Whole-genome and transcriptome analysis enhances precision cancer treatment options.

BACKGROUND: Recent advances are enabling delivery of precision genomic medicine to cancer clinics. While the majority of approaches profile panels of selected genes or hotspot regions, comprehensive data provided by whole-genome and transcriptome sequencing and analysis (WGTA) present an opportunity to align a much larger proportion of patients to therapies. PATIENTS AND METHODS: Samples from 570 patients with advanced or metastatic cancer of diverse types enrolled in the Personalized OncoGenomics (POG) program underwent WGTA. DNA-based data, including mutations, copy number and mutation signatures, were combined with RNA-based data, including gene expression and fusions, to generate comprehensive WGTA profiles. A multidisciplinary molecular tumour board used WGTA profiles to identify and prioritize clinically actionable alterations and inform therapy. Patient responses to WGTA-informed therapies were collected. RESULTS: Clinically actionable targets were identified for 83% of patients, of which 37% of patients received WGTA-informed treatments. RNA expression data were particularly informative, contributing to 67% of WGTA-informed treatments; 25% of treatments were informed by RNA expression alone. Of a total 248 WGTA-informed treatments, 46% resulted in clinical benefit. RNA expression data were comparable to DNA-based mutation and copy number data in aligning to clinically beneficial treatments. Genome signatures also guided therapeutics including platinum, poly-ADP ribose polymerase inhibitors and immunotherapies. Patients accessed WGTA-informed treatments through clinical trials (19%), off-label use (35%) and as standard therapies (46%) including those which would not otherwise have been the next choice of therapy, demonstrating the utility of genomic information to direct use of chemotherapies as well as targeted therapies. CONCLUSIONS: Integrating RNA expression and genome data illuminated treatment options that resulted in 46% of treated patients experiencing positive clinical benefit, supporting the use of comprehensive WGTA profiling in clinical cancer care.

Selected medical interventions in women with a deleterious BRCA mutation: a population-based study in British Columbia.

Background: We examined the uptake of risk-reducing interventions, including bilateral mastectomy, risk-reducing salpingo-oophorectomy, oral contraceptive pills, tamoxifen, and raloxifene, for the entire population of women with a deleterious BRCA1 or BRCA2 mutation in the Canadian province of British Columbia. Methods: This retrospective population-based study used data available in British Columbia for all women who, between 1996 and 2014, were tested and found to have a BRCA mutation. Rates of risk-reducing interventions stratified according to the type of BRCA mutation and prior history of breast or gynecologic cancer (ovary, fallopian tube, peritoneal) are presented. Cancers diagnosed in women with a BRCA mutation after disclosure of their mutation status are also presented. Results: The final study cohort consisted of 885 patients with a deleterious BRCA1 (n = 474) or BRCA2 (n = 411) mutation. Of the women with no prior breast cancer, 30.8% carrying a BRCA1 mutation and 28.3% carrying a BRCA2 mutation underwent bilateral mastectomy. Of women with no prior gynecologic cancer, 64.7% carrying a BRCA1 mutation and 62.2% carrying a BRCA2 mutation underwent risk-reducing bilateral salpingo-oophorectomy. Rates of chemoprevention with oral contraceptive pills and tamoxifen or raloxifene were low in all groups. In this cohort, 23 gynecologic and 70 breast cancers were diagnosed after disclosure of BRCA mutation status. Conclusions: Our results suggest reasonable uptake of risk-reducing interventions in high-risk women. To minimize the occurrence of breast and ovarian cancer in women with a BRCA1 or BRCA2 mutation, more attention could be paid to ensuring that affected women receive proper counselling and follow-up.

Response to angiotensin blockade with irbesartan in a patient with metastatic colorectal cancer.

BACKGROUND: A patient suffering from metastatic colorectal cancer, treatment-related toxicity and resistance to standard chemotherapy and radiation was assessed as part of a personalized oncogenomics initiative to derive potential alternative therapeutic strategies. PATIENTS AND METHODS: Whole-genome and transcriptome sequencing was used to interrogate a metastatic tumor refractory to standard treatments of a patient with mismatch repair-deficient metastatic colorectal cancer. RESULTS: Integrative genomic analysis indicated overexpression of the AP-1 transcriptional complex suggesting experimental therapeutic rationales, including blockade of the renin-angiotensin system. This led to the repurposing of the angiotensin II receptor antagonist, irbesartan, as an anticancer therapy, resulting in the patient experiencing a dramatic and durable response. CONCLUSIONS: This case highlights the utility of comprehensive integrative genomic profiling and bioinformatics analysis to provide hypothetical rationales for personalized treatment options.

An analysis of the association between prostate cancer risk loci, PSA levels, disease aggressiveness and disease-specific mortality.

BACKGROUND: Genome-wide association studies have identified multiple single-nucleotide polymorphsims (SNPs) associated with prostate cancer (PCa). Although these SNPs have been clearly associated with disease risk, their relationship with clinical outcomes is less clear. Our aim was to assess the frequency of known PCa susceptibility alleles within a single institution ascertainment and to correlate risk alleles with disease-specific outcomes. METHODS: We genotyped 1354 individuals treated for localised PCa between June 1988 and December 2007. Blood samples were prospectively collected and de-identified before being genotyped and matched to phenotypic data. We investigated associations between 61 SNPs and disease-specific end points using multivariable analysis and also determined if SNPs were associated with PSA at diagnosis. RESULTS: Seven SNPs showed associations on multivariable analysis (P<0.05), rs13385191 with both biochemical recurrence (BR) and castrate metastasis (CM), rs339331 (BR), rs1894292, rs17178655 and rs11067228 (CM), and rs11902236 and rs4857841 PCa-specific mortality. After applying a Bonferroni correction for number of SNPs (P<0.0008), the only persistent significant association was between rs17632542 (KLK3) and PSA levels at diagnosis (P=1.4 × 10(-5)). CONCLUSIONS: We confirmed that rs17632542 in KLK3 is associated with PSA at diagnosis. No significant association was seen between loci and disease-specific end points when accounting for multiple testing. This provides further evidence that known PCa risk SNPs do not predict likelihood of disease progression.

Mechanisms of Clostridium tyrobutyricum removal through natural creaming of milk: A microscopy study.

Clostridium tyrobutyricum is the main spoilage agent of late blowing defect (LBD) in Grana Padano and Parmigiano-Reggiano cheeses; LBD is characterized by openings and holes and is sometimes accompanied by cracks and an undesirable flavor. Even a very few spores remaining in the cheese curd may cause LBD; thus, it is essential to eradicate them during milk natural creaming. By this process, most of the bacteria, somatic cells, and spores rise to the top of the milk, together with the fat globules, and are removed with the cream. Previous studies suggested that milk immunoglobulins mediate the interactions between fat globules and bacteria that occur upon creaming but no direct evidence for this has been found. Moreover, other physical chemical interactions could be involved; for example, physical entrapment of spores among globule clusters. To maximize the efficiency of the natural creaming step in removing Cl. tyrobutyricum, it is essential to understand the nature of spore-globule interactions. With this aim, raw milk was contaminated with spores of Cl. tyrobutyricum before going to creaming overnight at 8°C, after which spore and bacteria removal was >90%. The obtained cream was analyzed by light interference contrast and fluorescence microscopy and by transmission electron microscopy (TEM). Results showed that most of the vegetative cells and spores, which were stained with malachite green before addition to milk, adhered tightly to the surface of single fat globules, the membranes of which appeared heterogeneous when stained with the fluorescent dye DilC18(3)-DS. Using the same dye, we observed transient and persistent interactions among globules, with formation of clusters of different sizes and partial coalescence of adhering membranes. Transmission electron microscopy examination of replicates of freeze-fractured cream allowed us to observe tight adhesion of spores to fat globules. Ultrathin sections revealed that this adhesion is mediated by an amorphous, slightly electron-opaque material, sometimes granular in appearance. Bacteria also adhered to different fat globules, linking them together, which suggests that adhesion was strong enough to maintain a stable contact. Although we cannot exclude physical entrapment of bacteria among fat globule clusters, we show for the first time that most of the bacteria are adhered to fat globules by an electron-opaque material whose nature has yet to be determined. Immunoglobulins are certainly the best candidates for adhesion but other compounds may be involved.

Evaluation of a modified pH-shift process to reduce 2-methylisoborneol and geosmin in spiked catfish and produce a consumer acceptable fried catfish nugget-like product.

UNLABELLED: Muddy and/or musty off-flavors in farmed-raised catfish occur as a result of the absorption of geosmin (GEO) and 2-methylisoborneol (MIB), compounds produced by algae. Previous research suggests the acid pH-shift method may be able to reduce off-flavors to produce a consumer acceptable product. The objective of this research was to evaluate application of the acid pH-shift method using a shaker sieve for protein recovery and to evaluate consumer acceptability of a resultant batter-coated fried nugget-like catfish product. Farm-raised catfish were either allowed to depurate (control) or treated with 1 ppb GEO or MIB. Fillets from each replicate were collected and ground and treated by the acid pH-shift process. Samples from all treatments and replicates were evaluated for residual GEO and MIB. In addition, batter-coated fried catfish samples were prepared for a consumer sensory evaluation. Results demonstrated that the pH-shift process decreased moisture, ash, and collagen content of catfish fillet tissue (P < 0.05). Flavor of control samples was preferred (P < 0.05). Texture of catfish samples treated by the pH-shift process was preferred (P < 0.05). Results demonstrate the pH-shift process can be utilized to reduce off-flavors and increase the acceptability of a processed catfish product. PRACTICAL APPLICATION: Use of a sieve as an economic alternative for the pH-shift process was evaluated for removing off-flavors from catfish. Difficulties were encountered with regard to protein recovery using the sieve and suggestions are made to, perhaps, make the process more applicable for a sieve-based recovery step. The process as described reduced off-flavors, but only 2-fold suggesting the process would work best on catfish near or just over off-flavor thresholds. Results also indicated the pH-shift process could be used to improve texture of a fried catfish product designed to be similar to chicken nuggets.

Assessment of Aquaflor(®) , copper sulphate and potassium permanganate for control of Aeromonas hydrophila and Flavobacterium columnare infection in sunshine bass, Morone chrysops female × Morone saxatilis male.

Two experiments were conducted to test the effectiveness of different therapeutants against a mixed infection of Aeromonas hydrophila and Flavobacterium columnare in sunshine bass. Experiment 1 evaluated copper sulphate, florfenicol-medicated feed and potassium permanganate (KMnO(4) ) against a natural mixed infection. Experiment 2 further evaluated copper sulphate as a treatment to control an experimental mixed infection. In experiment 1, naturally infected untreated fish had the lowest final survival per cent, at 71%, while florfenicol-medicated feed at 15mgkg(-1) body weight for 10days or copper sulphate at 2.1mgL(-1) (1% of the total alkalinity) for 24h produced the highest final survivals, at 90% and 88%, respectively. The final survival of the naturally infected fish administered florfenicol-medicated feed was significantly different (P<0.1) from the untreated fish. The survival curves for the florfenicol and the copper sulphate at 2.1mgL(-1) were significantly improved from the untreated fish. In experiment 2, fish were challenged by waterborne exposure to A. hydrophila and F. columnare and either not treated or treated with copper sulphate at 2.1mgL(-1) . At the end of experiment 2, the per cent survival of the challenged fish treated with copper sulphate (99%) was significantly higher (P<0.05) than the non-treated (61%). The results illustrate clear benefit of florfenicol and copper sulphate against a mixed infection of A. hydrophila and F. columnare.

Gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS): a new autosomal dominant syndrome.

OBJECTIVE: The purpose of this study was the clinical and pathological characterisation of a new autosomal dominant gastric polyposis syndrome, gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS). METHODS: Case series were examined, documenting GAPPS in three families from Australia, the USA and Canada. The affected families were identified through referral to centralised clinical genetics centres. RESULTS: The report identifies the clinical and pathological features of this syndrome, including the predominant dysplastic fundic gland polyp histology, the exclusive involvement of the gastric body and fundus, the apparent inverse association with current Helicobacter pylori infection and the autosomal dominant mode of inheritance. CONCLUSIONS: GAPPS is a unique gastric polyposis syndrome with a significant risk of gastric adenocarcinoma. It is characterised by the autosomal dominant transmission of fundic gland polyposis, including areas of dysplasia or intestinal-type gastric adenocarcinoma, restricted to the proximal stomach, and with no evidence of colorectal or duodenal polyposis or other heritable gastrointestinal cancer syndromes.

Germline mutations in CDH1 are infrequent in women with early-onset or familial lobular breast cancers.

BACKGROUND: Germline mutations in CDH1 are associated with hereditary diffuse gastric cancer; lobular breast cancer also occurs excessively in families with such condition. METHOD: To determine if CDH1 is a susceptibility gene for lobular breast cancer in women without a family history of diffuse gastric cancer, germline DNA was analysed for the presence of CDH1 mutations in 318 women with lobular breast cancer who were diagnosed before the age of 45 years or had a family history of breast cancer and were not known, or known not, to be carriers of germline mutations in BRCA1 or BRCA2. Cases were ascertained through breast cancer registries and high-risk cancer genetic clinics (Breast Cancer Family Registry, the kConFab and a consortium of breast cancer genetics clinics in the United States and Spain). Additionally, Multiplex Ligation-dependent Probe Amplification was performed for 134 cases to detect large deletions. RESULTS: No truncating mutations and no large deletions were detected. Six non-synonymous variants were found in seven families. Four (4/318 or 1.3%) are considered to be potentially pathogenic through in vitro and in silico analysis. CONCLUSION: Potentially pathogenic germline CDH1 mutations in women with early-onset or familial lobular breast cancer are at most infrequent.

Multiple granular cell tumors are an associated feature of LEOPARD syndrome caused by mutation in PTPN11.

We report a patient with a clinical and molecular diagnosis of LEOPARD syndrome (LS) associated with multiple granular cell tumors (MGCT). Bidirectional sequencing of exons 7, 12, and 13 of the PTPN11 gene revealed the T468M missense mutation in exon 12. This mutation has been previously reported in patients with LS. To our knowledge, this is the first report of MGCT associated with molecularly characterized LS and provides the first molecular evidence linking granular cell tumors (GCT) to the Ras/mitogen-activated protein (MAP) kinase pathway. We propose that MGCT can be associated with LS. Analysis of GCT from this case tested negatively for loss of heterozygosity (LOH) at the PTPN11 and NF1 loci and did not show deletions of the PTEN gene. The absence of LOH of PTPN11 supports published functional data that T468M is a dominant-negative mutation.

Comparative toxicity of the phytotoxins (8R,16R)-(-)-pyrenophorin and (5S,8R,13S,16R)-(-)-pyrenophorol on aquatic organisms.

The acute toxicities of the fungal phytotoxins (8R,16R)-(-)-pyrenophorin and (5S,8R,13S,16R)-(-)-pyrenophorol on Vibrio fischeri, Oscillatoria perornata, Pseudokirchneriella subcapitata, Lemna minor and Artemia fransiscana were evaluated. (8R,16R)-(-)-pyrenophorin was more toxic than (5S,8R,13S,16R)-(-)-pyrenophorol to V. fischeri, O. perornata, L. minor and A. fransiscana. The highest acute toxicity of (8R,16R)-(-)-pyrenophorin was exhibited on V. fischeri (5 min median effective concentration of 3.57 M 10(-5)) whereas the corresponding value for (5S,8R,13S,16R)-(-)-pyrenophorol was 801 M 10(-5). P. subcapitata exhibited a lack of sensitivity (median inhibitory concentration of >10 M 10(-5)) to both phytotoxins.

Relationship between physical properties of casein micelles and rheology of skim milk concentrate.

The properties of casein micelles in milk concentrates are of interest for the use of ultrafiltered (UF) skim milk concentrates in dairy products, and for the general understanding of colloidal stability and behavior of the casein micelle. The rheological behavior of UF skim milk concentrate with a casein concentration of 19.5% (wt/wt) was investigated at different pH and NaCl concentrations by analyzing flow viscometry and small amplitude oscillatory shear measurements. Viscometric flow curves were fitted to the Carreau-Yasuda model with the aim of determining values for the viscosity at infinite high shear rates and thereby estimate the voluminosity of the casein micelles (nu(casein)) in the UF concentrate. The voluminosity of the casein micelles increased with addition of NaCl and decreased when pH was decreased from 6.5 to 5.5. At pH 5.2, nu(casein) increased because of acid-induced aggregation of the casein micelles. The changes in nu(casein) could be interpreted from transmission electron microscopy of freeze-fractured samples of the UF concentrate and partly from dynamic light scattering measurements. Altered interactions between casein micelles due to different pH and NaCl concentrations are proposed to occur due to collapse of the kappa-casein layer, changed ionic strength, and altered distance between casein micelles.

Isolation and identification of antifungal and antialgal alkaloids from Haplophyllum sieversii.

Bioassay-guided fractionation of the hexane/ethyl acetate/water (H/EtOAc/H2O) crude extract of the aerial parts of Haplophyllum sieversii was performed because of preliminary screening data that indicated the presence of growth inhibitory components against Colletotrichum fragariae, Colletotrichum gloeosporioides, and Colletotrichum acutatum. Fractionation was directed using bioautographical methods resulting in the isolation of the bioactive alkaloids flindersine, anhydroevoxine, haplamine, and a lignan eudesmin. These four compounds were evaluated for activity against C. fragariae, C. gloeosporioides, C. acutatum, Botrytis cinerea, Fusarium oxysporum, and Phomopsis obscurans in a dose-response growth-inhibitory bioassay at 50.0, 100.0, and 150.0 microM. Of the four compounds tested, flindersine demonstrated the highest level of antifungal activity. Additionally, flindersine, eudesmin, and haplamine were screened against the freshwater phytoplanktons Oscillatoria perornata, Oscillatoria agardhii, Selenastrum capricornutum, and Pseudanabaena sp. (strain LW397). Haplamine demonstrated selective inhibition against the odor-producing cyanobacterium O. perornata compared to the activity against the green alga S. capricornutum, with lowest observed effect concentration values of 1.0 and 10.0 microM, respectively.

Ultrasound findings in follow-up investigations in a case of aspartoacylase deficiency (canavan disease).

Aspartoacylase deficiency is a neurodegenerative disease which typically starts in the first months of life with muscular hypotonia and developmental standstill. One of the first diagnostic procedures in this situation is an ultrasound of the brain. There is little information available about sonographic changes in Canavan disease. We present for the first time an ultrasound follow-up in a proven case of aspartoacylase deficiency from 3 weeks to 22 months. High echogenicity of the white matter was present in the neonatal period. Additional sonographic phenomena resulting in a characteristic pattern were shown in further investigations. The distinctive sonomorphology is compared to a few other cases in the literature. The correlation to the neuropathological course of the white matter changes is discussed. Recognition of the sonographic features in addition to the clinical presentation may contribute to an effective biochemical work-up.

Transdermal delivery of two antioxidants from different cosmetic formulations.

