Clinical evaluation of the cobas® MTB-RIF/INH reagent and the cobas® 6800 for the detection of isoniazid and rifampicin resistance.

We aimed to validate the performance of a newly developed real-time PCR assay using cobas® MTB-RIF/INH reagent on the cobas® 6800 system for detecting isoniazid (INH) and rifampicin (RIF) resistance, using Japanese Mycobacterium tuberculosis (MTB) isolates. In total, 119 mock sputum specimens spiked with resistant MTB were tested using the cobas® MTB-RIF/INH reagent. The whole genomes of all MTB isolates were sequenced by MiSeq and analysed for mutations/indels causing drug resistance. All isolates were tested for phenotypic drug susceptibility, then MTB negative sputa were collected and pooled to prepare mock sputum specimens for the study. The sensitivity and specificity for INH resistance at a concentration equal to 3 × the limit of detection were 77.8% and 90.0%, respectively; those for RIF resistance were 91.8% and 93.5%, respectively. The sensitivities for INH and RIF were statistically different (P = 0.014), but not the specificities (P = 0.624). Twenty-two false-susceptible and two false-resistant results were obtained in INH; meanwhile, six false-susceptible and three false-resistant results were obtained in RIF. False-resistance for INH and RIF was mainly due to disputed mutations. The cobas® MTB-RIF/INH reagent showed better performance than other rapid molecular tests.

Aneuploidy predicts outcome in patients with endometrial carcinoma and is related to lack of CDH13 hypermethylation.

PURPOSE: Many investigators have reported that aneuploidy detected by flow cytometry is a useful prognostic marker in patients with endometrial cancer. Laser scanning cytometry (LSC) is a technology similar to flow cytometry but is more feasible for clinical laboratory use. We evaluated the usefulness of DNA ploidy detected by LSC as a prognostic marker in patients with endometrial cancer and investigated genetic and epigenetic factors related to aneuploidy. EXPERIMENTAL DESIGN: Endometrial cancer specimens from 106 patients were evaluated. The methylation status of CDH13, Rassf1, SFRP1, SFRP2, SFRP4, SFRP5, p16, hMLH1, MGMT, APC, ATM, and WIF1 and mutations in the p53 and CDC4 genes were investigated. LSC was carried out to determine DNA ploidy. Fluorescence in situ hybridization was done with chromosome-specific centromeric probes to assess chromosomal instability. RESULTS: Univariate and multivariate analyses revealed that p53 mutation and lack of CDH13 hypermethylation associated positively with aneuploidy. Univariate analysis showed that aneuploidy, chromosomal instability, and lack of CDH13 hypermethylation as well as surgical stage were significantly predictive of death from endometrial cancer. Furthermore, multivariate analysis revealed that stage in combination with either DNA aneuploidy or lack of CDH13 hypermethylation was an independent prognostic factor. CONCLUSION: These results suggest that analysis of DNA ploidy and methylation status of CDH13 may help predict clinical outcome in patients with endometrial cancer. Prospective randomized trials are needed to confirm the validity of an individualized approach, including determination of tumor ploidy and methylation status of CDH13, to management of endometrial cancer patients.

Hypermethylation status of APC inversely correlates with the presence of submucosal invasion in laterally spreading colorectal tumors.

Little is known about epigenetic alterations in laterally spreading colorectal tumors (LSTs). The goal of the present study was to elucidate the epigenetic background of LSTs and compare the methylation status of DNA CpG islands (CGIs) with clinicopathologic features. Methylation of MINT1, MINT2, MINT31, p16, O(6)-methylguanine-DNA methyltransferase (MGMT), adenomatous polyposis coli (APC), and human MutL homologue 1 (hMLH1) in 42 LSTs was assessed by methylation-specific polymerase chain reaction (MSP) and compared with clinicopathologic parameters. The frequency of hypermethylation was 12.5% (4/32) for MINT1, 40.0% (16/40) for MINT2, 25.0% (10/40) for MINT31, 25.7% (9/35) for p16, 7.7% (3/39) for hMLH1, 26.5% (9/34) for MGMT, and 35.9% (14/39) for APC. APC methylation was inversely associated with submucosal invasion (P = 0.034), which was not found in any of 14 LST cases with APC methylation, whereas submucosal invasion was present in 8 of 25 (32.0%) cases without APC methylation. These data suggest that hypermethylation of APC could be a predictive marker for the absence of submucosal invasion of LSTs.

Determination of ancestral allele for possible human cancer-associated polymorphisms.

