Genome-wide identification and evolutionary analysis of WOX gene family in cucurbit crops

Li Chun,He Zhen,Liang Genyun,Yang Nan,Cai Peng,Liang Ying,Li Yuejian,Fang Chao,Liu Duchen,Xia Feng,Liu Xiaojun 한국원예학회 2024 Horticulture, Environment, and Biotechnology Vol.65 No.1

The WUSCHEL-related homeobox (WOX) gene family is essential for plant growth and development. However, the identifi cation and evolutionary analysis of WOX genes in the Cucurbitaceae have not been well investigated. In the present work, we performed a genome-wide analysis to identify WOX genes in eleven cucurbit crops. In total, 127 WOX genes were identifi ed in eleven cucurbit crops, and classifi ed into three diff erent clades: the ancient clade, the intermediate clade and the WUS clade. The same clade has comparable gene organization and conserved motif patterns. The cis -acting ele ment analysis revealed that WOX genes were involved in light, hormone and stress in cucurbit crops. Gene duplication analysis indicated that dispersed duplication and whole genome duplication were the two primary causes of WOX genes expansion. There were 24 and 129 gene pairs found within cucurbit crops, and between Cucumis sativus and other cucur bit crops, respectively. After gene duplication, all WOX genes were subjected to substantial purifying selection pressure according to the selective pressure analysis. Functional divergence analysis revealed that ancient and intermediate clades may have descended from some essential amino acid sites rather than diff erent evolution rate. Our research provides a comprehensive analysis of WOX genes which will be helpful for further research into their function study in Cucurbita ceae plants.

Ginsenoside Rg1 Induces Apoptosis through Inhibition of the EpoR-Mediated JAK2/STAT5 Signalling Pathway in the TF-1/Epo Human Leukemia Cell Line

Li, Jing,Wei, Qiang,Zuo, Guo-Wei,Xia, Jing,You, Zhi-Mei,Li, Chun-Li,Chen, Di-Long Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.6

Ginsenoside Rg1 is one effective anticancer and antioxidant constituent of total saponins of Panax ginseng (TSPG), which has been shown to have various pharmacological effects. Our previous study demonstrated that Rg1 had anti-tumor activity in K562 leukemia cells. The aim of this study was designed to investigate whether Rg1 could induce apoptosis in TF-1/Epo cells and further to explore the underlying molecular mechanisms. Here we found that Rg1 could inhibit TF-1/Epo cell proliferation and induce cell apoptosis in vitro in a concentration and time dependent manner. It also suppressed the expression of EpoR on the surface membrane and inhibited JAK2/STAT5 pathway activity. Rg1 induced up-regulation of Bax, cleaved caspase-3 and C-PAPR protein and down-regulation of Bcl-2 and AG490, a JAK2 specific inhibitor, could enhance the effects of Rg1. Our studies showed that EpoR-mediated JAK2/STAT5 signaling played a key role in Rg1-induced apoptosis in TF-1/Epo cells. These results may provide new insights of Rg1 protective roles in the prevention a nd treatment of leukemia.

Investigation of White Matter and Grey Matter Alterations in the Monkey Brain Following Ischemic Stroke Using Diffusion Tensor Imaging

Chun-Xia Li,Yuguang Meng,Yumei Yan,Doty Kempf,Leonard Howell,Frank Tong,Xiaodong Zhang 대한자기공명의과학회 2022 Investigative Magnetic Resonance Imaging Vol.26 No.4

