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Validation of biomarkers expressions by quantitative real-time polymerase chain reaction实时定量聚合酶链反应验证生物标志物的表达
Sixteen bone marrow samples were divided into 2 groups (Initial diagnosis =10, and Relapse = 6). They were lysed by 1 mL of TRIzol Reagent (Life Technologies, CA, USA) respectively, and the total RNA was isolated following the manufacturer’s instructions. After detecting the concentration and the purity of RNA, qualified RNA was reverse-transcribed to cDNA using the SureScript-First-strand-cDNA-synthesis-kit (Genecopoeia, Guangzhou, China) prior to qRT-PCR. The qRT-PCR reaction consisted of 3 µl of cDNA, 5 µl of 2xUniversal Blue SYBR Green qPCR Master Mix (Servicebio, Wuhan, China), and 1 µl each of forward and reverse primer. PCR was performed in a BIO-RAD CFX96 Touch TM PCR detection system (Bio-Rad Laboratories, Inc., USA) under the thermal cycling conditions: 40 cycles at 95°C for 60 s, 95°C for 20 s, 55°C for 20 s, and 72°C for the 30s. The 2-△△Ct method was used to calculate gene expressions, and Graphpad Prism 5 was applied to plot and calculated the statistic significance. Clinical characteristics of B-ALL patients from our study were exhibited in Supplementary Table S2 . The primer sequences used in the current study were given in following Supplementary Table S3 .
将 16 份骨髓样本分为两组(初诊 = 10 份,复发 = 6 份)。
Statistical analysis[...]
All statistical analyses were conducted in R software (3.6.1) and Graphpad Prism 5. The data from different groups were compared by the Wilcoxon test and t-test. If not specifically stated p value < 0.05 was considered statistically significant.
[...]
Results[...]
Identification and enrichment annotation of DE-NMRGs[...]
To identify the DE-NMRGs, expression levels of 33 NMRGs were extracted from GSE3912 according to the 51 NMRGs from previous analysis. The differential analysis showed that 23 DE-NMRGs were screened out between initially diagnosed and relapse samples, which were all up-regulated in relapse samples ( Figures 1A–C ). Moreover, 125 GO terms (107 BP and 18 MF) and 4 KEGG pathways were enriched by the 23 DE-NMRGs. For example, nucleoside phosphate metabolic process, nucleotide metabolic process, protein ADP−ribosylation, etc. were the main enriched terms in BP, and pentosyltransferase activity, NAD binding, NAD+ binding, etc, were the main enriched MF terms ( Supplementary Figure S2A ). The 4 enriched KEGG pathways were Nicotinate and nicotinamide metabolism, Nucleotide metabolism, Pyrimidine metabolism, and Purine metabolism ( Supplementary Figure S2B ).
为了识别DE-NMRGs,根据之前分析的51个NMRGs,从GSE3912中提取了33个NMRGs的表达水平。差异分析表明,在初诊样本和复发样本中筛选出了23个DE-NMRGs,它们在复发样本中均上调(图1A-C)。此外,23个DE-NMRGs还富集了125个GO术语(107个BP术语和18个MF术语)和4个KEGG通路。例如,核苷磷酸代谢过程、核苷酸代谢过程、蛋白质ADP-核糖基化等是BP的主要富集词,戊糖基转移酶活性、NAD结合、NAD+结合等是MF的主要富集词(附图S2A)。4 个富集的 KEGG 通路分别是烟酸和烟酰胺代谢、核苷酸代谢、嘧啶代谢和嘌呤代谢(附图 S2B)。
Discussion[...]
B-ALL is the most common hematological malignancy in children, and relapse is an important adverse factor affecting the survival of patients. About 20% of treated B-ALL patients will relapse and 10% of patients with diagnosed with ALL remain incurable (3). It has been reported that NMRGs in whole blood transcriptome data are biomarkers to predict clinical outcomes in muscular atrophy patients (14), and S Takao et al. have found that depletion of NAD + by KPT-9274 inhibitors may be a promising alternative to treat B-ALL patients (13). Moreover, Sarah K Tasianet al. have also expounded on the biological role of genomic and epigenomic analysis in the initial diagnosis and recurrent ALL (4). However, the mechanism of NMRGs in B-ALL recurrence is still unclear. Therefore, exploring NMRGs has biological importance in the initial diagnosis and recurrence of B-ALL.
[...]
