Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors.

Identification of prognostic and predictive genomic markers requires long-term clinical follow-up of patients. Extraction of high-quality DNA from archived formalin-fixed, paraffin-embedded material is essential for such studies. Of particular importance is a robust reproducible method of whole genome amplification for small tissue samples. This is especially true for high-resolution analytical approaches because different genomic regions and sequences may amplify differentially. We have tested a number of protocols for DNA amplification for array-based comparative genomic hybridization (CGH), in which relative copy number of the entire genome is measured at 1 to 2 mb resolution. Both random-primed amplification and degenerate oligonucleotide-primed amplification approaches were tested using varying amounts of fresh and paraffin-extracted normal and breast tumor input DNAs. We found that random-primed amplification was clearly superior to degenerate oligonucleotide-primed amplification for array-based CGH. The best quality and reproducibility strongly depended on accurate determination of the amount of input DNA using a quantitative polymerase chain reaction-based method. Reproducible and high-quality results were attained using 50 ng of input DNA, and some samples yielded quality results with as little as 5 ng input DNA. We conclude that random-primed amplification of DNA isolated from paraffin sections is a robust and reproducible approach for array-based CGH analysis of archival tumor samples.

Induction of atherosclerosis by human chylomicron remnants: a hypothesis.

Epidemiologic studies have provided support for the association between delayed remnant removal and premature atherosclerosis. Triglyceride-rich particles such as chylomicrons and chylomicron remnants that carry dietary derived fats, may play a role in the early stages of developing arteriosclerosis. Currently research focuses on these lipoprotein classes seeking distinguishing factors that causes some lipoproteins to be atherogenic while others are not. Such lipoproteins could be involved in atherogenesis directly or indirectly. Direct involvement occurs by interaction of triglyceride-rich particles with the arterial wall, possibly affecting the artery wall by oxidative stress, direct endothelial toxicity by constituents such as lysophosphatidylcholine or oxysterols, induction of prothrombotic changes, stimulation of endothelial expression of cell adhesion molecules and direct interaction with circulating blood cells. Indirect involvement refers to the influence of triglyceride-rich lipoproteins on other lipoproteins on the composition of low density lipoprotein (LDL) and high density lipoprotein (HDL) particles. We propose that in individuals with delayed removal of chylomicron remnants, the prolonged exposure of areas of endothelium that have been partially activated by turbulent flow, to specific components of the remnants, results in the endothelial cells becoming further activated and able to bind monocytes. During or shortly after the transcytosis to the intima and transformation of monocytes to macrophages, the macrophages become engorged with remnant derived lipids and form the nidus of a fatty streak.

Mutations of mtDNA in renal cell tumours arising in end-stage renal disease.

Toxic effects in the uraemic state or during maintenance dialysis have been suggested to be responsible for DNA damage and tumour development in end-stage renal disease (ESRD). This study therefore analysed the mitochondrial DNA alterations in six kidneys with ESRD and in nine renal cell tumours arising in these kidneys. Sequencing the entire 16 569 bp mitochondrial genome disclosed 94 sequence variations in normal and corresponding tumour tissues. Thirty-eight polymorphisms occurred in the D-loop region, 40 in the polypeptide coding regions, 12 in the rRNAs, and four in the tRNAs. Nine somatic nucleotide changes were found in seven of the nine tumours analysed; four of them were G to A transitions. Two of the G to A changes occurred in the D-loop region, one in the MTTA gene, and one in the MTND2 gene. An A to G substitution was seen in the control region at the mtTF1 binding site. A T to C transition also occurred also in the D-loop region. A T insertion was seen in MTRNR2 (16S rRNA). One C insertion in MTND4 and one A deletion in the polyA tract of the MTND5 gene resulted in frameshift mutations in two tumours. This study reveals a high mutational rate of the mitochondrial DNA in tumours, which may correspond to the increased level of reactive oxidative species in renal parenchymal cells in ESRD.

Somatic mitochondrial DNA mutations in human chromophobe renal cell carcinomas.

