1.Bioinformatics analysis of ferroptosis-related gene expression profile in primary open angle glaucoma
International Eye Science 2023;23(10):1699-1708
AIM:To investigate the ferroptosis-related key genes in the progression of primary open angle glaucoma(POAG)through bioinformatics analysis, aiming to gain a deeper understanding of the biological mechanism of ferroptosis in POAG.METHODS: The GSE27276 dataset, derived from the trabecular meshwork, was obtained from the GEO database. It consisted of 19 trabecular meshwork tissue samples and 17 normal trabecular meshwork tissue samples. The ferroptosis-related genes were obtained from the FerrDb database. Then the GSE27276 dataset with the ferroptosis gene set was mapped, differentially expressed ferroptosis-related genes(DE-FRGs)were identified in POAG, and the correlation analysis was performed. Additionally, the gene ontology(GO)function and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways of DE-FRGs were further analyzed. This study utilized two machine learning algorithms, namely the LASSO regression model and the SVM-RFE model, to identify the ferroptosis-related key genes of POAG. The screening results from both models were intersected to identify the most significant genes. The clinical diagnostic performance of these genes was evaluated using the receiver operating characteristic curve(ROC); the gene set enrichment analysis(GSEA)and gene set variation analysis(GSVA)were conducted on the most significant genes; the expression levels of these genes were validated using the GSE2378 and GSE9944 datasets obtained from the optic nerve head.RESULTS: In comparison to normal trabecular meshwork tissue, a total of 396 ferroptosis genes exhibited differential expression in POAG trabecular meshwork tissue. Among these, 39 genes were up-regulated while 64 genes were down-regulated. Spearman correlation analysis revealed certain correlation between the up-regulated genes and the down-regulated genes. The GO function and KEGG pathway enrichment analysis revealed that the differential genes were primarily enriched in the oxidative stress response and ferroptosis pathways. A total of 18 DE-FRGs were identified as key genes using LASSO and SVM-RFE algorithms, which demonstrated a higher diagnostic value. GSEA and GSVA revealed a significant association between GDF15, MFN2, and OTUB1 genes with the glutathione metabolic pathway. Moreover, it was observed that MFN2 activated the glutathione metabolic pathway in the high expression group, while OTUB1 activated it in the low expression group. The cross-validation of GSE2378 and GSE9944 datasets revealed a significant increase in the expression level of CREB1 in optic nerve specimens compared to normal optic nerve specimens, and it was consistent with the expression observed in trabecular meshwork samples from the GSE27276 dataset.CONCLUSION: Based on bioinformatics analysis, a total of 396 DE-FRGs were identified in POAG. By constructing a machine screening model and cross-validation of external datasets, CREB1 is expected to be the best characteristic gene for potential diagnostic biomarker, and provide targets for further elucidating the molecular mechanism and the diagnosis of ferroptosis in POAG. However, further in vivo and in vitro validation is required to elucidate the biological mechanism of ferroptosis in POAG.