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Validation of biomarkers expressions by quantitative real-time polymerase chain reaction实时定量聚合酶链反应验证生物标志物的表达
Sixteen bone marrow samples were divided into 2 groups (Initial diagnosis =10, and Relapse = 6). They were lysed by 1 mL of TRIzol Reagent (Life Technologies, CA, USA) respectively, and the total RNA was isolated following the manufacturer’s instructions. After detecting the concentration and the purity of RNA, qualified RNA was reverse-transcribed to cDNA using the SureScript-First-strand-cDNA-synthesis-kit (Genecopoeia, Guangzhou, China) prior to qRT-PCR. The qRT-PCR reaction consisted of 3 µl of cDNA, 5 µl of 2xUniversal Blue SYBR Green qPCR Master Mix (Servicebio, Wuhan, China), and 1 µl each of forward and reverse primer. PCR was performed in a BIO-RAD CFX96 Touch TM PCR detection system (Bio-Rad Laboratories, Inc., USA) under the thermal cycling conditions: 40 cycles at 95°C for 60 s, 95°C for 20 s, 55°C for 20 s, and 72°C for the 30s. The 2-△△Ct method was used to calculate gene expressions, and Graphpad Prism 5 was applied to plot and calculated the statistic significance. Clinical characteristics of B-ALL patients from our study were exhibited in Supplementary Table S2 . The primer sequences used in the current study were given in following Supplementary Table S3 .
将 16 份骨髓样本分为两组(初诊 = 10 份,复发 = 6 份)。
Statistical analysis[...]
All statistical analyses were conducted in R software (3.6.1) and Graphpad Prism 5. The data from different groups were compared by the Wilcoxon test and t-test. If not specifically stated p value < 0.05 was considered statistically significant.
[...]
Results[...]
Identification and enrichment annotation of DE-NMRGs[...]
To identify the DE-NMRGs, expression levels of 33 NMRGs were extracted from GSE3912 according to the 51 NMRGs from previous analysis. The differential analysis showed that 23 DE-NMRGs were screened out between initially diagnosed and relapse samples, which were all up-regulated in relapse samples ( Figures 1A–C ). Moreover, 125 GO terms (107 BP and 18 MF) and 4 KEGG pathways were enriched by the 23 DE-NMRGs. For example, nucleoside phosphate metabolic process, nucleotide metabolic process, protein ADP−ribosylation, etc. were the main enriched terms in BP, and pentosyltransferase activity, NAD binding, NAD+ binding, etc, were the main enriched MF terms ( Supplementary Figure S2A ). The 4 enriched KEGG pathways were Nicotinate and nicotinamide metabolism, Nucleotide metabolism, Pyrimidine metabolism, and Purine metabolism ( Supplementary Figure S2B ).
为了识别DE-NMRGs,根据之前分析的51个NMRGs,从GSE3912中提取了33个NMRGs的表达水平。差异分析表明,在初诊样本和复发样本中筛选出了23个DE-NMRGs,它们在复发样本中均上调(图1A-C)。此外,23个DE-NMRGs还富集了125个GO术语(107个BP术语和18个MF术语)和4个KEGG通路。例如,核苷磷酸代谢过程、核苷酸代谢过程、蛋白质ADP-核糖基化等是BP的主要富集词,戊糖基转移酶活性、NAD结合、NAD+结合等是MF的主要富集词(附图S2A)。4 个富集的 KEGG 通路分别是烟酸和烟酰胺代谢、核苷酸代谢、嘧啶代谢和嘌呤代谢(附图 S2B)。
Discussion[...]
B-ALL is the most common hematological malignancy in children, and relapse is an important adverse factor affecting the survival of patients. About 20% of treated B-ALL patients will relapse and 10% of patients with diagnosed with ALL remain incurable (3). It has been reported that NMRGs in whole blood transcriptome data are biomarkers to predict clinical outcomes in muscular atrophy patients (14), and S Takao et al. have found that depletion of NAD + by KPT-9274 inhibitors may be a promising alternative to treat B-ALL patients (13). Moreover, Sarah K Tasianet al. have also expounded on the biological role of genomic and epigenomic analysis in the initial diagnosis and recurrent ALL (4). However, the mechanism of NMRGs in B-ALL recurrence is still unclear. Therefore, exploring NMRGs has biological importance in the initial diagnosis and recurrence of B-ALL.
[...]
补充信息
刷新后重新翻译没有改变,使用梯子也不行
The text was updated successfully, but these errors were encountered: