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Gene expression profiling leads to discovery of correlation of matrix metalloproteinase 11 and heparanase 2 in breast cancer progression.

Fu J, Khaybullin R, Zhang Y, Xia A, Qi X - BMC Cancer (2015)

Bottom Line: A group of 28 promising genes were identified with ≥ 10-fold changes of expression level and p-values < 0.05.In particular, MMP11 and HPSE2 were closely examined due to the important roles they play in cancer cell growth and migration.Real-time RT-qPCR analyses of both training and testing sets validated the gene expression profiles of MMP11 and HPSE2.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1600 SW Archer Rd, Health Science Center P5-31, Gainesville, FL, 32610, USA. jfu@ufl.edu.

ABSTRACT

Background: In order to identify biomarkers involved in breast cancer, gene expression profiling was conducted using human breast cancer tissues.

Methods: Total RNAs were extracted from 150 clinical patient tissues covering three breast cancer subtypes (Luminal A, Luminal B, and Triple negative) as well as normal tissues. The expression profiles of a total of 50,739 genes were established from a training set of 32 samples using the Agilent Sure Print G3 Human Gene Expression Microarray technology. Data were analyzed using Agilent Gene Spring GX 12.6 software. The expression of several genes was validated using real-time RT-qPCR.

Results: Data analysis with Agilent GeneSpring GX 12.6 software showed distinct expression patterns between cancer and normal tissue samples. A group of 28 promising genes were identified with ≥ 10-fold changes of expression level and p-values < 0.05. In particular, MMP11 and HPSE2 were closely examined due to the important roles they play in cancer cell growth and migration. Real-time RT-qPCR analyses of both training and testing sets validated the gene expression profiles of MMP11 and HPSE2.

Conclusions: Our findings identified these 2 genes as a novel breast cancer biomarker gene set, which may facilitate the diagnosis and treatment in breast cancer clinical therapies.

No MeSH data available.


Related in: MedlinePlus

Validation of expression of HPSE2 and MMP11 using RT-qPCR. Seven samples were picked from the training set, representing Luminal A (C427 and C696), Luminal B (C927 and C369), Triple negative (C430 and C434), and normal tissue (N518) respectively. Fold changes of gene expression were calculated with the 2-ΔΔCT method, using β-actin as the house keeping gene. Results were shown as mean ± SEM from triplicates (n = 3). *p < 0.05 compared with N518, **p < 0.001 compared with N518
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Fig5: Validation of expression of HPSE2 and MMP11 using RT-qPCR. Seven samples were picked from the training set, representing Luminal A (C427 and C696), Luminal B (C927 and C369), Triple negative (C430 and C434), and normal tissue (N518) respectively. Fold changes of gene expression were calculated with the 2-ΔΔCT method, using β-actin as the house keeping gene. Results were shown as mean ± SEM from triplicates (n = 3). *p < 0.05 compared with N518, **p < 0.001 compared with N518

Mentions: To further validate the reliability of our gene array data, another 7 samples were randomly selected from the testing set (Fig. 1), including subtype Luminal A (C427 and C696), Luminal B (C927 and C369), Triple negative (C430 and C434), and normal control (N319). The results were shown in Fig. 5, which confirmed the gene expression profile for HPSE2 and MMP11 from microarray data. Validation with other samples from the testing set is still ongoing while our initial testing results demonstrated the reliability of the gene expression profiling generated by our genearray data.Fig. 5


Gene expression profiling leads to discovery of correlation of matrix metalloproteinase 11 and heparanase 2 in breast cancer progression.

Fu J, Khaybullin R, Zhang Y, Xia A, Qi X - BMC Cancer (2015)

Validation of expression of HPSE2 and MMP11 using RT-qPCR. Seven samples were picked from the training set, representing Luminal A (C427 and C696), Luminal B (C927 and C369), Triple negative (C430 and C434), and normal tissue (N518) respectively. Fold changes of gene expression were calculated with the 2-ΔΔCT method, using β-actin as the house keeping gene. Results were shown as mean ± SEM from triplicates (n = 3). *p < 0.05 compared with N518, **p < 0.001 compared with N518
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4477316&req=5

Fig5: Validation of expression of HPSE2 and MMP11 using RT-qPCR. Seven samples were picked from the training set, representing Luminal A (C427 and C696), Luminal B (C927 and C369), Triple negative (C430 and C434), and normal tissue (N518) respectively. Fold changes of gene expression were calculated with the 2-ΔΔCT method, using β-actin as the house keeping gene. Results were shown as mean ± SEM from triplicates (n = 3). *p < 0.05 compared with N518, **p < 0.001 compared with N518
Mentions: To further validate the reliability of our gene array data, another 7 samples were randomly selected from the testing set (Fig. 1), including subtype Luminal A (C427 and C696), Luminal B (C927 and C369), Triple negative (C430 and C434), and normal control (N319). The results were shown in Fig. 5, which confirmed the gene expression profile for HPSE2 and MMP11 from microarray data. Validation with other samples from the testing set is still ongoing while our initial testing results demonstrated the reliability of the gene expression profiling generated by our genearray data.Fig. 5

Bottom Line: A group of 28 promising genes were identified with ≥ 10-fold changes of expression level and p-values < 0.05.In particular, MMP11 and HPSE2 were closely examined due to the important roles they play in cancer cell growth and migration.Real-time RT-qPCR analyses of both training and testing sets validated the gene expression profiles of MMP11 and HPSE2.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1600 SW Archer Rd, Health Science Center P5-31, Gainesville, FL, 32610, USA. jfu@ufl.edu.

ABSTRACT

Background: In order to identify biomarkers involved in breast cancer, gene expression profiling was conducted using human breast cancer tissues.

Methods: Total RNAs were extracted from 150 clinical patient tissues covering three breast cancer subtypes (Luminal A, Luminal B, and Triple negative) as well as normal tissues. The expression profiles of a total of 50,739 genes were established from a training set of 32 samples using the Agilent Sure Print G3 Human Gene Expression Microarray technology. Data were analyzed using Agilent Gene Spring GX 12.6 software. The expression of several genes was validated using real-time RT-qPCR.

Results: Data analysis with Agilent GeneSpring GX 12.6 software showed distinct expression patterns between cancer and normal tissue samples. A group of 28 promising genes were identified with ≥ 10-fold changes of expression level and p-values < 0.05. In particular, MMP11 and HPSE2 were closely examined due to the important roles they play in cancer cell growth and migration. Real-time RT-qPCR analyses of both training and testing sets validated the gene expression profiles of MMP11 and HPSE2.

Conclusions: Our findings identified these 2 genes as a novel breast cancer biomarker gene set, which may facilitate the diagnosis and treatment in breast cancer clinical therapies.

No MeSH data available.


Related in: MedlinePlus