Expression analysis of transcription factors in sugarcane during cold stress / Análise de expressão de fatores de transcrição em cana-de-açúcar sob estresse por frio

Transcription factors (TF) are a wide class of genes in plants, and these can regulate the expression of other genes in response to various environmental stresses (biotic and abiotic). In the current study, transcription factor activity in sugarcane was examined during cold stress. Initially, RNA transcript reads of two sugarcane cultivars (ROC22 and GT08-1108) under cold stress were downloaded from SRA NCBI database. The reads were aligned into a reference genome and the differential expression analyses were performed with the R/Bioconductor edgeR package. Based on our analyses in the ROC22 cultivar, 963 TF genes were significantly upregulated under cold stress among a total of 5649 upregulated genes, while 293 TF genes were downregulated among a total of 3,289 downregulated genes. In the GT08-1108 cultivar, 974 TF genes were identified among 5,649 upregulated genes and 283 TF genes were found among 3,289 downregulated genes. Most transcription factors were annotated with GO categories related to protein binding, transcription factor binding, DNA-sequence-specific binding, transcription factor complex, transcription factor activity in RNA polymerase II, the activity of nucleic acid binding transcription factor, transcription corepressor activity, sequence-specific regulatory region, the activity of transcription factor of RNA polymerase II, transcription factor cofactor activity, transcription factor activity from plastid promoter, transcription factor activity from RNA polymerase I promoter, polymerase II and RNA polymerase III. The findings of above results will help to identify differentially expressed transcription factors during cold stress. It also provides a comprehensive analysis of the regulation of the transcription activity of many genes. Therefore, this study provides the molecular basis for improving cold tolerance in sugarcane and other economically important grasses.

Fatores de transcrição (FT) são uma ampla classe de genes em plantas e podem regular a expressão de outros genes em resposta a vários estresses ambientais (estresses bióticos e abióticos). No presente estudo, a atividade do fator de transcrição na cana-de-açúcar foi examinada durante o estresse pelo frio. Inicialmente, as leituras de transcrição de RNA de duas cultivares de cana-de-açúcar (ROC22 e GT08-1108) sob estresse frio foram baixadas do banco de dados SRA NCBI. As leituras foram alinhadas em um genoma de referência e as análises de expressão diferencial foram realizadas com o pacote R / Bioconductor edgeR. Com base em nossas análises no cultivar ROC22, 963 genes TF foram significativamente regulados positivamente sob estresse pelo frio entre um total de 5.649 genes regulados positivamente, enquanto 293 genes TF foram regulados negativamente entre um total de 3.289 genes regulados negativamente. No cultivar GT08-1108, 974 genes TF foram identificados entre 5.649 genes regulados positivamente e 283 genes TF foram encontrados entre 3.289 genes regulados negativamente. Os fatores de transcrição, em sua maioria, foram anotados com categorias GO relacionadas à ligação de proteína, ligação de fator de transcrição, ligação específica de sequência de DNA, complexo de fator de transcrição, atividade de fator de transcrição em RNA polimerase II, atividade de fator de transcrição de ligação de ácido nucleico, atividade de corepressor de transcrição, sequência específica da região reguladora, atividade do fator de transcrição da RNA polimerase II, atividade do cofator do fator de transcrição, atividade do fator de transcrição do promotor do plastídio, atividade do fator de transcrição do promotor da RNA polimerase I, polimerase II e RNA polimerase III. As descobertas dos resultados acima ajudarão a identificar fatores de transcrição expressos diferencialmente durante o estresse pelo frio. Ele também fornece uma análise abrangente da regulação da atividade [...].

Expression of e-cadherin and wnt pathway proteins betacatenin, apc, tcf-4 and survivin in gastric adenocarcinoma: clinical and pathological implication / Expressão da e-caderina e das proteínas da via de sinalização wnt betacatenina, apc, tcf-4 e survivina no adenocarcinoma gástrico: implicações clínica e patológica

ABSTRACT Background: Gastric cancer is the fifth most frequent cancer and the third most common cause of cancer-related deaths worldwide.It has been reported that Wnt/ betacatenin pathway is activated in 30-50% of these tumors. However,the deregulation of this pathway has not been fully elucidated. Aim: To determine the expression of E-cadherin, betacatenin, APC, TCF-4 and survivin proteins in gastric adenocarcinoma tissues and correlate with clinical and pathological parameters. Method: Seventy-one patients with gastric adenocarcinoma undergoing gastrectomy were enrolled. The expression of E-cadherin, betacatenin, APC, TCF-4 and survivin proteins was detected by immunohistochemistryand related to the clinical and pathological parameters. Results: The expression rates of E-cadherin in the membrane was 3%; betacatenin in the cytoplasm and nucleus were 23,4% and 3,1% respectively; APC in the cytoplasm was 94,6%; TCF-4 in the nucleus was 19,4%; and survivin in the nucleus 93,9%. The expression rate of E-cadherin was correlated with older patients (p=0,007), while betacatenin with tumors <5 cm (p=0,041) and APC with proximal tumors (p=0,047). Moreover, the expression of TCF-4 was significantly higher in the diffuse type (p=0,017) and T4 tumors (p=0,002). Conclusion: The Wnt/betacatenin is not involved in gastric carcinogenesis. However, the high frequency of survivin allows to suggest that other signaling pathways must be involved in the transformation of gastric tissue.

RESUMO Racional: O câncer gástrico encontra-se entre as principais neoplasias malignas do mundo sendo o quinto mais incidente e o terceiro em relação ao índice de mortalidade. Acredita-se que a via Wnt/betacatenina esteja ativada em 30-50% desses tumores, porém a desregulação dela ainda não está completamente esclarecida. Objetivo: Avaliar a imunoexpressão das proteínas E-caderina, betacatenina, APC, TCF-4 e survivina em tecidos de adenocarcinoma gástrico e correlacioná-las com as variáveis clínicas dos doentes e anatomopatológicas do tumor. Método: Foram coletados os dados clínicos e anatomopatológicos dos prontuários de 71 doentes com adenocarcinoma gástrico submetidos à gastrectomia. O material obtido na operação foi submetido à análise imunoistoquímica e a frequência da expressão de cada proteína pôde ser analisada de acordo com a sua localização na célula e relacionada com as variáveis clinicopatológicas. Resultados: A graduação percentualda expressão e da localização das proteínas foi a seguinte: E-caderina em 3% na membrana; betacatenina em 23,4% no citoplasma e 3,1% no núcleo; APC em 94,6% no citoplasma; TCF-4 em19,4% no núcleo; e survivina em 93,9% no núcleo. Houve relação entre expressão da proteína E-caderina com a idade mais avançada (p=0,007); betacatenina com tumores <5 cm de diâmetro (p=0,041);APC com tumores proximais (p=0,047); e TCF-4 com tipo difuso da classificação de Lauren (p=0,017) e com o grau de penetração tumoral (p=0,002). Conclusão: A via Wnt/betacatenina não está envolvida na carcinogênese gástrica. Porém, a frequência elevada de survivina permite sugerir que outras vias sinalizadoras devam estar envolvidas na transformação do tecido gástrico.

The NER-related gene GTF2H5 predicts survival in high-grade serous ovarian cancer patients / 부인종양

OBJECTIVE: We aimed to evaluate the prognostic and predictive value of the nucleotide excision repair-related gene GTF2H5, which is localized at the 6q24.2-26 deletion previously reported by our group to predict longer survival of high-grade serous ovarian cancer patients. METHODS: In order to test if protein levels of GTF2H5 are associated with patients' outcome, we performed GTF2H5 immunohistochemical staining in 139 high-grade serous ovarian carcinomas included in tissue microarrays. Upon stratification of cases into high- and low-GTF2H5 staining categories (> and < or = median staining, respectively) Kaplan-Meier and log-rank test were used to estimate patients' survival and assess statistical differences. We also evaluated the association of GTF2H5 with survival at the transcriptional level by using the on-line Kaplan-Meier plotter tool, which includes gene expression and survival data of 855 high-grade serous ovarian cancer patients from 13 different datasets. Finally, we determined whether stable short hairpin RNA-mediated GTF2H5 downregulation modulates cisplatin sensitivity in the SKOV3 and COV504 cell lines by using cytotoxicity assays. RESULTS: Low expression of GTF2H5 was associated with longer 5-year survival of patients at the protein (hazard ratio [HR], 0.52; 95% CI, 0.29 to 0.93; p=0.024) and transcriptional level (HR, 0.80; 95% CI, 0.65 to 0.97; p=0.023) in high-grade serous ovarian cancer patients. We confirmed the association with 5-year overall survival (HR, 0.55; 95% CI, 0.38 to 0.78; p=0.0007) and also found an association with progression-free survival (HR, 0.72; 95% CI, 0.54 to 0.96; p=0.026) in a homogenous group of 388 high-stage (stages III-IV using the International Federation of Gynecology and Obstetrics staging system), optimally debulked high-grade serous ovarian cancer patients. GTF2H5-silencing induced a decrease of the half maximal inhibitory concentration upon cisplatin treatment in GTF2H5-silenced ovarian cancer cells. CONCLUSION: Low levels of GTF2H5 are associated with enhanced prognosis in high-grade serous ovarian cancer patients and may contribute to cisplatin sensitization.