We sequenced the entire mitochondrial genome in 8 chromophobe renal cell carcinomas (RCCs) and corresponding normal kidneys. Our study disclosed 68 known and 45 new sequence variations occurring 132 and 45 times, respectively. We found 6 somatic nucleotide changes in 5 out of the 8 chromophobe RCCs. One A --> T substitution occurred in the D-loop region and an insertion of a 9-bp sequence in the noncoding region of the MTNC7. One G --> A substitution and one C --> T substitution were seen in the MTRNR1 and MTRNR2 genes, respectively. One C deletion in MTND5 and one T insertion in the MTND3 gene resulted in frameshift mutations in two tumors. All somatic alterations, with the exception of the 9-bp insertion, were heteroplasmic changes. Although somatic mtDNA mutations are found in chromophobe RCCs, their role in the maintenance of tumor cell phenotype or in tumorigenesis remains to be elucidated.

Alteration of the LRP1B gene region is associated with high grade of urothelial cancer.

We have delineated regions of interest at chromosome 2q21.2, 2q36.3, and 2q37.1 by deletion mapping of 114 urothelial cancers (UC). Altogether, 17%, 18%, and 63% of the G1, G2, and G3 tumors displayed loss of heterozygosity at chromosome 2q, respectively, The region at 2q21.2 was narrowed down to the LRP1B gene (NT_005129.6). Hemi- and homozygous deletion at the LRP1B gene region was seen in 31 of 114 UCs. Only 8% of the UCs with G1 and none with G2 tumors showed loss of heterozygosity at the LRP1B gene, whereas 49% of the G3 UCs had allelic loss at this region. RT-PCR analysis of the LRP1B gene showed the lack of expression of several exons in 2 of 9 cases analyzed. Our analysis suggests that the LRP1B gene is a candidate tumor suppressor gene in UCs.

Allelic loss on chromosomes 8 and 9 correlates with clinical outcome in locally advanced clear cell carcinoma of the kidney.

PURPOSE: We correlated allelic loss on chromosomes 8p, 9p and 14q with clinical outcome in locally advanced conventional renal cell carcinoma. MATERIALS AND METHODS: We analyzed radical nephrectomy specimens from 72 stage P3N0 conventional renal cell carcinomas by microsatellite loss of heterozygosity (LOH) analyses directed at chromosomes 3p, 8p, 9p and 14q (2 primers per chromosome). All patients were treated with surgery only. LOH results were correlated with disease-free survival using the Kaplan-Meier method. RESULTS: We detected LOH on chromosome 3p in 60 of 64 (94%), on chromosome 8p in 19 of 59 (32%), on 9p in 21 of 67 (31%) and on 14q in 18 of 70 (26%) informative cases. Of the 72 patients 24 (33%) had recurrence during followup. On univariate analysis patients with tumors demonstrating LOH on chromosomes 8p and 9q were at high risk for recurrence (p = 0.01). The correlation of recurrence with LOH approached significance for the individual chromosomes 8p and 9p (p = 0.10 and 0.14, respectively). No correlation was observed of LOH on chromosome 14q with recurrence (p = 0.42). The correlation of tumor grade with risk of relapse also approached significance (p = 0.12). On multivariate analysis LOH on chromosome 8p was a more powerful predictor of recurrence than tumor grade. When combinations of LOH on chromosomes were tested, LOH on chromosomes 8p and 9p was the most powerful predictor of recurrence (p = 0.006). CONCLUSIONS: LOH on chromosomes 8p or 9p may provide prognostic significance in patients with locally advanced renal cell carcinoma.

Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer.

Array-based comparative genomic hybridization (CGH) uses multiple genomic clones arrayed on a slide to detect relative copy number of tumor DNA sequences. Application of array CGH to tumor specimens makes genetic diagnosis of cancers possible and may help to differentiate relevant subsets of tumors, biologically and clinically, which would allow better prognostic and therapeutic decision making. In this study, we have used array-based CGH to detect DNA copy number alterations in distinct types of renal cell carcinomas for diagnostic purposes. We were able to correctly diagnose 33 of 34 malignant tumors by automated computational means and to group together eight benign neoplasms and normal kidney samples. These results indicate that array-based CGH is capable of diagnosing the vast majority of renal cell carcinomas based on their genetic profiles.