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Transcriptomic and Functional Pathway Analysis of Human Cervical Carcinoma Cancer Cells Response to Microtubule Inhibitor.

Wang J, Yan B, Liu SM, Sun H, Pan Y, Guan D, Zhang X, Xu J, Ma H - J Cancer (2015)

Bottom Line: We selected the concentration of vinblastine inducing 30% cell death for analyses assessing the DNA content, gene expression and transcriptional gene regulation of VBL-treated KB-3 cells.Transcriptomic and hierarchical clustering analysis demonstrated that treatment of KB-3 cells with VBL altered the expression of a diverse group of genes with G2/M arrest, which regulated by four oncogenic or tumor suppresser transcription factors (AP1, NFKB1, RELA, and TP53).Northern blots also confirmed that KRT-7, FN14, IER3, and ID1 were deregulated in VBL-treated KB-3 cells.

View Article: PubMed Central - PubMed

Affiliation: 1. Scientific Research Center, Shanghai Public Health Clinical Center, 2901 Caolang Road, Jinshan District, Shanghai 201508, China ; 2. Department of Translational Molecular Pathology, The University of Texas, M.D. Anderson Cancer Center, Houston, TX 77030, USA.

ABSTRACT

Background: There clearly is a need for effective chemotherapy for early-stage, high-risk patients with human cervical carcinoma. Vinblastine (VBL) is a key microtubule inhibitor, but unproven in its mechanisms as an important antitumor agent in cervical carcinoma.

Methods: We selected the concentration of vinblastine inducing 30% cell death for analyses assessing the DNA content, gene expression and transcriptional gene regulation of VBL-treated KB-3 cells.

Results: Transcriptomic and hierarchical clustering analysis demonstrated that treatment of KB-3 cells with VBL altered the expression of a diverse group of genes with G2/M arrest, which regulated by four oncogenic or tumor suppresser transcription factors (AP1, NFKB1, RELA, and TP53). Functional pathway analysis revealed the disease response to the biological effects of vinblastine in cervical carcinoma chemotherapy including protein ubiquitination pathway, RhoGDI signaling, integrin signaling, agranulocyte adhesion and biapedesis, and actin nucleation pathways. Northern blots also confirmed that KRT-7, FN14, IER3, and ID1 were deregulated in VBL-treated KB-3 cells.

Conclusion: Transcriptional time series profiles and a functional pathway analysis of VBL-treated KB-3 cells will provide a new strategy for improving microtubule inhibitor chemotherapy for cervical carcinoma.

No MeSH data available.


Related in: MedlinePlus

Cluster image showing the different classes of gene expression profiles. Five hundred thirty-six genes whose RNA levels changes in response to 2.5 x 10-4 µM of vinblastine were selected. This subset of genes was clustered hierarchically into groups on the basis of the similarity of their expression profiles. The graphs show the average expression profiles for the genes in the corresponding cluster A and B.
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Figure 2: Cluster image showing the different classes of gene expression profiles. Five hundred thirty-six genes whose RNA levels changes in response to 2.5 x 10-4 µM of vinblastine were selected. This subset of genes was clustered hierarchically into groups on the basis of the similarity of their expression profiles. The graphs show the average expression profiles for the genes in the corresponding cluster A and B.

Mentions: The VBL response gene candidates were selected based on the patterns from a heat-map figure (Fig. 2) from the 73 normalized gene lists via Partek Genomic Suite. The red is for the up-regulated genes, blue is for down-regulated genes, white is for the missing data in a time point, which were from differently expressed genes in KB-3 cells treated with 2.5 x 10-4 µM of vinblastine at 0, 2, 4, 8, 12, 16, 24, and 48 h, and identified to change in the transcriptome at a normal cutoff value ≥ ± 1.5-fold in 80% tested samples. Hierarchical clustering has the advantage that it is simple and the results can be easily visualized 13, and was used to partition data into two groups that have similar expression patterns (Fig. 2). These classes of genes could be distinguished into those whose mRNA levels remained induced for much longer (Fig. 2, cluster A) and those that responded early and whose induction was transient (Fig 2. cluster B), which included IER3, SCO2, SP140, ID1, DUSP6, ADRM1, U2AF1, NUDEL, SLC26A6, BCAA, PPID, SKD1, SPHK1, and SGK. Over-expressed genes in MDR KB-v1 cells can also be found in cluster A, which showed gradually increasing gene expression in VBL treatment of KB-3 cells as a function of time, including the genes that responded later (KRT 7, KRT 17, FN14, UGT2B7, ITGA5, and CD63) that appeared to be related to drug resistance involving cell wall metabolism, drug modification, and signal transduction 7. The transcriptional response to vinblastine suggests a multifaceted role for KB-3 cells in the physiology of drug metabolism.