2.Choice of surgical approaches for salvage surgery of primary lesion recurrence and residual cases of nasopharyngeal carcinoma
Zhong-Qiang TAO ; Yong-Feng SI ; Sheng-Yong LAN ; Zheng ZHANG ; Zhuo-Xia DENG ; Bo HUANG ; Ri-Jing ZHOU ; Jin-Long LU
Chinese Journal of Otorhinolaryngology Head and Neck Surgery 2011;46(2):108-113
Objective The choice of surgical approaches for salvage surgery based on the location and invasion of recurrent and residual lesions of nasopharyngeal carcinoma (NPC),surgical results,complications,and survival were assessed.Methods Thirty-seven cases with recurrent and residual lesions of NPC underwent salvage surgery between March 1991 and January 2005 were analysed retrospectively.Of 37 patients,23 were men and 14 women,with a median age of 46.5 years (26 -57 years) ;4 were at stage Ⅰ,10 at stage Ⅱ,14 at stage Ⅲ,and 9 at stage Ⅳ; 5 cases were with cervical metastasis,including 3 cases of N1 and 2 cases N2.All recurrent and residual lesions of NPC were determined by biopsy.On the location and invasion of recurrent and residual lesions of NPC,8 cases underwent endoscopic resection of lesions,12 cases of the palate nasopharyngectomy,5 cases of maxillary swing,4 cases of maxillary swing plus preronal approach,2 cases of lateral rhinotomy plus coronalflap approach,and 6 cases transfacial plus nasal pyramid swing approach.Five cases with cervical metastasis received neck dissection in addition to the operations for recurrent and residual lesions of NPC. Postoperatively 31 cases received radiotherapy with dosage of 60 Gy,among them 15 cases with concurrent chemoradiation therapy,and 6 cases with clear surgical margin did not received radiotherapy or chemotherapy. The cases were followed up for 12 - 72 months,with a median of 45 months.Results Total resection for the recurrent and residual lesions of NPC acounted for 91.8% (34/37) and subtotal resection for 8.2% (3/37). The accidence of perioperative complications was 24.3% (9/37). The 3- and 5-year overall disease-free survival rates (DFSR) were 62.1% and 43.3%,respectively. The 3- and 5-year overall survival rates (OSR) were 72.9% and 51.3%,respectively.The 5 year DFSR of cases at stage Ⅰ - Ⅳ were 100%,40%,28% and 11% (χ2 =10.0,P <0.01=,respectively.The 5 year OSR were 100%,70%,35% and 28% (χ2 = 11.5,P <0.01),respectively.Conclusions Salvage surgery is a justified treatment for the recurren and residual lesions of NPC,by which some patients with recurren and residual lesions of NPC can be salvaged.
3.Different dissecting orders of the pulmonary bronchus and vessels during right upper lobectomy are associated with surgical feasibility and postoperative recovery for lung cancer patients
Zhai HAO-RAN ; Yang XUE-NING ; Nie QIANG ; Liao RI-QIANG ; Dong SONG ; Li WEI ; Jiang BEN-YUAN ; Yang JIN-JI ; Zhou QING ; Tu HAI-YAN ; Zhang XU-CHAO ; Wu YI-LONG ; Zhong WEN-ZHAO
Chinese Journal of Cancer 2017;36(10):468-477,封3
Background: Right upper lobectomy (RUL) for lung cancer with different dissecting orders involves the most vari-able anatomical structures, but no studies have analyzed its effects on postoperative recovery. This study compared the conventional surgical approach, VAB (dissecting pulmonary vessels first, followed by the bronchus), and the alter-native surgical approach, aBVA (dissecting the posterior ascending arterial branch first, followed by the bronchus and vessels) on improving surgical feasibility and postoperative recovery for lung cancer patients. Methods: According to the surgical approach, consecutive lung cancer patients undergoing RUL were grouped into aBVA and VAB cohorts. Their clinical, pathologic, and perioperative characteristics were collected to compare periop-erative outcomes. Results: Three hundred one patients were selected (109 in the aBVA cohort and 192 in the VAB cohort). The mean operation time was shorter in the aBVA cohort than in the VAB cohort (164 vs. 221 min, P < 0.001), and less blood loss occurred in the aBVA cohort (92 vs. 141 mL, P < 0.001). The rate of conversion to thoracotomy was lower in the aBVA cohort than in the VAB cohort (0% vs. 11.5%, P < 0.001). The mean duration of postoperative chest drainage was shorter in the aBVA cohort than in the VAB cohort (3.6 vs. 4.5 days, P = 0.001). The rates of postoperative complica-tions were comparable (P = 0.629). The median overall survival was not arrived in both cohorts (P > 0.05). The median disease-free survival was comparable for all patients in the two cohorts (not arrived vs. 41.97 months) and for patients with disease recurrences (13.25 vs. 9.44 months) (both P > 0.05). The recurrence models in two cohorts were also comparable for patients with local recurrences (6.4% vs. 7.8%), distant metastases (10.1% vs. 8.3%), and both (1.8% vs. 1.6%) (all P > 0.05). Conclusions: Dissecting the right upper bronchus before turning over the lobe repeatedly and dissecting veins via the aBVA approach during RUL would promote surgical feasibility and achieve comparable postoperative recovery for lung cancer patients.