Purpose: Investigation of stroke lesions mostly focuses on the grey matter (GM). White matter (WM) degeneration during acute stroke has remained understudied. In the present study, monkeys were employed to investigate the alterations in GM and WM in the brain following ischemic occlusion using diffusion tensor imaging (DTI). Materials and Methods: Permanent middle cerebral artery occlusion was induced in rhesus monkeys (n = 6) using an interventional approach. Serial DTI was conducted on a clinical 3 T in the hyperacute phase (2–6 hours), 48, and 96 hours post-occlusion. Regions of interest in GM and WM of lesion areas were selected for data analysis. Results: Mean diffusivity (MD), radial diffusivity (RD), and axial diffusivity (AD) in WM decreased substantially during hyperacute stroke, similar to those seen in GM. No obvious fractional anisotropy changes were seen in WM during the hyperacute phase until 48 hours poststroke when significant fiber loss was observed. Pseudo-normalization of MD, AD, and RD was seen at 96 hours. Pathological changes in WM and GM were observed in ischemic areas at 8, 48, and 96 hours poststroke. Relative changes in MD, AD, and RD of WM were correlated negatively with infarction volumes at 6 hours poststroke. Conclusion: The present study revealed the microstructural changes in GM and WM of monkey brains during acute stroke using DTI. The preliminary results suggest that AD and RD may be sensitive surrogate markers to assess specific microstructural changes in WM during the hyperacute stroke.

Proteomic Analysis of Serum of Women with Elevated Ca-125 to Differentiate Malignant from Benign Ovarian Tumors

Li, Li,Xu, Yi,Yu, Chun-Xia Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.7

Clinically, elevated cancer antigen 125 (CA-125) in blood predicts tumor burden in a woman's body, especially in the ovary, but cannot differentiate between malignant or benign. We here used intensive modern proteomic approaches to identify predictive proteins in the serum of women with elevated CA-125 to differentiate malignant from benign ovarian tumors. We identified differentially expressed proteins in serum samples of ovarian cancer (OC) patients, benign ovarian tumor (BT) patients, and healthy control women using mass spectrometry-based quantitative proteomics. Both the OC and BT patients had elevated CA-125. Quantitation was achieved using isobaric tags for relative and absolute quantitation. We obtained 124 quantified differential serum proteins in OC compared with BT. Two proteins, apolipoprotein A-4 (APOA4) and natural resistance-associated macrophage 1, were verified using Western blotting. Proteome profiling applied to OC cases identified several differential serum proteins in the serum of women with elevated CA-125. A novel protein, APOA4, has the potential to be a marker for malignant tumor differentiation in the serum of women with elevated CA-125.

Isolation of Chemical Constituents from the Aerial Parts of Verbascum thapsus and Their Antiangiogenic and Antiproliferative Activities

Yan-Li Zhao,Yong-Ping Yang,Si-Feng Wang,Yang Li,Qiu-Xia He,Ke-Chun Liu,Xiao-Li Li 대한약학회 2011 Archives of Pharmacal Research Vol.34 No.5

Phytochemical investigation of Verbascum thapsus led to the isolation and identification of one new iridoid compound named verbathasin A, along with ten known compounds. The structure and relative stereochemistry of verbathasin A were elucidated by analysis of spectroscopic data. All the isolates except 10-deoxyeucommiol and ajugol were tested for antiangiogenic and antiproliferative activities, and compounds luteolin and 3-O-fucopyranosylsaikogenin F showed promising antiproliferative activities, with an obvious effect of inducing apoptosis of A549 lung cancer cells.

Predictive Value of XRCC1 and XRCC3 Gene Polymorphisms for Risk of Ovarian Cancer Death After Chemotherapy

Cheng, Chun-Xia,Xue, Min,Li, Kai,Li, Wu-Sheng Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.6

Objective: To investigate any association between XRCC1 and XRCC3 polymorphisms and outcome of platinum-based chemotherapy in ovarian cancer patients. Methods: With a prospective study design was cases were consecutively collected from January 2005 to January 2007. All 310 included patients were followed-up until the end of January 2010. Genotyping of XRCC1 and XRCC3 polymorphisms was conducted by TaqMan Gene Expression assays. Results: A total of 191 patients died during follow-up. Our study showed a lower survival rate in XRCC1 399 Arg/Arg genotype than Gln/Gln, with a significant increased risk of death (HR=1.69, 95%CI=1.07-2.78). Similarly, those carrying XRCC3 Thr/Thr genotype had a increased risk as compare to the Met/Met genotype, with a HR (95% CI) of 1.90 (1.12-3.41). There was no significant association between XRCC1 Arg194Trp and XRCC1Arg280His gene polymorphisms and ovarian cancer death. Conclusion: Our study demonstrates that polymorphisms in DNA repair genes have roles in the susceptibility and survival of ovarian cancer patients.