The efficacy of any cosmetic product containing a functional ingredient is determined by the skin delivery of the active molecule, which is influenced by the type of the vehicle and the molecule itself. This study was designed to compare the percutaneous absorption habits of the antioxidants carcinine and lipoic acid out of various formulations by means of the porcine skin model. Initial evaluation of the in vitro porcine skin model has demonstrated its feasibility for various substances and formulations [1, 2]. Increasing legal requirements for risk assessment in the cosmetic industry have led to the development of this alternative test method. The penetration properties are determined by the OECD Guideline TG 428: Skin Absorption: in vitro Method [3, 4], which allows the use of porcine skin for penetration studies. Porcine skin is used because of its similarity to human skin in terms of its morphology and the essential permeation characteristics [5]. The mass balances for each tested formulation type of the antioxidants show individual penetration behaviours with significant differences. The presented data plainly demonstrate that the lipophilic lipoic acid has a distinct higher penetration potential than the hydrophilic carcinine. The chosen vehicle can enhance or reduce the transdermal delivery of both tested antioxidants. Modern effective cosmetic formulations will work only, if the active ingredients penetrate into the epidermis. In conclusion, the correct selection of a suitable formulation plays an important role during product development.

Volatile components of the cyanobacterium Oscillatoria perornata (Skuja).

Volatile compounds were identified from unialgal continuous cultures of the cyanobacterium Oscillatoria perornata. Steam distillates of the unialgal cultures were continuously extracted with pentane, and the pentane extracts were analyzed by GC-MS. Retention indices and mass spectral data were used to identify 15 components. Relative amounts of individual components were expressed as percent peak area relative to total peak area. The main volatile components were heptadecane (57.0%), 2-methylisoborneol (29.4%), and benzaldehyde (1.2%). Together with the previously known 2-methylisoborneol, which is the major cause of the musty off-flavor problem in catfish farming operations in Mississippi, other components identified were dimethyl disulfide (1.0%), dimethyl trisulfide (0.5%), and benzothiazole (0.6%). These compounds and their organoleptic characteristics are discussed in relation to their possible contributions to cultured catfish off-flavor problems.

Phytotoxic and fungitoxic activities of the essential oil of kenaf (Hibiscus cannabinus L.) leaves and its composition.

The chemical composition of the essential oil of kenaf (Hibiscus cannabinus) was examined by GC-MS. Fifty-eight components were characterized from H. cannabinus with (E)-phytol (28.16%), (Z)-phytol (8.02%), n-nonanal (5.70%), benzene acetaldehyde (4.39%), (E)-2-hexenal (3.10%), and 5-methylfurfural (3.00%) as the major constituents. The oil was phytotoxic to lettuce and bentgrass and had antifungal activity against Colletotrichum fragariae, Colletotrichum gloeosporioides, and Colletotrichum accutatum but exhibited little or no algicidal activity.

Effects of carbon source, phosphorus concentration, and several micronutrients on biomass and geosmin production by Streptomyces halstedii.

The effects of various carbon sources, phosphorus concentration, and different concentrations of the micronutrients calcium, cobalt, copper, iron, manganese, potassium, and zinc were determined on biomass dry weight production, geosmin production, and geosmin/biomass (G/B) values for Streptomyces halstedii, a geosmin-producing actinomycete isolated from the sediment of an aquaculture pond. Of the substrates tested, maltose as a sole carbon source promoted maximal growth by S. halstedii while mannitol promoted maximal geosmin production, and galactose yielded the highest G/B values. Fish-food pellets and galactose were poor substrates for growth. Increasing phosphorus concentrations enhanced geosmin production and G/B values. Of the seven micronutrients tested, zinc, iron, and copper had the most profound effects on biomass and geosmin production. Increasing zinc concentrations promoted biomass production while inhibiting geosmin production and G/B values; increasing concentrations of copper and iron inhibited biomass and geosmin production. Increased copper concentrations had the greatest effect in preventing growth and geosmin production by S. halstedii.