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Expression of pre-selected TMEMs with predicted ER localization as potential classifiers of ccRCC tumors

View Article: PubMed Central - PubMed

ABSTRACT

Background: VHL inactivation is the most established molecular characteristic of clear cell renal cell carcinoma (ccRCC), with only a few additional genes implicated in development of this kidney tumor. In recently published ccRCC gene expression meta-analysis study we identified a number of deregulated genes with limited information available concerning their biological role, represented by gene transcripts belonging to transmembrane proteins family (TMEMs). TMEMs are predicted to be components of cellular membranes, such as mitochondrial membranes, ER, lysosomes and Golgi apparatus. Interestingly, the function of majority of TMEMs remains unclear. Here, we analyzed expression of ten TMEM genes in the context of ccRCC progression and development, and characterized these proteins bioinformatically.

Methods: The expression of ten TMEMs (RTP3, SLC35G2, TMEM30B, TMEM45A, TMEM45B, TMEM61, TMEM72, TMEM116, TMEM207 and TMEM213) was measured by qPCR. T-test, Pearson correlation, univariate and multivariate logistic and Cox regression were used in statistical analysis. The topology of studied proteins was predicted with Metaserver, together with PSORTII, Pfam and Localizome tools.

Results: We observed significant deregulation of expression of 10 analyzed TMEMs in ccRCC tumors. Cluster analysis of expression data suggested the down-regulation of all tested TMEMs to be a descriptor of the most advanced tumors. Logistic and Cox regression potentially linked TMEM expression to clinical parameters such as: metastasis, Fuhrman grade and overall survival. Topology predictions classified majority of analyzed TMEMs as type 3 and type 1 transmembrane proteins, with predicted localization mainly in ER.

Conclusions: The massive down-regulation of expression of TMEM family members suggests their importance in the pathogenesis of ccRCC and the bioinformatic analysis of TMEM topology implies a significant involvement of ER proteins in ccRCC pathology.

Electronic supplementary material: The online version of this article (doi:10.1186/s12885-015-1530-4) contains supplementary material, which is available to authorized users.

No MeSH data available.


Predicted topologies of TMEMs. Signal sequences are in orange, transmembrane domains in green, functional domains derived from Pfam database in violet. All structures were generated using Localizome server
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Fig6: Predicted topologies of TMEMs. Signal sequences are in orange, transmembrane domains in green, functional domains derived from Pfam database in violet. All structures were generated using Localizome server

Mentions: The up-regulated TMEM22 and TMEM45A encoded proteins were predicted to localize in endoplasmic reticulum. TMEM22 contains a domain similar to E.coli multidrug-resistance antiporter Emre, while TMEM45A (together with TMEM45B) was assigned to DUF716 protein family of unknown function in humans (Fig. 6). TMEM22 (SLC35G2) encodes a member G2 protein of solute carrier family 35, a polytopic transmembrane protein found in Golgi apparatus, endosomes and lysosomes [65, 66] possibly involved in nucleoside-sugar transport [67]. Differential regulation in SLC35G2 expression in intrahepatic cholangiocarcinoma [68] and promoter hypermethylation of SLC35G2 in melanoma were previously reported [69]. Dobashi et al. found up-regulation of SLC35G2 in Caki-1 and Caki-2 RCC cell lines and tumor samples; additionally, siRNA silencing of SLC35G2 diminished cell growth in those cell lines, suggesting its potential involvement in cancer progression and development [29]. Here, we also observe up-regulation of SLC35G2 expression in our tumor set. Additionally, we find SLC35G2 expression to be up-regulated in PBMCs collected from patients a year post-nephrectomy, as compared to PBMCs of healthy volunteers. This finding is very promising, although it requires additional conformation in an independent cohort.Fig. 6


Expression of pre-selected TMEMs with predicted ER localization as potential classifiers of ccRCC tumors
Predicted topologies of TMEMs. Signal sequences are in orange, transmembrane domains in green, functional domains derived from Pfam database in violet. All structures were generated using Localizome server
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5015219&req=5

Fig6: Predicted topologies of TMEMs. Signal sequences are in orange, transmembrane domains in green, functional domains derived from Pfam database in violet. All structures were generated using Localizome server
Mentions: The up-regulated TMEM22 and TMEM45A encoded proteins were predicted to localize in endoplasmic reticulum. TMEM22 contains a domain similar to E.coli multidrug-resistance antiporter Emre, while TMEM45A (together with TMEM45B) was assigned to DUF716 protein family of unknown function in humans (Fig. 6). TMEM22 (SLC35G2) encodes a member G2 protein of solute carrier family 35, a polytopic transmembrane protein found in Golgi apparatus, endosomes and lysosomes [65, 66] possibly involved in nucleoside-sugar transport [67]. Differential regulation in SLC35G2 expression in intrahepatic cholangiocarcinoma [68] and promoter hypermethylation of SLC35G2 in melanoma were previously reported [69]. Dobashi et al. found up-regulation of SLC35G2 in Caki-1 and Caki-2 RCC cell lines and tumor samples; additionally, siRNA silencing of SLC35G2 diminished cell growth in those cell lines, suggesting its potential involvement in cancer progression and development [29]. Here, we also observe up-regulation of SLC35G2 expression in our tumor set. Additionally, we find SLC35G2 expression to be up-regulated in PBMCs collected from patients a year post-nephrectomy, as compared to PBMCs of healthy volunteers. This finding is very promising, although it requires additional conformation in an independent cohort.Fig. 6

View Article: PubMed Central - PubMed

ABSTRACT

Background: VHL inactivation is the most established molecular characteristic of clear cell renal cell carcinoma (ccRCC), with only a few additional genes implicated in development of this kidney tumor. In recently published ccRCC gene expression meta-analysis study we identified a number of deregulated genes with limited information available concerning their biological role, represented by gene transcripts belonging to transmembrane proteins family (TMEMs). TMEMs are predicted to be components of cellular membranes, such as mitochondrial membranes, ER, lysosomes and Golgi apparatus. Interestingly, the function of majority of TMEMs remains unclear. Here, we analyzed expression of ten TMEM genes in the context of ccRCC progression and development, and characterized these proteins bioinformatically.

Methods: The expression of ten TMEMs (RTP3, SLC35G2, TMEM30B, TMEM45A, TMEM45B, TMEM61, TMEM72, TMEM116, TMEM207 and TMEM213) was measured by qPCR. T-test, Pearson correlation, univariate and multivariate logistic and Cox regression were used in statistical analysis. The topology of studied proteins was predicted with Metaserver, together with PSORTII, Pfam and Localizome tools.

Results: We observed significant deregulation of expression of 10 analyzed TMEMs in ccRCC tumors. Cluster analysis of expression data suggested the down-regulation of all tested TMEMs to be a descriptor of the most advanced tumors. Logistic and Cox regression potentially linked TMEM expression to clinical parameters such as: metastasis, Fuhrman grade and overall survival. Topology predictions classified majority of analyzed TMEMs as type 3 and type 1 transmembrane proteins, with predicted localization mainly in ER.

Conclusions: The massive down-regulation of expression of TMEM family members suggests their importance in the pathogenesis of ccRCC and the bioinformatic analysis of TMEM topology implies a significant involvement of ER proteins in ccRCC pathology.

Electronic supplementary material: The online version of this article (doi:10.1186/s12885-015-1530-4) contains supplementary material, which is available to authorized users.

No MeSH data available.