Compound HRAS/PIK3CA Mutations in Chinese Patients with Alveolar Rhabdomyosarcomas

Liu, Chun-Xia,Li, Xiao-Ying,Li, Cheng-Fang,Chen, Yun-Zhao,Cui, Xiao-Bin,Hu, Jian-Ming,Li, Feng Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.4

The rhabdomyosarcoma (RMS) is the most common type of soft tissue tumor in children and adolescents; yet only a few screens for oncogenic mutations have been conducted for RMS. To identify novel mutations and potential therapeutic targets, we conducted a high-throughput Sequenom mass spectrometry-based analysis of 238 known mutations in 19 oncogenes in 17 primary formalin-fixed paraffin-embedded RMS tissue samples and two RMS cell lines. Mutations were detected in 31.6% (6 of 19) of the RMS specimens. Specifically, mutations in the NRAS gene were found in 27.3% (3 of 11) of embryonal RMS cases, while mutations in NRAS, HRAS, and PIK3CA genes were identified in 37.5% (3 of 8) of alveolar RMS (ARMS) cases; moreover, PIK3CA mutations were found in 25% (2 of 8) of ARMS specimens. The results demonstrate that tumor profiling in archival tissue samples is a useful tool for identifying diagnostic markers and potential therapeutic targets and suggests that these HRAS/ PIK3CA mutations play a critical role in the genesis of RMS.

Prognostic Value of PLCE1 Expression in Upper Gastrointestinal Cancer: a Systematic Review and Meta-analysis

Cui, Xiao-Bin,Peng, Hao,Li, Su,Li, Ting-Ting,Liu, Chun-Xia,Zhang, Shu-Mao,Jin, Ting-Ting,Hu, Jian-Ming,Jiang, Jin-Fang,Liang, Wei-Hua,Li, Na,Li, Li,Chen, Yun-Zhao,Li, Feng Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.22

Background: A number of studies have identified a shared susceptibility locus in phospholipase C epsilon 1 (PLCE1) for esophageal squamous cell carcinoma (ESCC) and gastric cardia adenocarcinomas (GCA). However, the results of PLCE1 expression in esophageal and gastric cancer remain inconsistent and controversial. Moreover, the effects on clinicopathological features remain undetermined. This study aimed to provide a precise quantification of the association between PLCE1 expression and the risk of ESCC and GCA through meta-analysis. Materials and Methods: Eligible studies were identified from PubMed, Wanfang Data, ISI Web of Science, and the Chinese National Knowledge Infrastructure databases. Using RevMan5.2 software, pooled odds ratios (ORs) with 95% confidence intervals (CIs) were employed to assess the association of PLCE1 expression with clinicopathological features relative to ESCC or GCA. Results: Seven articles were identified, including 761 esophageal and gastric cancer cases and 457 controls. Overall, we determined that PLCE1 expression was associated with tumor progression in both esophageal cancers (pooled OR=5.93; 95%CI=3.86 to 9.11) and gastric cancers (pooled OR=9.73; 95%CI=6.46 to 14.7). Moreover, invasion depth (pooled OR=3.62; 95%CI=2.30 to 5.70) and lymph node metastasis (pooled OR=4.21; 95%CI=2.69 to 6.59) were linked with PLCE1 expression in gastric cancer. However, no significant associations were determined between PLCE1 overexpression and the histologic grade, invasion depth, and lymph node metastasis in esophageal cancer. Conclusions: Our metaanalysis results indicated that upregulated PLCE1 is significantly associated with an increased risk of tumor progression in ESCC and GCA. Therefore, PLCE1 expression can be appropriately regarded as a promising biomarker for ESCC and GCA patients.

