Genome-wide single nucleotide polymorphism analysis has revealed large-scale cryptic regions of acquired homozygosity in the form of segmental uniparental disomy in f20% of acute myeloid leukemias. We have investigated whether such regions, which are the consequence of mitotic recombination, contain homozygous mutations in genes known to be mutational targets in leukemia. In 7 of 13 cases with uniparental disomy, we identified concurrent homozygous mutations at four distinct loci (WT1, FLT3, CEBPA, and RUNX1). This implies that mutation precedes mitotic recombination which acts as a ''second hit'' responsible for removal of the remaining wildtype allele, as has recently been shown for the JAK2 gene in myeloproliferative disorders.

MicroRNAs (miRNAs) are short single-stranded RNAs that have a potentially important role in gene regulation. Using a quantitative real-time polymerase chain reaction assay specific to the mature miRNA, the expression level of a selected group of haematopoietic tissue-specific miRNAs was measured across a set of 30 primary adult acute myeloid leukaemia (AML) with a normal karyotype. The expression levels of each miRNA were correlated with the genome-wide mRNA expression profiles in the same leukaemias. This revealed that miR181a correlated strongly with the AML morphological sub-type and with the expression of genes previously identified through sequence analysis as potential interaction targets. Three other miRNAs, miR-10a, miR-10b and miR-196a-1, showed a clear correlation with HOX gene expression. Leukemia (2007) 21, 912-916.

Basal cell carcinoma is the most common human cancer with increasing incidence reported worldwide. Despite the aberrant signaling role of the Hedgehog pathway, little is known about the genetic mechanisms underlying basal cell carcinomas. Towards a better understanding of global genetic events, we have employed the Affymetrix Mapping 10K single nucleotide polymorphism (SNP) microarray technique for ''fingerprinting'' genomewide allelic imbalance in 14 basal cell carcinoma-blood pair samples. This rapid high-resolution SNP genotyping technique has revealed a somatic recombination event-uniparental disomy, leading to a loss of heterozygosity (LOH), as a key alternative genetic mechanism to allelic imbalances in basal cell carcinomas. A highly conserved LOH region at 9q21-q31 was found in 13 of 14 (93%) basal cell carcinomas. Further statistical and fluorescence in situ hybridization analyses confirmed that the 9q LOH was a result of uniparental disomy in 5 of 13 (38%) basal cell carcinomas. De novo mutations in the Patched 1 gene (PTCH) were found in 9 of 13 (69%) basal cell carcinomas with 9q LOH. A second important locus, containing LOH at 6q23-q27 was found in 5 of 14 (36%) basal cell carcinomas, suggesting that the presence of an additional putative tumor suppressor gene may be contributing to basal cell carcinoma development. This study shows that the rate of 9q LOH in basal cell carcinomas has been previously underestimated. Furthermore, we provide the first evidence that uniparental disomy due to somatic recombination constitutes one of the mechanisms of LOH in basal cell carcinoma tumorigenesis.

