Epigenetic silencing of AXIN2 in colorectal carcinoma with microsatellite instability.

Mutation or epigenetic silencing of mismatch repair genes, such as MLH1 and MSH2, results in microsatellite instability (MSI) in the genome of a subset of colorectal carcinomas (CRCs). However, little is yet known of genes that directly contribute to tumor formation in such cancers. To characterize MSI-dependent changes in gene expression, we have now compared transcriptomes between fresh CRC specimens positive or negative for MSI (n=10 for each) with the use of high-density oligonucleotide microarrays harboring >44,000 probe sets. Correspondence analysis of the expression patterns of isolated MSI-associated genes revealed that the transcriptome of MSI+ CRCs is clearly distinct from that of MSI- CRCs. Such MSI-associated genes included that for AXIN2, an important component of the WNT signaling pathway. AXIN2 was silenced, apparently as a result of extensive methylation of its promoter region, specifically in MSI+ CRC specimens. Forced expression of AXIN2, either by treatment with 5'-azacytidine or by transfection with AXIN2 cDNA, resulted in rapid cell death in an MSI+ CRC cell line. These data indicate that epigenetic silencing of AXIN2 is specifically associated with carcinogenesis in MSI+ CRCs.

DNA microarray analysis of natural killer cell-type lymphoproliferative disease of granular lymphocytes with purified CD3-CD56+ fractions.

Natural killer (NK) cell-type lymphoproliferative disease of granular lymphocytes (LDGL) is characterized by the outgrowth of CD3(-)CD16/56(+) NK cells, and can be further subdivided into two distinct categories: aggressive NK cell leukemia (ANKL) and chronic NK lymphocytosis (CNKL). To gain insights into the pathophysiology of NK cell-type LDGL, we here purified CD3(-)CD56(+) fractions from healthy individuals (n=9) and those with CNKL (n=9) or ANKL (n=1), and compared the expression profiles of >12 000 genes. A total of 15 'LDGL-associated genes' were identified, and a correspondence analysis on such genes could clearly indicate that LDGL samples share a 'molecular signature' distinct from that of normal NK cells. With a newly invented class prediction algorithm, 'weighted distance method', all 19 samples received a clinically matched diagnosis, and, furthermore, a detailed cross-validation trial for the prediction of normal or CNKL status could achieve a high accuracy (77.8%). By applying another statistical approach, we could extract other sets of genes, expression of which was specific to either normal or LDGL NK cells. Together with sophisticated statistical methods, gene expression profiling of a background-matched NK cell fraction thus provides us a wealth of information for the LDGL condition.

DNA microarray analysis of hematopoietic stem cell-like fractions from individuals with the M2 subtype of acute myeloid leukemia.

Acute myeloid leukemia (AML) may develop de novo or secondarily to myelodysplastic syndrome (MDS). Although the clinical outcome of MDS-related AML is worse than that of de novo AML, it is not easy to differentiate between these two clinical courses without a record of prior MDS. Large-scale profiling of gene expression by DNA microarray analysis is a promising approach with which to identify molecular markers specific to de novo or MDS-related AML. This approach has now been adopted with AC133-positive hematopoietic stem cell-like fractions purified from 10 individuals, each with either de novo or MDS-related AML of the M2 subtype. Sets of genes whose activity was associated with either disease course were identified. Furthermore, on the basis of the expression profiles of these genes, it was possible to predict correctly the clinical diagnosis for 17 (85%) of the 20 cases in a cross-validation trial. Similarly, different sets of genes were identified whose expression level was associated with clinical outcome after induction chemotherapy. These data suggest that, at least in terms of gene expression profiles, de novo AML and MDS-related AML are distinct clinical entities.

Flat and depressed lesions of the colon and rectum: Pathogenesis and clinical management.

INTRODUCTION: It is not clear whether flat lesions play a role in the pathogenesis of colorectal carcinoma. Flat lesions are being increasingly recognised with new colonoscopic techniques. MATERIALS AND METHODS: A total of 10,939 consecutive colonoscopies were performed over a 9-year period. After bowel preparation with polyethylene glycol electrolyte lavage solution, high-resolution video colonoscopy and indigocarmine spraying were performed to detect flat lesions. All lesions suggesting neoplastic change were removed by polypectomy or surgery. Cancers invading beyond the submucosal layer were excluded from this analysis. The gross appearance of flat-type lesions was classified as flat elevated type or flat depressed type based on the presence or absence of central depression. RESULTS: A total of 5408 neoplastic lesions were index lesions, including 5035 adenomas and 373 carcinomas (124 with submucosal invasion). The prevalence of flat depressed and flat elevated lesions were 2.8% and 18.1%, respectively. Submucosal invasion rates were 17.1% in the flat depressed, 0.8% in the flat elevated, 1.6% in the sessile, 4.0% in pedunculated lesions and 9.3% in creeping lesions. The submucosal invasion rate in the flat depressed lesions was significantly higher than in any others, except for creeping lesions (P = 0.06). The percentage of flat elevated and flat depressed carcinomas among all carcinomas invading the submucosa was 6.5% and 21.0%, respectively. CONCLUSION: Flat lesions were common during routine colonoscopy. One-quarter of colorectal cancers may be derived from flat lesions. Training in dye spray technique may result in a higher detection rate of flat colonic lesions.

SSR analysis of genetic diversity among maize inbred lines adapted to cold regions of Japan.

Information regarding diversity and relationships among breeding material is necessary for hybrid maize ( Zea mays L.) breeding. Simple-sequence repeat (SSR) analysis of the 60 loci distributed uniformly throughout the maize genome was carried out for 65 inbred lines adapted to cold regions of Japan in order to assess genetic diversity among the inbred lines and to assign them to heterotic groups. The mean value (0.69) of the polymorphic-index content (PIC) for the SSR loci provided sufficient discrimination-ability for the assessment of genetic diversity among the inbred lines. The correlation between the genetic-similarity (GS) estimates and the coancestry coefficient was significant ( r = 0.70). The average-linkage (UPGMA) cluster analysis and principal-coordinate analysis (PCOA) for a matrix of the GS estimates showed that the Northern flint inbred lines bred in Japan were similar to a Canadian Northern flint inbred line CO12 and a European flint inbred line F283, and that dent inbred lines bred in Japan were similar to BSSS inbred lines such as B73. These associations correspond to the known pedigree records of these inbred lines. The results indicate that SSR analysis is effective for the assessment of genetic diversity among maize inbred lines and for the assignment of inbred lines to heterotic groups.