5.Cloning and Expression Patterns of LmC3H1 Gene in Lonicera macranthoides and Its Correlation with Chlorogenic Acid Content
Ya CHEN ; An-qi WANG ; Cong LIU ; Yu-qing LONG ; Xia LIU ; Juan ZENG ; Can LI ; Xiang-dan LIU ; Ri-bao ZHOU
Chinese Journal of Experimental Traditional Medical Formulae 2020;26(9):167-175
Objective::To clone
6.Cloning and function analysis of chalcone isomerase gene and chalcone synthase gene in Lonicera macranthoides.
Juan ZENG ; Yu-Qing LONG ; Can LI ; Mei ZENG ; Min YANG ; Xin-Ru ZHOU ; Xiang-Dan LIU ; Ri-Bao ZHOU
China Journal of Chinese Materia Medica 2022;47(9):2419-2429
In order to explore the functions of genes of key rate-limiting enzymes chalcone isomerase(CHI) and chalcone synthase(CHS) in the biosynthesis of flavonoids in Lonicera macranthoides, this study screened and cloned the cDNA sequences of CHI and CHS genes from the transcriptome data of conventional variety and 'Xianglei' of L. macranthoides. Online bioinformatics analysis software was used to analyze the characteristics of the encoded proteins, and quantitative reverse-transcription polymerase chain reaction(qRT-PCR) to detect the expression of CHI and CHS in different parts of the varieties at different flowering stages. The content of luteo-loside was determined by high performance liquid chromatography(HPLC) and the correlation with the expression of the two genes was analyzed. The results showed that the CHI and CHS of the two varieties contained a 627 bp and 1170 bp open reading frame(ORF), respectively, and the CHI protein and CHS protein were stable, hydrophilic, and non-secretory. qRT-PCR results demonstrated that CHI and CHS of the two varieties were differentially expressed in stems and leaves at different flowering stages, particularly the key stages. Based on HPLC data, luteoloside content was in negative correlation with the relative expression of the genes. Thus, CHI and CHS might regulate the accumulation of flavonoids in L. macranthoides, and the specific functions should be further studied. This study cloned CHI and CHS in L. macranthoides and analyzed their expression for the first time, which laid a basis for investigating the molecular mechanism of the differences in flavonoids such as luteoloside in L. macranthoides and variety breeding.
Acyltransferases/metabolism*
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Chalcone
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Cloning, Molecular
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Intramolecular Lyases
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Lonicera/metabolism*
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Plant Breeding
7.Mining and identification of members of MYB transcription factor family in Lonicera macranthoides.
Juan ZENG ; Yu-Qing LONG ; Xue-Sen FU ; Ling WANG ; Zi-Xuan LIU ; Ri-Bao ZHOU ; Xiang-Dan LIU
China Journal of Chinese Materia Medica 2023;48(8):2103-2115
As a large family of transcription factors, the MYB family plays a vital role in regulating flower development. We studied the MYB family members in Lonicera macranthoides for the first time and identified three sequences of 1R-MYB, 47 sequences of R2R3-MYB, two sequences of 3R-MYB, and one sequence of 4R-MYB from the transcriptome data. Further, their physicochemical properties, conserved domains, phylogenetic relationship, protein structure, functional information, and expression were analyzed. The results show that the 53 MYB transcription factors had different conserved motifs, physicochemical properties, structures, and functions in wild type and 'Xianglei' cultivar of L. macranthoides, indicating their conservation and diversity in evolution. The transcript level of LmMYB was significantly different between the wild type and 'Xianglei' cultivar as well as between flowers and leaves, and some genes were specifically expressed. Forty-three out of 53 LmMYB sequences were expressed in both flowers and leaves, and 9 of the LmMYB members showed significantly different transcript levels between the wild type and 'Xianglei' cultivar, which were up-regulated in the wild type. The results provide a theoretical basis for further studying the specific functional mechanism of the MYB family.
Transcription Factors/metabolism*
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Lonicera/metabolism*
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Phylogeny
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Plant Proteins/metabolism*
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Gene Expression Regulation, Plant