Human hepatoma cell line (Hep G2) cellular response to hypothermic stress with recovery: Induction of Hsp70, Hsp60 and Hsf1 expression / Respuesta celular de línea de hepatoma humano (HepG2) al estrés hipotérmico con recuperación: Inducción de la expresión de Hsp60, Hsp70, y Hsf1

The cell response of human HepG2 cells exposed to hypothermia with rewarming was analyzed. Ultrastructural findings in hypothermic stressed cells showed swollen mitochondria, dispersed chromatin, vacuoles and ring-shape nucleolar reorganization. These changes were coupled with significative differences in the induction of Hsp60, inducible Hsp70 and monomeric Hsf1 in all treated samples, but not in Hsc 70 expression. Cellular response to hypothermia could be associated with the synergistic induction of Hsp expression.

En este trabajo se analizó la respuesta celular de células HepG2 expuestas a hipotermia con posterior recuperación. Los hallazgos ultraestructurales en células sometidas a estrés hipotérmico incluyeron mitocondrias edematizadas, núcleos picnóticos, vacuolas y reorganización nucleolar en forma de anillo. Tales cambios están relacionados con diferencias significativas en la inducción de la expresión de Hsp60, Hsp70 inducible y Hsf 1 monomérico en todas las muestras tratadas, pero no de Hsc70. La respuesta celular a la hipotermia puede ser relacionada con la inducción sinergística de las Hsp.

Effect of antisense MBD1 gene eukaryotic expression plasmid on expression of MBD1 gene in human biliary tract carcinoma cells / 华中科技大学学报（医学）（英德文版）

Hypermethylation of the promoter region is one of the major mechanism of tumor suppressor gene inactivation. In order to provide a research tool for the study on the function of MBD1 gene in DNA methylation and tumorigenesis, antisense MBD1 gene eukaryotic expression plasmid was constructed and transfected into human biliary tract carcinoma cell line QBC-939 to observe its effect on the expression of MBD1 mRNA and protein by using RT-PCR and FCM respectively. Following the transfection, the mRNA level of MBD1 gene decreased from 0. 912 +/- 0.022 to 0.215 +/- 0. 017, and the protein level of MBD1 gene also decreased from (80.19 +/- 5.05) % to (35.11 +/- 4.05) %. There were very significant differences in the expression both at the transcription and post-transcription levels of MBD1 gene between non-tranfection group and the antisense MBD1 gene eukaryotic expression plasmid transfection group (P < 0.01). It was suggested that transfection with the antisense MBD1 gene eukaryotic expression plasmid can significantly reduce the expression level of MBD1 gene in QBC-939, and this study may provide a valid tool for the investigation of the function of MBD1 gene and its role in biliary tract carcinoma.

Expression of CD99 in Pleomorphic Carcinomas of the Lung

Pleomorphic carcinoma of the lung (PCL) is characterized by a mixture of sarcomatoid and carcinoma components, and a poor prognosis. However, no immunophenotype of tumor markers has been characterized in PCL. To charaterize the immunophenotype for CD99 in PCL, we performed an immunohistochemical evaluation of PCLs for thyroid transcription factor-1 (TTF-1), cytokeratin (CK) 7 and 20, and for CD99. CD99 was found to be expressed in both carcinomatous (47%) and sarcomatous components such as spindle cells (92%) and giant cells (57%). In the case of spindle cells, CK7 was expressed in 6 cases (46%) and TTF-1 in 2 cases (15%), whereas for giant cells CK7 was expressed in 8 cases (57%) and TTF-1 in one case (7%). However, CK20 was not expressed in either the carcinomatous or sarcomatous components in any case. Thus, CD99 was found to be widely expressed in both sarcomatous and carcinoma component in PCL. A clinicopathological analysis showed no direct correlation between the expression of CD99 and the clinical indices (stage, survival rate, invasion) of PCL.

Inhibition of expression of hypoxia-inducible factor-1alpha mRNA by nitric oxide in hypoxic pulmonary hypertension rats / 华中科技大学学报（医学）（英德文版）

