Smoking may cause genetic alterations at 5q22.2 approximately q23.1 in clear-cell renal cell carcinoma

Genetic profile and immunohistochemical study of clear cell renal carcinoma: Pathological-anatomical correlation and prognosis

INTRODUCTION

Renal cell carcinoma (RCC) accounts for 2-3% of all tumors being the most frequent solid lesion in the kidney.

OBJECTIVE

To determine what genetic alterations and immunohistochemical (IHC) of clear cell renal carcinoma (ccRCC) are associated with prognosis and tumor aggressiveness.

PATIENTS AND METHODS

Experimental analytical study with 57 patients who underwent radical and partial nephrectomy between 2005 and 2011, all with diagnosis of ccRCC and minimum post-operative follow-up of 36 months. The pathological study included IHC determination of biomarkers associated (CAIX, CAM 5.2, CD10, c-erbB-2, EGFR, HIF-1a, Ki67, MDM2, PAX-2 y 8, p53, survivin and VEGFR 1 and 2). Genetic analysis was carried out using multiplex ligation-dependent probe amplification (MLPA). Clinical data were collected and summarized using an access-type database, adding genetic analysis and IHC data of each patient's tumor sample. IHC statistical analysis included Chi-square, Kruskal-Wallis and multivariate analysis. The genetic analysis was performed using multivariate logistic regression (normal/deletion-duplication). Significance level p<0.05.

RESULTS

Pathologic stage was: pT1 (61.8%), pT2 (32.7%); pT3-T4 (5.4%); 16.3% were pN+ and 19.3% M1. 23.6% recurred being predominantly to distance in 83.3%. 27.3% of patients died (73.3% ccCCR). CAIX (Carbonic anhydrase IX) and tumor size were associated with worse Fuhrman grade (p = 0.035; p = 0.001 respectively). Deletion-duplication of genes increased the likelihood: of death (APC, Bcl-2 and CDKN2A by 11, 7 and 4 respectively and SMAD4 reduced the probability by 88%); tumor recurrence (CDKN2A by fifteen fold and VHL reduced the probability by 87%); pT greater than 2 (CCND2, MDM2 and WT1 multiplied by 6, 7 and 9); risk of N+ (CDK4 and EBF1 by 13); distant metastases (BRCA2 and DLEU1 by 5); Fuhrman grade ≥3 (BRCA1, BRCA2 and p53 by 40, 75 and 34 respectively, while that FHIT reduced by 96%). Deletion-duplication of CDK4 and DCC increased survival by a factor of 13 and 16, while that DLEU1 and RUNX1 decreased survival time by 80%.

CONCLUSION

CAIX and tumor size are associated with increased aggressiveness. The mutations to level 5q, 9p, 11p, 12, 13q, 17, 18q and 21q are associated with more aggressive tumors and with worse survival rate.

Combined analysis with copy number variation identifies risk loci in lung cancer

Background. Lung cancer is the most important cause of cancer mortality worldwide, but the underlying mechanisms of this disease are not fully understood. Copy number variations (CNVs) are promising genetic variations to study because of their potential effects on cancer. Methodology/Principal Findings. Here we conducted a pilot study in which we systematically analyzed the association of CNVs in two lung cancer datasets: the Environment And Genetics in Lung cancer Etiology (EAGLE) and the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial datasets. We used a preestablished association method to test the datasets separately and conducted a combined analysis to test the association accordance between the two datasets. Finally, we identified 167 risk SNP loci and 22 CNVs associated with lung cancer and linked them with recombination hotspots. Functional annotation and biological relevance analyses implied that some of our predicted risk loci were supported by other studies and might be potential candidate loci for lung cancer studies. Conclusions/Significance. Our results further emphasized the importance of copy number variations in cancer and might be a valuable complement to current genome-wide association studies on cancer.

Genomic alterations in breast cancer patients in betel quid and non betel quid chewers

Betel Quid (BQ) chewing independently contributes to oral, hepatic and esophageal carcinomas. Strong association of breast cancer risk with BQ chewing in Northeast Indian population has been reported where this habit is prodigal. We investigated genomic alterations in breast cancer patients with and without BQ chewing exposure. Twenty six BQ chewers (BQC) and 17 non BQ chewer (NBQC) breast cancer patients from Northeast India were analyzed for genomic alterations and pathway networks using SNP array and IPA. BQC tumors showed significantly (P<0.01) higher total number of alterations, as compared with NBQC tumors, 48±17% versus 32±25 respectively. Incidence of gain in fragile sites in BQC tumors were significantly (P<0.001) higher as compared with NBQC tumors, 34 versus 23% respectively. Two chromosomal regions (7q33 and 21q22.13) were significantly (p<0.05) associated with BQC tumors while two regions (19p13.3–19p12 and 20q11.22) were significantly associated with NBQC tumors. GO terms oxidoreductase and aldo-keto reductase activity in BQC tumors in contrast to G-protein coupled receptor protein signaling pathway and cell surface receptor linked signal transduction in NBQC tumors were enriched in DAVID. One network “Drug Metabolism, Molecular Transport, Nucleic Acid Metabolism” including genes AKR1B1, AKR1B10, ETS2 etc in BQC and two networks “Molecular Transport, Nucleic Acid Metabolism, Small Molecule Biochemistry” and “Cellular Development, Embryonic Development, Organismal Development” including genes RPN2, EMR3, VAV1, NNAT and MUC16 etc were seen in NBQC. Common alterations (>30%) were seen in 27 regions. Three networks were significant in common regions with key roles of PTK2, RPN2, EMR3, VAV1, NNAT, MUC16, MYC and YWHAZ genes. These data show that breast cancer arising by environmental carcinogens exemplifies genetic alterations differing from those observed in the non exposed ones. A number of genetic changes are shared in both tumor groups considered as crucial in breast cancer progression.