.05 and |log2 (fold change)| ≥ 2). Conversely, in RE samples there was a markedly greater methylation ratio of IGFBP3 and IGF1R genes. The results of KEGG analysis indicated that these genes were involved in the signalling pathways for insulin, mitogen-activated protein kinase, gonadotropin-releasing hormone, vascular endothelial growth factor and progesterone-mediated oocyte maturation, which participated in differential regulation of goat endometrial development during receptive and prereceptive phases. The results of previous and the present study indicate resulting proteins of IGF2BP2, PTGDS, VEGFB, PGR, IGFBP3 and IGF1R gene expression may have important functions in regulating endometrial receptivity for the embryo.
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Affiliation(s)
- Yuxuan Song
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Jincheng Han
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Fangjun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Haidong Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Binyun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xiaopeng An
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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Wen M, Zhou B, Lin X, Chen Y, Song J, Li Y, Zacksenhaus E, Ben-David Y, Hao X. Associations Between XPD Lys751Gln Polymorphism and Leukemia: A Meta-Analysis. Front Genet 2018; 9:218. [PMID: 30100919 PMCID: PMC6073102 DOI: 10.3389/fgene.2018.00218] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/28/2018] [Indexed: 12/15/2022] Open
Abstract
Objectives: The aim of the present study was to define the potential relationship between xeroderma pigmentosum group D (XPD) Lys751Gln polymorphisms and the risk of leukemia. Methods: A comprehensive search of Pubmed, Web of Science, EBSCO, the Cochrane Library and China National Knowledge Infrastructure was conducted to identify original articles published before March 2017 concerning the association between XPD Lys751Gln polymorphisms and leukemia risk. A literature quality assessment was performed using the Newcastle-Ottawa Scale. Heterogeneity across studies was assessed using I2 statistics. Random- or fixed-effects models were used to calculate pooled odds ratios (ORs) in the presence or absence of heterogeneity, respectively. Sensitivity analysis was used to assess the influence of individual studies on the pooled estimate. Publication bias was investigated using funnel plots and Egger’s regression test. All data analyses were performed using Stata 14.0 and Revman 5.3. Results: Fourteen studies with a total of 7525 participants (2,757 patients; 4,768 controls) were included in this meta-analysis. We found that XPD Lys751Gln polymorphisms significantly increased the risk of developing leukemia in both dominant OR = 1.21, 95%CI [1.10–1.35], P ≤ 0.001) and heterozygote (OR = 1.22, 95%CI [1.09–1.36], P ≤ 0.001) model. An allele model showed a borderline significant increase in leukemia risk (OR = 1.13, 95%CI [1.00–1.27], P = 0.05). A subgroup analysis revealed a consistent association between XPD Lys751Gln polymorphisms and leukemia risk for some genetic models in Caucasian populations, adult or chronic groups, and in almost all models of childhood or acute groups. Conclusion: Our results indicate that XPD Lys751Gln polymorphism increases the risk of leukemia, especially in childhood and acute cases.
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Affiliation(s)
- Min Wen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China.,College of Basic Medicine, Guizhou Medical University, Guiyang, China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academy of Sciences, Guiyang, China
| | - Bo Zhou
- College of Basic Medicine, Guizhou Medical University, Guiyang, China
| | - Xin Lin
- College of Basic Medicine, Guizhou Medical University, Guiyang, China
| | - Yunhua Chen
- College of Basic Medicine, Guizhou Medical University, Guiyang, China
| | - Jialei Song
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academy of Sciences, Guiyang, China
| | - Yanmei Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academy of Sciences, Guiyang, China
| | - Eldad Zacksenhaus
- Department of Medicine, Toronto General Research Institute, University Health Network, Toronto, ON, Canada
| | - Yaacov Ben-David
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academy of Sciences, Guiyang, China
| | - Xiaojiang Hao
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academy of Sciences, Guiyang, China
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