In order to study the effect of nitric oxide (NO) on the expression of hypoxia-inducible factor-1 alpha (HIF-1alpha) mRNA in hypoxic pulmonary hypertension (HPH) rats, 30 healthy male Wistar rats were randomly divided into normoxic control group, chronic hypoxic group and hypoxia plus L-arginine (L-Arg) group. The animal model of HPH was developed. The mean pulmonary arterial pressure (mPAP) was measured by inserting a microcatheter into the pulmonary artery. The HIF-1alpha mRNA expression levels were detected by in situ hybridization (ISH) and semiquantitative RT-PCR. It was found that after 14 days hypoxia, the mPAP in normoxic control group (17.6 +/- 2.7 mmHg, 1 mmHg=0.133 kPa) was significantly lower than that in chronic hypoxic group (35.8 +/- 6.1 mmHg, t=0.2918, P<0.05) and mPAP in chronic hypoxic group was higher than that in hypoxia plus L-arginine group (24.4 +/- 3.8 mmHg, t=0.2563, P<0.05). ISH showed that the expression of HIF-1alpha mRNA in the intraacinar pulmonary arteriolae (IAPA) in normoxic control group (0.1076 +/- 0.0205) was markedly weaker than that in chronic hypoxic group (0.3317 +/- 0.0683, t=3.125, P<0.05) and that in chronic hypoxic group was stronger than that in hypoxia plus L-arginine group (0.1928 +/- 0.0381, t=2.844, P<0.05). RT-PCR showed that the content of HIF-1alpha mRNA in chronic hypoxic group (2.5395 +/- 0.6449) was 2.16 times and 1.75 times higher than that in normoxic control group (1.1781 +/- 0.3628) and hypoxia plus L-arginine group (1.4511 +/- 0.3981), respectively. It is concluded that NO can reduce the mPAP by the inhibition of the expression of HIF-1alpha mRNA, which may be one of the mechanisms through which NO affects the pathogenesis of HPH.

Nerve growth factor(NGF) induces mRNA expression of the new transcription factor protein p48ZnF

Apoptosis, the cell's intrinsic death program, plays a crucial role in the regulation of tissue homeostasis, and abnormal inhibition of apoptosis is an indicator of cancer and autoimmune diseases, whereas excessive cell death is implicated in neurodegenerative disorders such as Alzheimer's disease (AD). Using cDNA subtraction analysis, we compared p60TRP (p60 transcription regulator protein) expressing cells with control cells during the process of apoptosis and we identified the new zinc-finger protein p48ZnF that is predominantly located in the cytoplasm of the cell. Additionally, we demonstrate here that p48ZnF is up-regulated in rat neuronal PC12 cells upon stimulation with the neurotrophic factor NGF (50 ng/ml). These findings point to a possible pivotal role of p48ZnF in the control of neuronal survival.

Thyroid Transcription Factor-1 (TTF-1) Expression in Human Lung Carcinomas: Its Prognostic Implication and Relationship with Expressions of p53 and Ki-67 Proteins

This study was aimed to evaluate the prevalence and prognostic implication of thyroid transcription factor-1 (TTF-1) immunoreactivity in 81 human lung carcinomas, including 65 cases of non-small cell lung carcinoma (NSCLC) and 16 cases of small cell lung carcinoma (SCLC); and also to investigate its relationship with the cell proliferation and regulation by immunostaining of Ki-67 and p53 proteins, respectively. The immunohistochemical staining for TTF-1(clone 8G7G3/1) was performed and several clinicopathologic variables and the follow-up data were obtained. The immuno-staining results for TTF-1 were semiquantitatively interpreted as negative and positive. Of NSCLCs, TTF-1 is highly expressed in adenocarcinomas (76%), whereas squamous cell carcinomas revealed no immunoreactivity (0%). SCLCs showed strong TTF-1 expression (88%). In NSCLC, TTF-1 expression was inversely correlated with Ki-67 proliferative activity and independent of p53 overexpression. TTF-1(+) group tended to show better survival than TTF-1(-) group in NSCLC. Conclusively, these observations suggest that TTF-1 is a sensitive and specific diagnostic marker for pulmonary adenocarcinomas and SCLCs; that TTF-1 might have a good prognostic implication based on its inverse correlation with Ki-67 proliferative activity and tendency for better survival in NSCLC; that this cell lineage marker may play a role in the molecular pathogenesis of lung cancers at the level of transcription.

Expression of interferons-alpha and -beta, tumor necrosis factor-alpha and transcription factors, IRF-1 and IRF-2, in leukocytes induced during interferon production

Analysis of gene expression in peripheral blood lymphocytes is of special interest because it could reflect physiological conditions. We have examined the expression and compared the relative amounts of specific mRNAs for interferons (IFN-alpha and IFN-beta), tumor necrosis factor-alpha (TNF-alpha) and interferon regulatory factors (IRF-1 and IRF-2) from interferon primed and Sendai virus induced peripheral blood leukocytes. Results obtained showed that IRF-1 was highly inducible by IFN treatment, IFN-alpha, TNF-alpha and IRF-2 were weakly induced by IFN treatment, and IFN-beta was not inducible by priming the cells with recombinant human IFN-alpha 2b. The IFN-alpha, IFN-beta, IRF-2 and TNF-alpha transcripts increased upon viral infection. The IRF-1 mRNA was rapidly induced by IFN treatment and decreased after Sendai virus infection. Our results show that, in peripheral blood lymphocytes, IFN-alpha and -beta genes have a different response to IFN induction, thus suggesting different regulatory mechanisms for IFN induction of type I IFN genes in peripheral blood lymphocytes