To determine ancestral allele in possible cancer-associated polymorphisms, DNA samples from 10 chimpanzees (Pan troglodytes) were sequenced for alleles corresponding to 17 polymorphisms: 8 short tandem repeats [IL1RN (alias IL-1RA) variable number tandem repeat (VNTR); TYMS (previously TS) VNTR; AR CAG repeat; dinucleotide repeats of UGT1A1, IGF1, IFNG (alias IFN-gamma), ESR1 (alias ER-alpha), and EGFR] and 9 single nucleotide polymorphisms (MMP1-1607 1G/2G, MMP3-1171 5A/6A, OGG1 Ser326Cys, ALDH2 Gly487Lys, TP53 Arg72Pro, ABCG2 Gln141Lys, MGMT Leu84Phe, SOD2 Ala-9Val, and MTHFR Ala222Val). No chimpanzee polymorphism corresponded to human IL1RN VNTR; the ancestral allele was a repeat lost in humans. Dinucleotide repeat polymorphisms of IGF1, IFNG, ESR1, and EGFR were shared by chimpanzees, but the length of repeats tended to be longer in humans than in chimpanzees. This tendency was particularly evident for IGF1. All of the SNPs tested are human-specific nucleotide changes. The ancestral allele 7A was shown to be lost in MMP3-1171 5A/6A. Thus, all of the possible cancer-associated polymorphisms tested have human-specific alleles, and the ancestral allele is lost in three polymorphisms (IL1RN VNTR, UGT1A1 CA repeat, and MMP3-1171 5A/6A), suggesting a possible involvement of human-specific alleles in cancer susceptibility.

A simple immunomonitoring procedure for mRNA-loaded dendritic cell therapy.

To develop a simple immunomonitoring method for dendritic cell therapy using messenger RNA (mRNA) as antigen, we evaluated whether Mycobacterium tuberculosis antigen 85A (Ag85A) mRNA-transfected peripheral blood mononuclear cells (PBMCs) could be used to stimulate the induction of interferon (IFN)-gamma-producing T cells. PBMCs from 10 healthy donors were cocultured with autologous PBMCs transfected with mRNA overnight, and the number of IFN-gamma-producing T cells was measured by flow cytometry. IFN-gamma-producing CD4+ and CD8+ T cells were detected in 4 and 5 donors, respectively. PBMCs from 3 donors with negative results were then cocultured with Ag85A mRNA-transfected autologous PBMCs for 1 week to achieve in vitro primary induction of Ag85A-specific T cells. After restimulation with freshly prepared stimulator cells, a small but significant number of IFN-gamma-producing CD8+ T cells was detected. The induction of IFN-gamma-producing CD8+ T cells by overnight coculture was completely abolished by anti-class II or anti-interleukin-12 antibodies, whereas it was partially inhibited by anti-class I antibody. These data suggest that Ag85A mRNA-transfected PBMCs induce specific IFN-gamma-producing T cells and might be applicable for immunomonitoring of mRNA-loaded dendritic cell therapy.

Frizzled-7 as a potential therapeutic target in colorectal cancer.

We investigated whether one of the Wnt receptors, frizzled-7 (FZD7), functions in the canonical Wnt signaling pathway of colorectal cancer (CRC) cells harboring an APC or CTNNB1 mutation and may be a potential therapeutic target for sporadic CRCs. The expression level of FZD gene family members in colon cancer cells and primary CRC tissues were determined by real-time PCR. Activation of the Wnt signaling pathway was evaluated by TOPflash assay. The expression level of Wnt target genes was determined by real-time polymerase chain reaction and/or Western blot analysis. Cell growth and cell invasion were assessed by MTS and matrigel assays, respectively. Among 10 FZD gene family members, FZD7 mRNA was predominantly expressed in six colon cancer cell lines with APC or CTNNB1 mutation. These six cell lines were transfected with FZD7 cDNA together with a TOPflash reporter plasmid, resulting in a 1.5- to 24.3-fold increase of Tcf transcriptional activity. The mRNA expression levels of seven known Wnt target genes were also increased by 1.5- to 3.4-fold after transfection of FZD7 cDNA into HCT-116 cells. The six cell lines were then cotransfected with FZD7-siRNA and a TOPflash reporter plasmid, which reduced Tcf transcriptional activity to 20% to 80%. FZD7-siRNA was shown to significantly decrease cell viability and in vitro invasion activity after transfection into HCT-116 cells. Our present data demonstrated that FZD7 activates the canonical Wnt pathway in colon cancer cells despite the presence of APC or CTNNB1 mutation and that FZD7-siRNA may be used as a therapeutic reagent for CRCs.