Screening and analysis on the differentially expression genes between diploid and autotetraploid watermelon by using of digital gene expression profile / Triagem e análise da expressão diferencial dos genes entre melancia diplóide e autotetraplóide através do perfil de expressão gênica digital

Abstract Synthetic polyploids are key breeding materials for watermelon. Compared with diploid watermelon, the tetraploid watermelon often exhibit wide phenotypic differences and differential gene expression. Digital gene expression (DGE) profile technique was performed in this study to present gene expression patterns in an autotetraploid and its progenitor diploid watermelon, and deferentially expressed genes (DEGs) related to the abiotic and biotic stress were also addressed. Altogether, 4,985 DEGs were obtained in the autotetraploid against its progenitor diploid, and 66.02% DEGs is up-regulated. GO analysis shows that these DEGs mainly distributed in 'metabolic process', 'cell' and 'catalytic activity'. KEGG analysis revealed that these DEGs mainly cover 'metabolic pathways', 'secondary metabolites' and 'ribosome'. Moreover, 134 tolerance related DEGs were identified which cover osmotic adjustment substance, protective enzymes/protein, signaling proteins and pathogenesis-related proteins. This study present the differential expression of stress related genes and global gene expression patterns at background level in autotetraploid watermelons. These new evidences could supplement the molecular theoretical basis for the better resistance after the genome doubling in the gourd family.

Resumo Poliploides sintéticos são materias fundamentais para melhoramento genético da melancia. Comparativamente ao seu homólogo diploide, a melancia tetraploide apresenta amplas diferenças genotípica e fenotípica e diferença de expressão gênica. A expressão gênica digital ou DGE (digital gene expression) foi utilizada neste estudo para representar o perfil de expressão gênica da melancia autotetraploide e seu progenitor diploide e a expressão diferencial de genes relacionados ao estresse biótico e abiótico. Os resultados mostraram que 4.985 DEGs foram observados no organismo autotetraploide, sendo que, deste total, 66.02%foram supra-regulados. A análise de ontologia gênica (GO) mostrou que estes DEGs estão relacionados principalmente com processos metabólicas, célula e atividade catalítica, abrangendo de acordo com a análise de genes e genoma (KEGG) rotas metabólicas, metabolismo secundário e ribossomos. Além disso, 134 genes de defesa foram identificados, abrangendo substâncias de ajuste osmótico, enzimas/proteínas de proteção, proteínas sinalizadoras e proteínas relacionadas à patogênese. Este estudo mostrou a expressão diferencial de genes relacionados ao estresse e o perfil global de expressão gênica de melancia autotetraploide, estes resultados podem complementar, a nível molecular, o entendimento do fator resistência após a duplicação do genoma em cucurbitáceas.

Screening and analysis on the differentially expression genes between diploid and autotetraploid watermelon by using of digital gene expression profile

Abstract Synthetic polyploids are key breeding materials for watermelon. Compared with diploid watermelon, the tetraploid watermelon often exhibit wide phenotypic differences and differential gene expression. Digital gene expression (DGE) profile technique was performed in this study to present gene expression patterns in an autotetraploid and its progenitor diploid watermelon, and deferentially expressed genes (DEGs) related to the abiotic and biotic stress were also addressed. Altogether, 4,985 DEGs were obtained in the autotetraploid against its progenitor diploid, and 66.02% DEGs is up-regulated. GO analysis shows that these DEGs mainly distributed in metabolic process, cell and catalytic activity. KEGG analysis revealed that these DEGs mainly cover metabolic pathways, secondary metabolites and ribosome. Moreover, 134 tolerance related DEGs were identified which cover osmotic adjustment substance, protective enzymes/protein, signaling proteins and pathogenesis-related proteins. This study present the differential expression of stress related genes and global gene expression patterns at background level in autotetraploid watermelons. These new evidences could supplement the molecular theoretical basis for the better resistance after the genome doubling in the gourd family.

Resumo Poliploides sintéticos são materias fundamentais para melhoramento genético da melancia. Comparativamente ao seu homólogo diploide, a melancia tetraploide apresenta amplas diferenças genotípica e fenotípica e diferença de expressão gênica. A expressão gênica digital ou DGE (digital gene expression) foi utilizada neste estudo para representar o perfil de expressão gênica da melancia autotetraploide e seu progenitor diploide e a expressão diferencial de genes relacionados ao estresse biótico e abiótico. Os resultados mostraram que 4.985 DEGs foram observados no organismo autotetraploide, sendo que, deste total, 66.02%foram supra-regulados. A análise de ontologia gênica (GO) mostrou que estes DEGs estão relacionados principalmente com processos metabólicas, célula e atividade catalítica, abrangendo de acordo com a análise de genes e genoma (KEGG) rotas metabólicas, metabolismo secundário e ribossomos. Além disso, 134 genes de defesa foram identificados, abrangendo substâncias de ajuste osmótico, enzimas/proteínas de proteção, proteínas sinalizadoras e proteínas relacionadas à patogênese. Este estudo mostrou a expressão diferencial de genes relacionados ao estresse e o perfil global de expressão gênica de melancia autotetraploide, estes resultados podem complementar, a nível molecular, o entendimento do fator resistência após a duplicação do genoma em cucurbitáceas.

DNA Ploidy Study in 1,673 Fresh Solid Tumors / 대한암학회지

PURPOSE: To evaluate the possible role of DNA content abnomrality in solid tumors as a diagnostic indicator in Korean patients, the incidence of aneuploidy in the major organs were analyzed and compared with the incidences which have been reported in the literatures. MATERIALS AND METHODS: Flow cytometric analysis of DNA content were performed on the 1673 fresh tissues of neoplastic lesions which were obtained for the last five years in Hospital. RESULTS: The frequency of aneuploidy was more than 50% in the primary malignant tumors of the stomach, colon, esophagus, liver, biliary tract, pancreas, head and neck organs, salivary gland, lung, breast, ovary, CNS and urinary tract. However, the frequency of aneuploidy was as low as 7% in papillary carcinoma of thyroid and about 30% in renal cell carcinoma and malignant lymphomas. High frequency of aneuploidy (more than 70%) was seen in the metastatic tumors in liver, brain, ovary and lymph nodes. Aneuploidy was also found in benign tumors of salivary gland, adenomas of endocrine organs, meningiomas, smooth muscle tumors and schwannomas. CONCLUSION: The results of present study were in concordant with those of the other domestic and foreign studies. Although aneuploidy can be observed in some benign tumors, DNA ploidy pattern is considered to be an important diagnostic and prognostic factors in malignant lesions of the various organs.

Prognostic Significance of Flow Cytometric Nuclear DNA Content and S-phase Fraction in Non-small Cell Lung Cancer / 대한내과학회지

OBJECTIVES: In surgically treated non-small cell lung cancer, patients have a wide difference in prognosis even though they may be in the same stage. Therefore it is difficult to establish the prognosis for individual lung cancer patients. In this study, by using flow cytometric analysis of nuclear DNA content and S-phase fraction(SPF) of surgically treated non-small cell lung cancer patients, we proposed to establish other prognostic factors and their validity in comparison with the existing ones. METHODS: Paraffin-embedded tissue specimens from 81 surgically treated patients, diagnosed with non-small cell lung cancer ranging from stage I to stage IIIa, were analyzed by flow cytometrically determined nulear DNA content and S-phase fraction. Cellular DNA content stained with propidium iodide was analyzed by flow cytometry: histograms with a coefficient of variation exceeding 8% were not used. RESULTS: 1) DNA content analysis was carried out for 59 of 81 patients. Of the 59 patients who were investigated by flow cytometry, 45 (76.3%) of the tumors were DNA aneuploidy and 14 (23.7%) were DNA diploidy. The proportion of DNA aneuploidy tumors showed no significant difference between cell types or stage. 2) S-phase fraction was evaluated for 36 of 81 patients. Mean value of SPF was 19.2% (+/-12.62)%. The value of SPF had nothing to do with stage. 3) The proportion of the high SPF group (more than 10% of cell proliferation cycle) was 75% With advance staging, the proportion of the high SPF group increased. 4) Significant difference in the median survival time was observed between the low SPF group and the high SPF group (32 months in low SPF, 12 months in high SPF) (p<0.05). No significant difference in the median survival time was observed between the aneuploidy group and the diploidy group (19 months in aneuploidy, 34 months in diploidy). 5) Significant difference in the disease free median survival time was observed between the low SPF group and the high SPF group (5 months in low SPF, 19 months in high SPF) (p<0.05). No significant difference in the disease free median survival time was observed between the aneuploidy group and the diploidy group (12 months in aneuploidy, 34 months in diploidy). 6) Upon multivariate analysis, stage and high SPF (more than 10% of cell proliferation cycle) were significant prognostic factors in surgically treated non-small cell lung cancer patients. CONCLUSION: The TNM stage and high SPF were significant as prognostic factors in surgically treated non-small cell lung cancer patients. Therefore new treatment plan should be needed in the patients who have high SPF.

Hydatidiform Mole with a Coexisting Fetus: Report of three cases with nuclear DNA ploidy analysis by flow cytometry or chromosomal analysis

Three cases of hydatidiform mole with a coexisting fetus are described. In two cases, flow cytometric analysis of nuclear DNA content from paraffin-embedded, molar tissues and normal-appearing placental tissues showed diploid pattern. One case had karyotypes of 46, XX both in fetal skin fibroblasts and in molar tissues. Microscopically, the villi showed diffuse hydropic swelling with circumferential trophoblastic proliferations and consistent with the diagnosis of complete mole. Two patient had persistent gestational trophoblastic neoplasia on the follow-up. Therefore, in cases of hydatidiform mole with a coexisting fetus, dizygotic twin pregnancies composed of a normal pregnancy from one ovum and a complete mole pregnancy from the other ovum must be considered and the patients should be followed with serum beta-hCG measurements.