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Genome-wide association studies approach and post-GWAS study in rice
Gang Li,Min-Young Yoon,Won-Hee Ra,Jae-Wan Park,Qiang He,Aye Aye Khaing,Xiao-Qiang Wang,Win Htet Oo,Feng-Peng Li,Byoung Kook Yun,Chang-Yong Lee,Yong-Jin Park 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07
AGenome-wide association studies (GWAS) have proven a useful technique for identifying genetic loci responsible for natural variation in rice. With the fast developed next-generation sequencing technology, it is possible for people to carry out GWAS by phenotyping different traits. However, how to make full use of huge data, abandon unnecessary data, and solve the problem of data application effectively seems still an obstacle for many researchers. Taking the case of whole-genome resequencing of Korean authentic rice core set, here we present a general technological path of GWAS including: 1) a schematic view of sequencing-based GWAS in rice; 2) a user-friendly and interactive web application for GWAS in rice by the aid of experience from Arabidopsis; 3) Haplotype and association analysis of candidate genes in a certain mechanism pathway, giving 10 starch synthesis genes as example; and 4) functional validation by Trans- and Mata-Omics analysis.
Gang Wang,Peng-yu Duan,Yuan Ma,Xi-na Li,Feng-zhi Qu,Liang Ji,Xiao-yu Guo,Wang-jun Zhang,Fan Xiao,Le Li,Ji-sheng Hu,Bei Sun 생화학분자생물학회 2019 Experimental and molecular medicine Vol.51 No.-
Currently, preliminary results have confirmed the existence of receptor-interacting protein kinase 3 (RIPK3) and mixed lineage kinase domain-like protein (MLKL)-dependent necroptosis of pancreatic acinar cells during early acute pancreatitis (AP), which might be a potential target for the effective regulation of necroinflammatory injury. However, the exact effect of receptor-interacting protein kinase 1 (RIPK1)-dependent regulated acinar cell necrosis on AP is still uncertain. In our study, we first explored the changes in the degree of local and systemic inflammation in AP rats when the activation of acinar cell RIPK1 was inhibited. The RIPK1 inhibitor Nec-1 was used to treat rats, and the levels of related inflammatory markers, necrosis indicators and apoptotic indicators were measured. Changes in pancreatic nuclear factor κB (NF-κB) and aquaporin 8 (AQP8) expression were noted. Next, the expression of AQP8 in AR42J cells was inhibited, and the degree of cell necrosis and inflammatory damage was found to be significantly reduced. Most importantly, we demonstrated that the RIPK1/NF-ĸB/AQP8 axis might be a potential regulatory pathway mediating RIPK1-dependent regulated acinar cell necrosis in early AP. Finally, we used the NF-κB inhibitor PDTC and Nec-1 to treat rats in different groups and measured the degree of pathological pancreatic injury, the activation of RIPK1, and the expression of NF-κB and AQP8. In summary, we hypothesized that there might be a RIPK1/NF-ĸB/AQP8 pathway controlling RIPK1-dependent regulated necrosis of acinar cells in AP, which might be a promising therapeutic target against AP-related injury.
Fu, Xiao-Gang,Zhang, Li-Ping,Wu, Li-Zhu,Tung, Chen-Ho Korean Society of Photoscience 2003 Journal of Photosciences Vol.10 No.1
Zeolite, Nafion membranes and vesicles were used as microreactors to control the pathway of photosensitized oxidation of alkenes and remarkable selectivity was achieved.
miR-98 suppresses melanoma metastasis through a negative feedback loop with its target gene IL-6
Fei Li,Xin-ji Li,Li Qiao,Fei Shi,Wen Liu,You Li,Yu-ping Dang,Weijie Gu,Xiao-gang Wang,Wei Liu 생화학분자생물학회 2014 Experimental and molecular medicine Vol.46 No.-
Dysregulated microRNA (miRNA) expression has a critical role in tumor development and metastasis. However, the mechanism by which miRNAs control melanoma metastasis is unknown. Here, we report reduced miR-98 expression in melanoma tissues with increasing tumor stage as well as metastasis; its expression is also negatively associated with melanoma patient survival. Furthermore, we demonstrate that miR-98 inhibits melanoma cell migration in vitro as well as metastatic tumor size in vivo. We also found that IL-6 is a target gene of miR-98, and IL-6 represses miR-98 levels via the Stat3-NF-κB-lin28B pathway. In an in vivo melanoma model, we demonstrate that miR-98 reduces melanoma metastasis and increases survival in part by reducing IL-6 levels; it also decreases Stat3 and p65 phosphorylation as well as lin28B mRNA levels. These results suggest that miR-98 inhibits melanoma metastasis in part through a novel miR-98-IL-6-negative feedback loop.
