Genome wide DNA-profiling of HIV-related B-cell lymphomas

Abstract

Non-Hodgkin lymphomas (NHL) represent a frequent complication of human immunodeficiency virus (HIV) infection. To elucidate HIV-NHL pathogenesis, we performed a genome-wide DNA profiling based on a single nucleotide polymorphism-based microarray comparative genomic hybridization in 57 HIV-lymphomas and, for comparison, in 105 immunocompetent diffuse large B-cell lymphomas (IC-DLBCL). Genomic complexity varied across HIV-NHL subtypes. HIV-Burkitt lymphoma showed a significantly lower number of lesions than HIV-DLBCL (P = 0.032), whereas the median number of copy number changes was significantly higher in Epstein-Barr virus negative (EBV-) HIV-DLBCL (42.5, range 8-153) compared to EBV+ cases (22; range 3-41; P = 0.029). Compared to IC-DLBCL, HIV-DLBCL displayed a distinct genomic profile with no gains of 18q and specific genetic lesions. Fragile sites-associated genes, including FHIT (FRA3B), WWOX (FRA16D), DCC (FRA18B) and PARK2 (FRA6E) were frequently inactivated in HIV-NHL by interstitial deletions, and a significantly higher prevalence of FHIT alterations was observed in HIV-DLBCL compared to IC-DLBCL. The same genes involved by fragile site deletions were also frequently affected by aberrant methylation of regulative regions.

Fig 1

Frequency of DNA gains (up) and losses (down) observed in 11 HIV-BL (A), 25 HIV-DLBCL (B), 105 IC-DLBCL (C), four HIV-PCNSL (D) and eight HIV-PEL (E). X-axis, chromosome localization and physical mapping; Y-axis, percentage of cases showing the aberrations.

Fig 2

Expression analysis of FHIT and WWOX mRNA by real-time quantitative RT-PCR. Levels of FHIT (A) and WWOX (B) mRNA in HIV-NHL samples with and without genetic and/or epigenetic alterations of the gene were normalized to the endogenous reference GUSB mRNA to obtain the normalized threshold cycle (ΔCt) for each sample. The median ΔCt value was set to 1. The ΔCt value of FHIT (A) and WWOX (B) of cases without alterations of the gene was related to the ΔCt value of FHIT (A) and WWOX (B) of cases displaying genetic and/or epigenetic alterations to obtain the relative threshold cycle (ΔΔCt). The (2^−ΔΔCt) algorithm was used to determine the relative expression of FHIT and WWOX mRNA. Statistical analysis, performed by the non parametric Mann-Whitney test with Bonferroni adjustment, revealed a significant difference in FHIT and WWOX expression between samples without genetic and/or epigenetic alterations and HIV-NHL cases displaying alterations of the gene (p=0.01 for FHIT, and p<0.001 for WWOX).