Transcriptomic and Functional Pathway Analysis of Human Cervical Carcinoma Cancer Cells Response to Microtubule Inhibitor.

Wang J, Yan B, Liu SM, Sun H, Pan Y, Guan D, Zhang X, Xu J, Ma H - J Cancer (2015)

Cluster image showing the different classes of gene expression profiles. Five hundred thirty-six genes whose RNA levels changes in response to 2.5 x 10-4 µM of vinblastine were selected. This subset of genes was clustered hierarchically into groups on the basis of the similarity of their expression profiles. The graphs show the average expression profiles for the genes in the corresponding cluster A and B.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4543753&req=5

Figure 2: Cluster image showing the different classes of gene expression profiles. Five hundred thirty-six genes whose RNA levels changes in response to 2.5 x 10-4 µM of vinblastine were selected. This subset of genes was clustered hierarchically into groups on the basis of the similarity of their expression profiles. The graphs show the average expression profiles for the genes in the corresponding cluster A and B.
Mentions: The VBL response gene candidates were selected based on the patterns from a heat-map figure (Fig. 2) from the 73 normalized gene lists via Partek Genomic Suite. The red is for the up-regulated genes, blue is for down-regulated genes, white is for the missing data in a time point, which were from differently expressed genes in KB-3 cells treated with 2.5 x 10-4 µM of vinblastine at 0, 2, 4, 8, 12, 16, 24, and 48 h, and identified to change in the transcriptome at a normal cutoff value ≥ ± 1.5-fold in 80% tested samples. Hierarchical clustering has the advantage that it is simple and the results can be easily visualized 13, and was used to partition data into two groups that have similar expression patterns (Fig. 2). These classes of genes could be distinguished into those whose mRNA levels remained induced for much longer (Fig. 2, cluster A) and those that responded early and whose induction was transient (Fig 2. cluster B), which included IER3, SCO2, SP140, ID1, DUSP6, ADRM1, U2AF1, NUDEL, SLC26A6, BCAA, PPID, SKD1, SPHK1, and SGK. Over-expressed genes in MDR KB-v1 cells can also be found in cluster A, which showed gradually increasing gene expression in VBL treatment of KB-3 cells as a function of time, including the genes that responded later (KRT 7, KRT 17, FN14, UGT2B7, ITGA5, and CD63) that appeared to be related to drug resistance involving cell wall metabolism, drug modification, and signal transduction 7. The transcriptional response to vinblastine suggests a multifaceted role for KB-3 cells in the physiology of drug metabolism.

Bottom Line: We selected the concentration of vinblastine inducing 30% cell death for analyses assessing the DNA content, gene expression and transcriptional gene regulation of VBL-treated KB-3 cells.Transcriptomic and hierarchical clustering analysis demonstrated that treatment of KB-3 cells with VBL altered the expression of a diverse group of genes with G2/M arrest, which regulated by four oncogenic or tumor suppresser transcription factors (AP1, NFKB1, RELA, and TP53).Northern blots also confirmed that KRT-7, FN14, IER3, and ID1 were deregulated in VBL-treated KB-3 cells.

View Article: PubMed Central - PubMed

Affiliation: 1. Scientific Research Center, Shanghai Public Health Clinical Center, 2901 Caolang Road, Jinshan District, Shanghai 201508, China ; 2. Department of Translational Molecular Pathology, The University of Texas, M.D. Anderson Cancer Center, Houston, TX 77030, USA.

ABSTRACT

Background: There clearly is a need for effective chemotherapy for early-stage, high-risk patients with human cervical carcinoma. Vinblastine (VBL) is a key microtubule inhibitor, but unproven in its mechanisms as an important antitumor agent in cervical carcinoma.

Methods: We selected the concentration of vinblastine inducing 30% cell death for analyses assessing the DNA content, gene expression and transcriptional gene regulation of VBL-treated KB-3 cells.

Results: Transcriptomic and hierarchical clustering analysis demonstrated that treatment of KB-3 cells with VBL altered the expression of a diverse group of genes with G2/M arrest, which regulated by four oncogenic or tumor suppresser transcription factors (AP1, NFKB1, RELA, and TP53). Functional pathway analysis revealed the disease response to the biological effects of vinblastine in cervical carcinoma chemotherapy including protein ubiquitination pathway, RhoGDI signaling, integrin signaling, agranulocyte adhesion and biapedesis, and actin nucleation pathways. Northern blots also confirmed that KRT-7, FN14, IER3, and ID1 were deregulated in VBL-treated KB-3 cells.

Conclusion: Transcriptional time series profiles and a functional pathway analysis of VBL-treated KB-3 cells will provide a new strategy for improving microtubule inhibitor chemotherapy for cervical carcinoma.

No MeSH data available.


Related in: MedlinePlus