The Association of GSDMB and ORMDL3 Gene Polymorphisms With Asthma: A Meta-Analysis

Chun-Ni Zhao,Ye Fan,Jian-Jun Huang,Hai-Xia Zhang,Tao Gao,Cong Wang,Tong Wang,Li-Fang Hou 대한천식알레르기학회 2015 Allergy, Asthma & Immunology Research Vol.7 No.2

Purpose: ORM1-like 3 (ORMDL3) belongs to a highly conserved protein family which is anchored as transmembrane protein in the endoplasmic reticulum. Gasdermin B (GSDMB) is adjacent to ORMDL3 on chromosome 17q21.2 and belongs to the gasdermin-domain containing the protein family(GSDM family). Recent reports suggest that GSDMB and ORMDL3 are associated with asthma in several populations. However, genetic associationstudies that examined the association of GSDMB and ORMDL3 gene variants with asthma showed conflicting results. To assess whether combinedevidence shows the association between GSDMB/ORMDL3 polymorphism and asthma. Methods: A bibliographic search from MEDLINE identified13 original articles using the search keywords ‘GSDMB’, ‘ORMDL3’, and ‘asthma’. An updated literature-based meta-analysis involving 6,691 subjectswith asthma, 9,281 control individuals, and 1,360 families were conducted. Meta-odds ratios (ORs) and 95% confidence intervals (CIs) basedon the fixed effects model or the random effects model depended on Cochran’s Q-statistic and I2 values. Data from case-control and TDT studieswere analyzed in an allelic model using the Catmap software. Results: We selected and identified 3 SNPs of ORMDL3 associated with asthma(rs8076131: OR=1.10; 95% CI, 1.02-1.20; P=0.012. rs12603332: OR=1.15; 95% CI, 1.05-1.25; P=0.002. rs3744246: OR=1.10; 95% CI, 1.02-1.17;P=0.008) and 1 SNP of GSDMB associated with asthma (rs7216389: OR=1.37; 95% CI, 1.27-1.47; P<0.01). Publication bias was estimated usingmodified Egger’s linear regression test proposed by Harbordetal and revealed no evidence of biases. Furthermore, cumulative meta-analysis in chronologicalorder showed the inclination toward significant association for rs7216389 and rs12603332 with continually adding studies, and the inclinationtoward null-significant association for rs3744246 and rs8076131. Conclusions: Moderate evidence exists for associations of the ORMDL3rs8076131, rs12603332, and rs3744246 and GSDMB rs7216389 variants with asthma. Large sample size and representative population-based studiesand TDT studies with homogeneous asthmatic patients and well-matched controls are warranted to confirm this finding.

Comparative Genomic Analysis Reveals That the 20K and 38K Prophages in Listeria monocytogenes Serovar 4a Strains Lm850658 and M7 Contribute to Genetic Diversity but Not to Virulence

( Chun Fang ),( Tong Cao ),( Ying Shan ),( Ye Xia ),( Yong Ping Xin ),( Chang Yong Cheng ),( Houhui Song ),( John Bowman ),( Xiao Liang Li ),( Xiang Yang Zhou ),( Wei Huan Fang ) 한국미생물 · 생명공학회 2016 Journal of microbiology and biotechnology Vol.26 No.1

Listeria monocytogenes is a foodborne pathogen of considerable genetic diversity with varying pathogenicity. Initially, we found that the strain M7 was far less pathogenic than the strain Lm850658 though both are serovar 4a strains belonging to the lineage III. Comparative genomic approaches were then attempted to decipher the genetic basis that might govern the strain-dependent pathotypes. There are 2,761 coding sequences of 100% nucleotide identity between the two strains, accounting for 95.7% of the total genes in Lm850658 and 92.7% in M7. Lm850658 contains 33 specific genes, including a novel 20K prophage whereas strain M7 has 130 specific genes, including two large prophages (38K and 44K). To examine the roles of these specific prophages in pathogenicity, the 20K and 38K prophages were deleted from their respective strains. There were virtually no differences of pathogenicity between the deletion mutants and their parent strains, although some putative virulent factors like VirB4 are present in the 20K region or holin-lysin in the 38K region. In silico PCR analysis of 29 listeria genomes show that only strain SLCC2540 has the same 18 bp integration hotspot as Lm850658, whereas the sequence identity of their 20K prophages is very low (21.3%). The 38K and 44K prophages are located in two other different hotspots and are conserved in low virulent strains M7, HCC23, and L99. In conclusion, the 20K and 38K prophages of L. monocytogenes serovar 4a strains Lm850658 and M7 are not related to virulence but contribute to genetic diversity.