Many cases of AML have either a normal karyotype or non-recurrent chromosomal abnormalities and hence their pathogenesis remains obscure. The introduction of array-based analysis of single nucleotide polymorphisms (SNPs) allows the rapid determination of genome-wide allelic information at a high density for a DNA sample. High-resolution SNP genotype analysis was performed on 64 presentation AML samples with full karyotype information as follows: normal karyotype [40], t(8;21) [5], t(15;17) [4], inv16 [3], 11q23 [2],−7 [3],+8 [2] and other structural abnormalities [7]. Using the 10K SNP array (Affymetrix, Inc., Santa Clara) 9, a mean call rate of 93.3% yielded more than 10,000 SNP genotype calls per sample. Large unexpected regions of homozygosity were observed in 12 AMLs (18.75%). These regions ranged in size from 16 million base pairs to 113 million base pairs and would have been visible in the karyotypes if due to deletion. Remission bone marrow samples from 5 of those patients were subjected to SNP genotype analysis. The SNP call data demonstrated clearly that the homozygosity seen in the leukemic DNA was not present in the respective remission bone marrow DNA. Fluorescence in situ hybridisation (FISH) demonstrated 2 signals for probes within regions of homozygosity. Furthermore, hybridisation signal values on the SNP arrays demonstrated that regions of homozygosity did not differ from the rest of the chromosome. It was therefore concluded that such homozygous regions corresponded to uniparental disomy (UPD) due to somatic recombination events occurring during development of the leukemias. There appears to be a non-random distribution of UPD with 5 events on chromosome 11, 2 on chromosome 6, 2 on chromosome 9 and 1 on chromosomes 13, 19 and 21. As expected for somatic recombination, homozygosity continued to the telomere in most cases. Any parental bias in UPD could be evidence of a role for imprinted genes. This issue was investigated using the H19 gene, which is located at 11p15 and is normally methylated only on the paternal allele. Two leukemias exhibited UPD including 11p15 and the methylation status of the H19 gene was therefore determined by bisulfite sequencing. One leukemia with UPD11p exhibited a homozygous methylated paternal pattern, while the other example of UPD11p showed a homozygous non-methylated maternal pattern. These data show that the UPD seen on 11p is not restricted to a single parental origin. In a previous analysis, the leukemia with UPD19q was shown to be homozygous for a CEBPA mutation and FISH demonstrated 2 copies of the CEBPA gene. This gene is located at 19q13.1, within the area of UPD and we conclude that the mutation occurred prior to the UPD. We can therefore speculate that an important consequence of UPD could be to unmask pre-existing mutations. A total of 8 different chromosomal regions have been shown to be affected by UPD in this study and this may suggest that there are at least this number of mutational targets. The discovery of widespread, somatically acquired, UPD in leukemias has potentially important clinical implications. 20% of the normal karyotype AMLs was found to have UPD, and this could offer a valuable new approach to the classification of this important subgroup of AML. The prognostic consequences of such cryptic abnormalities for the patient are uncertain, and larger studies will be required to assess the clinical significance of this phenomenon.

The chromosomal translocation t(8;21) is associated with 10-15% of all cases of acute myeloid leukaemia (AML). The resultant fusion protein AML1/MTG8 interferes with haematopoietic gene expression and is an important regulator of leukaemogenesis. We studied the effects of small interfering RNA (siRNA)-mediated AML1/MTG8 depletion on global gene expression in t(8;21)-positive leukaemic cell lines and in primary AML blasts using cDNA arrays, oligonucleotide arrays and real-time reverse transcription-polymerase chain reaction (RT-PCR). Suppression of AML1/MTG8 results in the increased expression of genes associated with myeloid differentiation, such as AZU1, BPI, CTSG, LYZ and RNASE2 as well as of antiproliferative genes such as IGFBP7, MS4A3 and SLA both in blasts and in cell lines. Furthermore, expression levels of several genes affiliated with drug resistance or indicative of poor prognosis AML (BAALC, CD34, PRG2, TSPAN7) are affected by AML1/MTG8 depletion. In conclusion, siRNA-mediated suppression of AML1/MTG8 cause very similar changes in gene expression pattern in t(8;21)-positive cell lines and in primary AML blasts. Furthermore, the results suggest that the specific targeting of AML1/MTG8 function may be a promising approach for complementing existing treatment strategies.

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The genotype of a tumor determines its biology and clinical behavior. The genetic alterations associated with the unique embryonal morphology of nonseminomatous subtypes of testicular germ cell tumors remain to be established. Using single nucleotide polymorphism microarray analysis, we found in all of the 15 nonseminomas analyzed, large-scale chromosomal homozygosities, most of which were not associated with relative chromosome loss. This unusual genotype, distinguishing nonseminoma from seminomas and other human tumors, may be associated with the special embryonal development morphologic transition of this malignancy. Based on these genetic data, we hypothesized a new potential origin of nonseminomas through sperm fusion. Nonrandom involvement of certain chromosomes also suggests that genes on these chromosome regions may play an important role in nonseminoma development. (Cancer Res 2005; 65(20): 9137-41)

We consider the application of logarithmic conformal field theory in finding solutions to the turbulent phases of 2-dimensional models of magnetohydrodynamics. These arise upon dimensional reduction of standard (infinite conductivity) 3-dimensional magnetohydrodynamics, after taking various simplifying limits. We show that solutions of the corresponding Hopf equations and higher order integrals of motion can be found within the solutions of ordinary turbulence proposed by Flohr, based on the tensor product of the logarithmic extensionc 6,1 of the non-unitary minimal model c 6,1 . This possibility arises because of the existence of a continuous hidden symmetry present in the latter models, and the fact that there appear several distinct dimension -1 and -2 primary fields. 1