title: Renal cell carcinoma primary cultures maintain genomic and phenotypic profile of parental tumor tissues.
abstract: BACKGROUND
  Clear cell renal cell carcinoma (ccRCC) is characterized by recurrent copy number alterations (CNAs) and loss of heterozygosity (LOH), which may have potential diagnostic and prognostic applications. Here, we explored whether ccRCC primary cultures, established from surgical tumor specimens, maintain the DNA profile of parental tumor tissues allowing a more confident CNAs and LOH discrimination with respect to the original tissues.
  
  
  METHODS
  We established a collection of 9 phenotypically well-characterized ccRCC primary cell cultures. Using the Affymetrix SNP array technology, we performed the genome-wide copy number (CN) profiling of both cultures and corresponding tumor tissues. Global concordance for each culture/tissue pair was assayed evaluating the correlations between whole-genome CN profiles and SNP allelic calls. CN analysis was performed using the two CNAG v3.0 and Partek software, and comparing results returned by two different algorithms (Hidden Markov Model and Genomic Segmentation).
  
  
  RESULTS
  A very good overlap between the CNAs of each culture and corresponding tissue was observed. The finding, reinforced by high whole-genome CN correlations and SNP call concordances, provided evidence that each culture was derived from its corresponding tissue and maintained the genomic alterations of parental tumor. In addition, primary culture DNA profile remained stable for at least 3 weeks, till to third passage. These cultures showed a greater cell homogeneity and enrichment in tumor component than original tissues, thus enabling a better discrimination of CNAs and LOH. Especially for hemizygous deletions, primary cultures presented more evident CN losses, typically accompanied by LOH; differently, in original tissues the intensity of these deletions was weaken by normal cell contamination and LOH calls were missed.
  
  
  CONCLUSIONS
  ccRCC primary cultures are a reliable in vitro model, well-reproducing original tumor genetics and phenotype, potentially useful for future functional approaches aimed to study genes or pathways involved in ccRCC etiopathogenesis and to identify novel clinical markers or therapeutic targets. Moreover, SNP array technology proved to be a powerful tool to better define the cell composition and homogeneity of RCC primary cultures.
authors.affiliation: Institute for Biomedical Technologies (ITB), National Research Council (CNR), via Fratelli Cervi 93, 20090 Segrate, Milan, Italy.
authors.forename: Ingrid
authors.initials: I
authors.lastname: Cifola
authors.forename: Cristina
authors.initials: C
authors.lastname: Bianchi
authors.forename: Eleonora
authors.initials: E
authors.lastname: Mangano
authors.forename: Silvia
authors.initials: S
authors.lastname: Bombelli
authors.forename: Fabio
authors.initials: F
authors.lastname: Frascati
authors.forename: Ester
authors.initials: E
authors.lastname: Fasoli
authors.forename: Stefano
authors.initials: S
authors.lastname: Ferrero
authors.forename: Vitalba
authors.initials: V
authors.lastname: Di Stefano
authors.forename: Maria A
authors.initials: MA
authors.lastname: Zipeto
authors.forename: Fulvio
authors.initials: F
authors.lastname: Magni
authors.forename: Stefano
authors.initials: S
authors.lastname: Signorini
authors.forename: Cristina
authors.initials: C
authors.lastname: Battaglia
authors.forename: Roberto A
authors.initials: RA
authors.lastname: Perego
mesh_terms: D002292:Carcinoma, Renal Cell / Q000737:chemistry / Q000235:genetics / Q000473:pathology*; D045744:Cell Line, Tumor / Q000737:chemistry / Q000166:cytology* / Q000648:ultrastructure; D048430:Cell Shape; D004273:DNA, Neoplasm / Q000032:analysis / Q000235:genetics; D018628:Gene Dosage; D020869:Gene Expression Profiling; D042822:Genomic Instability; D005838:Genotype; D006801:Humans; D016130:Immunophenotyping; D007680:Kidney Neoplasms / Q000737:chemistry / Q000235:genetics / Q000473:pathology*; D019656:Loss of Heterozygosity; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D017384:Sequence Deletion
chemical_list: D004273:DNA, Neoplasm