Limits...
Meta-Analysis of Public Microarray Datasets Reveals Voltage-Gated Calcium Gene Signatures in Clinical Cancer Patients.

Wang CY, Lai MD, Phan NN, Sun Z, Lin YC - PLoS ONE (2015)

Bottom Line: Voltage-gated calcium channels (VGCCs) are well documented to play roles in cell proliferation, migration, and apoptosis; however, whether VGCCs regulate the onset and progression of cancer is still under investigation.The VGCC family consists of five members, which are L-type, N-type, T-type, R-type and P/Q type.This bioinformatics analysis revealed that different subtypes of VGCCs (CACNA1C, CACNA1D, CACNA1B, CACNA1G, and CACNA1I) are implicated in the development and progression of diverse types of cancer and show dramatic up-regulation in breast cancer.

View Article: PubMed Central - PubMed

Affiliation: Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America; Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.

ABSTRACT
Voltage-gated calcium channels (VGCCs) are well documented to play roles in cell proliferation, migration, and apoptosis; however, whether VGCCs regulate the onset and progression of cancer is still under investigation. The VGCC family consists of five members, which are L-type, N-type, T-type, R-type and P/Q type. To date, no holistic approach has been used to screen VGCC family genes in different types of cancer. We analyzed the transcript expression of VGCCs in clinical cancer tissue samples by accessing ONCOMINE (www.oncomine.org), a web-based microarray database, to perform a systematic analysis. Every member of the VGCCs was examined across 21 different types of cancer by comparing mRNA expression in cancer to that in normal tissue. A previous study showed that altered expression of mRNA in cancer tissue may play an oncogenic role and promote tumor development; therefore, in the present findings, we focus only on the overexpression of VGCCs in different types of cancer. This bioinformatics analysis revealed that different subtypes of VGCCs (CACNA1C, CACNA1D, CACNA1B, CACNA1G, and CACNA1I) are implicated in the development and progression of diverse types of cancer and show dramatic up-regulation in breast cancer. CACNA1F only showed high expression in testis cancer, whereas CACNA1A, CACNA1C, and CACNA1D were highly expressed in most types of cancer. The current analysis revealed that specific VGCCs likely play essential roles in specific types of cancer. Collectively, we identified several VGCC targets and classified them according to different cancer subtypes for prospective studies on the underlying carcinogenic mechanisms. The present findings suggest that VGCCs are possible targets for prospective investigation in cancer treatment.

No MeSH data available.


Related in: MedlinePlus

Expression of voltage-gated calcium channel (VGCC) genes in different types of cancer.Expression of voltage-gated calcium channel (VGCC) genes in 21 types of cancers compared to normal tissue controls. The gene name of each channel is shown. Each gene was found in its tissue of origin, and the color gradient correlates with decreasing gene rank percentile. The search criteria threshold was set at p-value<0.05 with fold change >1.5 and gene rank percentile <10% for screening microarray datasets of cancer versus normal cases.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4493072&req=5

pone.0125766.g001: Expression of voltage-gated calcium channel (VGCC) genes in different types of cancer.Expression of voltage-gated calcium channel (VGCC) genes in 21 types of cancers compared to normal tissue controls. The gene name of each channel is shown. Each gene was found in its tissue of origin, and the color gradient correlates with decreasing gene rank percentile. The search criteria threshold was set at p-value<0.05 with fold change >1.5 and gene rank percentile <10% for screening microarray datasets of cancer versus normal cases.

Mentions: The P/Q-type, T-type, N-type, R-type, and L type VGCCs all contain the α1 subunit responsible for assembling the calcium-selective pore [41, 69]. This subunit is encoded by various genes spreading from the L-type (CACNA1S, CACNA1C, CACNA1D and CACNA1F) to the T-type (CACNA1G, CACNA1H and CACNA1I) [70]. However, to date, no holistic approach has been taken to the screening VGCC family genes in different types of cancer. The present study used a holistic approach to explore VGCC expression in different types of cancer by employing the web-based ONCOMINE microarray database to analyze altered VGCC mRNA expression in 21 types of cancer. We compared the cancer tissue to normal tissue controls and set threshold criteria for screening a suitable dataset from the ONCOMINE database. Inclusion of a suitable dataset for further analysis required that comparisons of gene expression between cancer and normal tissues obeyed specific threshold criteria: the fold change must be above 1.5, the p-value must be less than 0.05, and the gene-ranking percentile must be less than 10%. The fold change, p-value, and the top gene-ranking percentile are presented in Fig 1 for different VGCC genes in different types of cancer tissues.


