Phase II study of nab-paclitaxel in refractory small bowel adenocarcinoma and CpG island methylator phenotype (CIMP)-high colorectal cancer.

Background: Hypermethylation of promoter CpG islands [CpG island methylator phenotype (CIMP)] represents a unique pathway for the development of colorectal cancer (CRC), characterized by lack of chromosomal instability and a low rate of adenomatous polyposis coli (APC) mutations, which have both been correlated with taxane resistance. Similarly, small bowel adenocarcinoma (SBA), a rare tumor, also has a low rate of APC mutations. This phase II study evaluated taxane sensitivity in SBA and CIMP-high CRC. Patients and methods: The primary objective was Response Evaluation Criteria in Solid Tumors version 1.1 response rate. Eligibility included Eastern Cooperative Oncology Group performance status 0/1, refractory disease, and SBA or CIMP-high metastatic CRC. Nab-paclitaxel was initially administered at a dose of 260 mg/m2 every 3 weeks but was reduced to 220 mg/m2 owing to toxicity. Results: A total of 21 patients with CIMP-high CRC and 13 with SBA were enrolled from November 2012 to October 2014. The efficacy-assessable population (patients who received at least three doses of the treatment) comprised 15 CIMP-high CRC patients and 10 SBA patients. Common grade 3 or 4 toxicities were fatigue (12%), neutropenia (9%), febrile neutropenia (9%), dehydration (6%), and thrombocytopenia (6%). No responses were seen in the CIMP-high CRC cohort and two partial responses were seen in the SBA cohort. Median progression-free survival was significantly greater in the SBA cohort than in the CIMP-high CRC cohort (3.2 months compared with 2.1 months, P = 0.03). Neither APC mutation status nor CHFR methylation status correlated with efficacy in the CIMP-high CRC cohort. In vivo testing of paclitaxel in an SBA patient-derived xenograft validated the activity of taxanes in this disease type. Conclusion: Although preclinical studies suggested taxane sensitivity was associated with chromosomal stability and wild-type APC, we found that nab-paclitaxel was inactive in CIMP-high metastatic CRC. Nab-paclitaxel may represent a novel therapeutic option for SBA.

Microsatellite genotyping reveals a signature in breast cancer exomes.

Genomic instability at microsatellite loci is a hallmark of many cancers, including breast cancer. However, much of the genomic variation and many of the hereditary components responsible for breast cancer remain undetected. We hypothesized that variation at microsatellites could provide additional genomic markers for breast cancer risk assessment. A total of 1,345 germline and tumor DNA samples from individuals diagnosed with breast cancer, exome sequenced as part of The Cancer Genome Atlas, were analyzed for microsatellite variation. The comparison group for our analysis, representing healthy individuals, consisted of 249 females which were exome sequenced as part of the 1,000 Genomes Project. We applied our microsatellite-based genotyping pipeline to identify 55 microsatellite loci that can distinguish between the germline of individuals diagnosed with breast cancer and healthy individuals with a sensitivity of 88.4 % and a specificity of 77.1 %. Further, we identified additional microsatellite loci that are potentially useful for distinguishing between breast cancer subtypes, revealing a possible fifth subtype. These findings are of clinical interest as possible risk diagnostics and reveal genes that may be of potential therapeutic value, including genes previously not associated with breast cancer.

Comparison of Phenotypic and Genotypic Methods Used for the Species Identification of Lactobacillus NP51 and Development of a Strain-Specific PCR Assay.

The species level identity of Lactobacillus NP51, a commercial direct-fed microbial previously identified as Lactobacillus acidophilus NP51, was re-evaluated to determine whether new technologies resulted in changes in the original identification. The phenotypic methods for species identification included API 50 CHL kit and two automated systems, Vitek 2 and MIDI (FAME analysis; a total of three independent FAME analyses). Discrepancies among the identification results with all methods of phenotypic analysis were reported. MicroSeqID 500 16S rRNA system (SeqWright Inc., Houston, TX), a genotypic method, identified the organism as Lactobacillus animalis. Cloning, sequencing and subsequent sequence comparison of NP51 16S-23S intergenic spacer region (ISRs) to nucleotide sequence databases using the BLAST search tool indicated that NP51 can now be named L. animalis. When NP51 was originally identified as L. acidophilus, the designation of L. animalis did not exist taxonomically. The NP51 sequence comparisons using BLAST also revealed that NP51 and a strain previously identified as L. animalis LA51 HOFG1 by Flint and Angert are identical strains under different names. A strain-specific primer pair was also identified for HOFG1 by the same research group. A primer pair (using HOFG1 forward pair) also produced an amplicon unique to NP51. These methods demonstrate the significance of genetic-based detection methods both for scientific identification of organisms from biological samples and to prevent misidentification in food and health industry related microorganisms in which proprietary considerations are an important concern.