Causes, Features, and Outcomes of Drug-Induced Liver Injury in 69 Children from China
( Yun Zhu ),( Yong Gang Li ),( Jia Bo Wang ),( Shu Hong Liu ),( Li Fu Wang ),( Yan Ling Zhao ),( Yun Feng Bai ),( Zhong Xia Wang ),( Jian Yu Li ),( Xiao He Xiao ) 대한소화기학회 2015 Gut and Liver Vol.9 No.4
Background/Aims: Drug-induced liver injury (DILI) is a frequent cause of pediatric liver disease; however, the data on DILI are remarkably limited. Methods: All 69 children hospitalized with DILI between January 2009 and December 2011 were retrospectively studied. Results: A total of 37.7% of the children had medical histories of respiratory infection. The clinical injury patterns were as follows: hepatocellular 89.9%, cholestatic 2.9%, and mixed 7.2%. Liver biopsies from 55 children most frequently demonstrated chronic (47.3%) and acute (27.3%) hepatitis. Hypersensitivity features, namely, fever (31.9%), rash (21.7%), and eosinophilia (1.4%), were found. Twenty-four children (34.8%) developed chronic DILI. Antibiotics (26.1%) were the most common Western medicines (WMs) causing DILI, and the major implicated herbs were Ephedra sinica and Polygonum multiflorum. Compared with WM, the children whose injuries were caused by Chinese herbal medicine (CHM) showed a higher level of total bilirubin (1.4 mg/dL vs 16.6 mg/dL, p=0.004) and a longer prothrombin time (11.8 seconds vs 17.3 seconds, p=0.012), but they exhibited less chronic DILI (2/15 vs 18/39, p=0.031). Conclusions: Most cases of DILI in children are caused by antibiotics or CHM used to treat respiratory infection and present with hepatocellular injury. Compared with WM, CHM is more likely to cause severe liver injury, but liver injury caused by CHM is curable. (Gut Liver 2015;9:525-533)
Yan, Jian,Liu, Xiao-Long,Han, Lu-Zhe,Xiao, Gang,Li, Ning-Lei,Deng, Yi-Nan,Yin, Liang-Chun,Ling, Li-Juan,Yu, Xiao-Yuan,Tan, Can-Liang,Huang, Xiao-Ping,Liu, Li-Xin Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.2
The aim of the present study was to investigate the expression of the transcription factor Ki-67, ER, PR, Her2/neu, p21, EGFR, and TOP II-${\alpha}$ in the tumor tissue of patients with invasive ductal carcinoma(IDC); in addition, we examined correlations between these markers. Two hundred and sixteen IDC patients, who were not previously been treated with chemo- or radiotherapy, were included in the study. All tumors were grade I-III. Expression of molecular markers was determined by immunohistochemical analysis on paraffin-embedded tissue sections. Follow-up data were collected for 3 months to 10 years and analyzed for tumor recurrence, survival time, and prognostic risk factors. We determined Ki-67 expression correlates with the expression of ER, PR, HER-2, EGFR, and TOP-${\alpha}$, as well as lymph node involvement, high tumor grade, lymphovascular invasion, high tumor stage, and high TNM stage in IDC. Positive Ki-67 expression was a risk factor for rapid tumor recurrence and may help tumor progression, leading to poor prognosis in IDC. Ki-67 was directly correlated with EGFR, TOP II-${\alpha}$, lymph node involvement, high tumor grade, lymphovascular invasion, high tumor stage, and high TNM stage in the hormone receptor subtypes of breast cancer. In triple negative breast cancer, Ki-67 correlated with TOP II-${\alpha}$. Expression of Ki-67 correlated with that of ER, PR, HER-2, EGFR, TOP II-${\alpha}$, and p21. In addition, the biomarker Ki-67 has a role as a prognostic factor and indicates a poor prognosis in IDC.
Ying Yang,Dong Wang,Lei Cui,Hong-Hao Ma,Li Zhang,Hong-Yun Lian,Qing Zhang,Xiao-Xi Zhao,Li-Ping Zhang,Yun-Ze Zhao,Na Li,Tian-You Wang,Zhi-Gang Li,Rui Zhang 대한암학회 2021 Cancer Research and Treatment Vol.53 No.1
Purpose We sought to investigate the effectiveness and safety of dabrafenib in children with BRAFV600E-mutated Langerhans cell histiocytosis (LCH). Materials and Methods A retrospective analysis was performed on 20 children with BRAFV600E-mutated LCH who were treated with dabrafenib. Results The median age at which the patients started taking dabrafenib was 2.3 years old (range, 0.6 to 6.5 years). The ratio of boys to girls was 2.3:1. The median follow-up time was 30.8 months (range, 18.9 to 43.6 months). There were 14 patients (70%) in the risk organ (RO)+ group and six patients (30%) in the RO– group. All patients were initially treated with traditional chemotherapy and then shifted to targeted therapy due to poor control of LCH or intolerance to chemotherapy. The overall objective response rate and the overall disease control rate were 65% and 75%, respectively. During treatment, circulating levels of cell-free BRAFV600E (cfBRAFV600E) became negative in 60% of the patients within a median period of 3.0 months (range, 1.0 to 9.0 months). Grade 2 or 3 adverse effects occurred in five patients. Conclusion Some children with BRAFV600E-mutated LCH may benefit from monotherapy with dabrafenib, especially high-risk patients with concomitant hemophagocytic lymphohistiocytosis and intolerance to chemotherapy. The safety of dabrafenib is notable. A prospective study with a larger sample size is required to determine the optimal dosage and treatment duration.
Ifosfamide-containing Regimens for Treating Patients with Osteosarcomas
Li, Yan-Yan,Jiang, Xiao-Ming,Dong, Yi-Guo,Xu, Gang,Ma, Yu-Bo Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.22
Background: This systemic analysis was conducted to evaluate the efficacy and safety of an ifosfamide-containing regimen in treating patients with osteosarcoma. Methods: Clinical studies evaluating the efficacy and safety of Ifosfamide-containing regimen on response and safety for patients with osteosarcoma were identified by using a predefined search strategy. Pooled response rate (RR) of treatment were calculated. Results: When ifosfamide-containing regimens were evaluated, 4 clinical studies which including 134 patients with osteosarcoma were considered eligible for inclusion. Systemic analysis suggested that, in all patients, pooled RR was 44.8% (60/134) in ifosfamide-containing regimens. Major adverse effects were neutropenia, leukopenia, and fatigue inIfosfamide-containing regimens; No treatment related death occurred in cantharidin combined regimens. Conclusion: This systemic analysis suggests that ifosfamide-containing regimens are associated with good response rate and acceptable toxicity in treating patients with osteosarcoma, but this result should be confirmed by randomized clinical trials.