Meta-Analysis of Public Microarray Datasets Reveals Voltage-Gated Calcium Gene Signatures in Clinical Cancer Patients.

Wang CY, Lai MD, Phan NN, Sun Z, Lin YC - PLoS ONE (2015)

Expression of voltage-gated calcium channel (VGCC) genes in different types of cancer.Expression of voltage-gated calcium channel (VGCC) genes in 21 types of cancers compared to normal tissue controls. The gene name of each channel is shown. Each gene was found in its tissue of origin, and the color gradient correlates with decreasing gene rank percentile. The search criteria threshold was set at p-value<0.05 with fold change >1.5 and gene rank percentile <10% for screening microarray datasets of cancer versus normal cases.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493072&req=5

pone.0125766.g001: Expression of voltage-gated calcium channel (VGCC) genes in different types of cancer.Expression of voltage-gated calcium channel (VGCC) genes in 21 types of cancers compared to normal tissue controls. The gene name of each channel is shown. Each gene was found in its tissue of origin, and the color gradient correlates with decreasing gene rank percentile. The search criteria threshold was set at p-value<0.05 with fold change >1.5 and gene rank percentile <10% for screening microarray datasets of cancer versus normal cases.
Mentions: The P/Q-type, T-type, N-type, R-type, and L type VGCCs all contain the α1 subunit responsible for assembling the calcium-selective pore [41, 69]. This subunit is encoded by various genes spreading from the L-type (CACNA1S, CACNA1C, CACNA1D and CACNA1F) to the T-type (CACNA1G, CACNA1H and CACNA1I) [70]. However, to date, no holistic approach has been taken to the screening VGCC family genes in different types of cancer. The present study used a holistic approach to explore VGCC expression in different types of cancer by employing the web-based ONCOMINE microarray database to analyze altered VGCC mRNA expression in 21 types of cancer. We compared the cancer tissue to normal tissue controls and set threshold criteria for screening a suitable dataset from the ONCOMINE database. Inclusion of a suitable dataset for further analysis required that comparisons of gene expression between cancer and normal tissues obeyed specific threshold criteria: the fold change must be above 1.5, the p-value must be less than 0.05, and the gene-ranking percentile must be less than 10%. The fold change, p-value, and the top gene-ranking percentile are presented in Fig 1 for different VGCC genes in different types of cancer tissues.

Bottom Line: Voltage-gated calcium channels (VGCCs) are well documented to play roles in cell proliferation, migration, and apoptosis; however, whether VGCCs regulate the onset and progression of cancer is still under investigation.The VGCC family consists of five members, which are L-type, N-type, T-type, R-type and P/Q type.This bioinformatics analysis revealed that different subtypes of VGCCs (CACNA1C, CACNA1D, CACNA1B, CACNA1G, and CACNA1I) are implicated in the development and progression of diverse types of cancer and show dramatic up-regulation in breast cancer.

View Article: PubMed Central - PubMed

Affiliation: Department of Anatomy, University of California San Francisco, San Francisco, California, United States of America; Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.

ABSTRACT
Voltage-gated calcium channels (VGCCs) are well documented to play roles in cell proliferation, migration, and apoptosis; however, whether VGCCs regulate the onset and progression of cancer is still under investigation. The VGCC family consists of five members, which are L-type, N-type, T-type, R-type and P/Q type. To date, no holistic approach has been used to screen VGCC family genes in different types of cancer. We analyzed the transcript expression of VGCCs in clinical cancer tissue samples by accessing ONCOMINE (www.oncomine.org), a web-based microarray database, to perform a systematic analysis. Every member of the VGCCs was examined across 21 different types of cancer by comparing mRNA expression in cancer to that in normal tissue. A previous study showed that altered expression of mRNA in cancer tissue may play an oncogenic role and promote tumor development; therefore, in the present findings, we focus only on the overexpression of VGCCs in different types of cancer. This bioinformatics analysis revealed that different subtypes of VGCCs (CACNA1C, CACNA1D, CACNA1B, CACNA1G, and CACNA1I) are implicated in the development and progression of diverse types of cancer and show dramatic up-regulation in breast cancer. CACNA1F only showed high expression in testis cancer, whereas CACNA1A, CACNA1C, and CACNA1D were highly expressed in most types of cancer. The current analysis revealed that specific VGCCs likely play essential roles in specific types of cancer. Collectively, we identified several VGCC targets and classified them according to different cancer subtypes for prospective studies on the underlying carcinogenic mechanisms. The present findings suggest that VGCCs are possible targets for prospective investigation in cancer treatment.

No MeSH data available.


Related in: MedlinePlus