Reduction of Escherichia coli O157 and Salmonella in feces and on hides of feedlot cattle using various doses of a direct-fed microbial.

In this study, the effectiveness of direct-fed microbials at reducing Escherichia coli O157 and Salmonella in beef cattle was evaluated. Steers (n=240) received one of the following four treatment concentrations: control = lactose carrier only; low = 1 X 10(7) CFU per steer daily Lactobacillus acidophilus NP51; medium = 5 x 10(8) CFU per steer daily L. acidophilus NP51; and high = 1 x 10(9) CFU per steer daily L. acidophilus NP51. Low, medium, and high diets also included 1 x 10(9) CFU per steer Propionibacterium freudenreichii NP24. Feces were collected from each animal at allocation of treatment and found to have no variation (P = 0.54) between cohorts concerning E. coli O157 recovery. Feces and hide swabs were collected at harvest and analyzed for the presence of E. coli O157 by immunomagnetic separation and Salmonella by PCR. No significant dosing effects were detected for E. coli O157 recovery from feces at the medium dose or from hides at the medium and high doses. E. coli O157 was 74% (P < 0.01) and 69% (P < 0.01) less likely to be recovered in feces from animals receiving the high and low diets, respectively, compared with controls. Compared with controls, E. coli O157 was 74% (P = 0.05) less likely to be isolated on hides of cattle receiving the low dose. No significant dosing effects were detected for Salmonella recovery from feces at the medium and low doses or from hides at any doses. Compared with controls, Salmonella was 48% (P = 0.09) less likely to be shed in feces of cattle receiving the high dose. No obvious dose-response of L. acidophilus NP51 on recovery of E. coli O157 or Salmonella was detected in our study.

An investigation into techniques for cleaning mold-contaminated home contents.

This study examined the efficacy of the following treatments to reduce selected fungal spore and mycotoxin levels on materials commonly found in home contents: (1) gamma irradiation at a 10-13 kiloGray exposure, (2) a detergent/bleach wash, and (3) a steam cleaning technique. A minimum of six replicates were performed per treatment. Paper, cloth, wood, and carpet were inoculated with either fungal spores (Stachybotrys chartarum, Aspergillus niger, Penicillium chrysogenum, or Chaetomium globosum) at 240,000 spores/2.54 cm2 of material or with the mycotoxins roridin A, T-2, and verrucarin A at 10 microg per 2.54 cm2 of material. Treatments were evaluated with an agar plating technique for fungal spores and a yeast toxicity culture assay for mycotoxins. Results showed that gamma irradiation inactivated fungal spores, but the treatment was not successful in inactivating mycotoxins. The washing technique completely inactivated or removed spores on all materials except for C. globosum, which was reduced on all items except paper (p < 0.05). Washing inactivated all mycotoxins on paper and cloth but not on carpet or untreated wood (p < 0.001). The steam cleaning treatment did not completely eliminate any fungal spores; however, it reduced P. chrysogenum numbers on all materials, C. globosum was reduced on wood and carpet, and S. chartarum was reduced on wood (p < 0.05). Steam cleaning was unsuccessful in inactivating any of the tested mycotoxins. These results show that the bleach/detergent washing technique was more effective overall in reducing spore and mycotoxin levels than gamma irradiation or steam cleaning. However, the other examined techniques were successful in varying degrees.

Evaluation of fungal growth on cellulose-containing and inorganic ceiling tile.

Buildings with poor indoor air quality (IAQ) frequently have many areas with surface fungal contamination. Studies have demonstrated that certain fungal genera (e.g., Cladosporium, Penicillium, and Stachybotrys) are able to grow on building materials such as wallpaper, drywall, and ceiling tiles, particularly after water damage has occurred. Due to the increasing awareness of sick building syndrome (SBS), it has become essential to identify building materials that prevent the interior growth of fungi. The objective of this study was to identify building materials that would not support the growth of certain fungal genera, regardless of whether an external food source was made available. The growth of three fungal genera (Cladosporium, Penicillium, and Stachybotrys) was evaluated on cellulose-containing ceiling tile (CCT) and inorganic ceiling tile (ICT). Both types of ceiling tile were exposed to environmental conditions which can occur inside a building. Our results show that ICT did not support the growth of these three fungal genera while CCT did. Our data demonstrate that ICT could serve as an ideal replacement for CCT.