title: Expression of pre-selected TMEMs with predicted ER localization as potential classifiers of ccRCC tumors.
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.
authors.affiliation: Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland. twrzes@amu.edu.pl.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Wrzesiński
authors.affiliation: Department of Human Molecular Genetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland. grete@amu.edu.pl.
authors.forename: Malgorzata
authors.initials: M
authors.lastname: Szelag
authors.affiliation: Department of Urology and Urological Oncology, Poznan University of Medical Sciences, Szwajcarska 3, 61-285, Poznan, Poland. w.cieslikowski@gmail.com.
authors.forename: Wojciech A
authors.initials: WA
authors.lastname: Cieślikowski
authors.affiliation: Department of Urology and Urological Oncology, Poznan University of Medical Sciences, Szwajcarska 3, 61-285, Poznan, Poland. agnieszka.ida@gmail.com.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Ida
authors.affiliation: Department of Nephrology and Hypertension, University Medical Center, Postbus 85500, 3508 GA, Utrecht, Netherlands. R.Giles@umcutrecht.nl.
authors.forename: Rachel
authors.initials: R
authors.lastname: Giles
authors.affiliation: Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland. eladop21@wp.pl.
authors.forename: Elżbieta
authors.initials: E
authors.lastname: Zodro
authors.affiliation: Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland. aisasz89@wp.pl.
authors.forename: Joanna
authors.initials: J
authors.lastname: Szumska
authors.affiliation: Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland. asia.pozniak@gmail.com.
authors.forename: Joanna
authors.initials: J
authors.lastname: Poźniak
authors.affiliation: Department of Urology and Urological Oncology, Poznan University of Medical Sciences, Szwajcarska 3, 61-285, Poznan, Poland. zbigniew.kwias@poczta.onet.pl.
authors.forename: Zbigniew
authors.initials: Z
authors.lastname: Kwias
authors.affiliation: Department of Human Molecular Genetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland. h.bluyss@amu.edu.pl.
authors.forename: Hans A R
authors.initials: HA
authors.lastname: Bluyssen
authors.affiliation: Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland. j.wesoly@amu.edu.pl.
authors.forename: Joanna
authors.initials: J
authors.lastname: Wesoly
mesh_terms: D000328:Adult; D000368:Aged; D002292:Carcinoma, Renal Cell / Q000235:genetics* / Q000378:metabolism* / Q000473:pathology; D016000:Cluster Analysis; D019295:Computational Biology; D018450:Disease Progression; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D007680:Kidney Neoplasms / Q000235:genetics* / Q000378:metabolism* / Q000473:pathology; D008297:Male; D008565:Membrane Proteins / Q000235:genetics* / Q000378:metabolism; D008875:Middle Aged; D005810:Multigene Family; D060787:Neoplasm Grading; D009362:Neoplasm Metastasis; D009367:Neoplasm Staging; D016017:Odds Ratio; D021381:Protein Transport; D011960:Receptors, Estrogen / Q000378:metabolism*; D047368:Tumor Burden
chemical_list: D008565:Membrane Proteins; D011960:Receptors, Estrogen