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

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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.


TMEMs - prediction of orientation in plasma membrane. ‘N’ in red indicates N-terminus of proteins, transmembrane segments are in green, functional domains derived from Pfam database are in violet. All structures were generated using Localizome server
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Fig5: TMEMs - prediction of orientation in plasma membrane. ‘N’ in red indicates N-terminus of proteins, transmembrane segments are in green, functional domains derived from Pfam database are in violet. All structures were generated using Localizome server

Mentions: TMEM213 was the most down-regulated gene of all TMEMs tested in ccRCC samples. According to Pfam database TMEM213 gene encodes a protein from the family of unknown function and average length of 154 aa, present in all eukaryotes. The Metaserver prediction suggests TMEM213 might contain two transmembrane (TM) helix segments (aa 7–26 and 71–91) with no tertiary homology to any protein crystal structures, currently available in RCSB PDB database. PSORT II classified TMEM213 as type 1a topology protein with one TM domain (aa 75–90). In contrast to Metaserver, PSORT II assigned aa 1–27 as a cleavable N-terminal signal peptide instead of TM domain (Additional file 7: Table S4). PSORT II NNCN Reinhardt’s method for cytoplasmic/nuclear discrimination [52] scored TMEM213 as nuclear protein with reliability of 55.5. k-NN prediction for subcellular localization [56] determined TMEM213 to be connected to endoplasmic reticulum with probability of 44.4 %. Localizome analysis resulted in similar prediction to PSORT II (Fig. 5). Similar analyses were performed for the remaining 9 TMEMs as shown in Table 4.Fig. 5


Expression of pre-selected TMEMs with predicted ER localization as potential classifiers of ccRCC tumors
TMEMs - prediction of orientation in plasma membrane. ‘N’ in red indicates N-terminus of proteins, transmembrane segments are in green, functional domains derived from Pfam database are 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

Fig5: TMEMs - prediction of orientation in plasma membrane. ‘N’ in red indicates N-terminus of proteins, transmembrane segments are in green, functional domains derived from Pfam database are in violet. All structures were generated using Localizome server
Mentions: TMEM213 was the most down-regulated gene of all TMEMs tested in ccRCC samples. According to Pfam database TMEM213 gene encodes a protein from the family of unknown function and average length of 154 aa, present in all eukaryotes. The Metaserver prediction suggests TMEM213 might contain two transmembrane (TM) helix segments (aa 7–26 and 71–91) with no tertiary homology to any protein crystal structures, currently available in RCSB PDB database. PSORT II classified TMEM213 as type 1a topology protein with one TM domain (aa 75–90). In contrast to Metaserver, PSORT II assigned aa 1–27 as a cleavable N-terminal signal peptide instead of TM domain (Additional file 7: Table S4). PSORT II NNCN Reinhardt’s method for cytoplasmic/nuclear discrimination [52] scored TMEM213 as nuclear protein with reliability of 55.5. k-NN prediction for subcellular localization [56] determined TMEM213 to be connected to endoplasmic reticulum with probability of 44.4 %. Localizome analysis resulted in similar prediction to PSORT II (Fig. 5). Similar analyses were performed for the remaining 9 TMEMs as shown in Table 4.Fig. 5

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.