Cell-Free DNA Next-Generation Sequencing in Pancreatobiliary Carcinomas.

UNLABELLED: Patients with pancreatic and biliary carcinomas lack personalized treatment options, in part because biopsies are often inadequate for molecular characterization. Cell-free DNA (cfDNA) sequencing may enable a precision oncology approach in this setting. We attempted to prospectively analyze 54 genes in tumor and cfDNA for 26 patients. Tumor sequencing failed in 9 patients (35%). In the remaining 17, 90.3% (95% confidence interval, 73.1%-97.5%) of mutations detected in tumor biopsies were also detected in cfDNA. The diagnostic accuracy of cfDNA sequencing was 97.7%, with 92.3% average sensitivity and 100% specificity across five informative genes. Changes in cfDNA correlated well with tumor marker dynamics in serial sampling (r = 0.93). We demonstrate that cfDNA sequencing is feasible, accurate, and sensitive in identifying tumor-derived mutations without prior knowledge of tumor genotype or the abundance of circulating tumor DNA. cfDNA sequencing should be considered in pancreatobiliary cancer trials where tissue sampling is unsafe, infeasible, or otherwise unsuccessful. SIGNIFICANCE: Precision medicine efforts in biliary and pancreatic cancers have been frustrated by difficulties in obtaining adequate tumor tissue for next-generation sequencing. cfDNA sequencing reliably and accurately detects tumor-derived mutations, paving the way for precision oncology approaches in these deadly diseases.

The Cultural Climate of Southwest Dental Colleges: Dentistry and Dental Hygiene.

PURPOSE: The purpose of this study was to identify the cultural climate of southwestern dental colleges, from the perspective of dental hygiene and dental students. METHODS: The Cultural Attitudes and Climate Questionnaire was used to measure cultural climate. It contained 57 items related to campus experiences, cultural comfort, diversity awareness, racial pressures, fair treatment, respect, lack of support, patient care and overall satisfaction. The survey was administered to 508 dental and dental hygiene students at 5 dental colleges. RESULTS: The response rate was 41% (n=239/508). Students reported not experiencing racial conflict or pressures (71 to 90%), being treated fairly and with respect (86 to 90%) and being comfortable interacting with and treating other cultures (70 to 91%). They also practiced culturally appropriate behaviors (54 to 92%). Those reporting diversity training (77.8%) were more likely to engage in 3 of the 6 awareness practices (p<0.033). Although all groups agreed their educational experience was rewarding (89.5%), African-Americans reported a significantly lower level of agreement than Whites (p=0.003) and Asians (p=0.008). Among all groups, satisfaction with their educational experience was significantly correlated with fair treatment (rho=0.441 to 0.511, p<0.001) and respect for other cultures (rho=0.391 to 0.441, p<0.001). CONCLUSION: The students generally reported a positive cultural climate. Improvements could be made by focusing on fair treatment, respect for cultures and the African-American experience. Cultural competence training could be key to improving cultural climate, as positive outcomes from training were identified.

New allergies after cord blood transplantation.

BACKGROUND AIMS: Umbilical cord blood transplantation (CBT) is an effective treatment for benign and malignant diseases. Late effects of CBT are not well described in the literature. In the present study, we present our experience of new-onset allergies in long-term survivors after CBT. METHODS: After an initial patient had a severe peanut allergic reaction after CBT, all CBT patients were prospectively followed for new allergy development. Fifty patients received CBT between March 2006 and June 2011. RESULTS: The median follow-up after CBT was 447 days (range, 12-2022). At the time of analysis, 30 patients were alive, with 3-year survival of 55.5%; median follow-up of surviving patients was 910 days (range, 68-2022). The allergic syndrome developed in five patients, with the cumulative incidence of new allergies at 2 years of 18.4% (95% confidence interval, 10.8-26). The median time to onset of new allergy after transplantation was 298 days (range, 250-809). CONCLUSIONS: Allergy development has been linked to a delayed maturation of the immune system in several studies. We present the first case series of patients who had new allergies after CBT. Further study of this novel complication as well as counseling of patients after CBT would be important.

Patterns and determinants of dementia pharmacotherapy in a population-based cohort of home care clients.

BACKGROUND: Little is known about the needs of older home care clients with dementia or their key quality of care issues, including their use of pharmacotherapy for Alzheimer's disease. OBJECTIVES: The objectives of this study were to (1) describe the sociodemographic, psychosocial, and health characteristics of clients with dementia (relative to two control subgroups) from a population-based home care cohort; and, (2) determine the distribution and associated characteristics of cholinesterase inhibitor (ChEI) and/or memantine use among dementia clients overall and according to medication class, comorbid illness, and year of assessment. METHODS: This cross-sectional study included all home care clients aged 50 years or older assessed with the Resident Assessment Instrument-Home Care (RAI-HC) in Ontario, Canada from January 2003 to December 2010. Multivariable logistic regression models were used to identify factors associated with receiving a dementia medication (a ChEI and/or memantine). RESULTS: There were 104,802 (21.5 %) clients with a diagnosis of dementia, 92,529 (18.9 %) cognitively impaired clients without a dementia diagnosis, and 290,929 (59.6 %) cognitively intact clients. Relative to the comparison groups, dementia clients were more likely to have reported conflicts with others, a distressed caregiver, greater levels of cognitive and functional impairment, and to exhibit wandering, aggressive behaviors, anxiety, hallucinations or delusions, and swallowing problems. Approximately half of dementia clients were taking a dementia medication, most commonly donepezil. Characteristics most strongly associated with use of ChEI monotherapy included age greater than 64 (especially 75-84), absence of economic barriers, availability of a primary caregiver, year of assessment, moderate to severe cognitive impairment, relative independence in function, health stability, no depressive symptoms or hallucinations/delusions, no recent hospitalization, use of at least 9 medications, the absence of chronic health and neurological conditions, and the use of an antipsychotic or antidepressant. For combination therapy, strong positive associations were observed for younger age, year of assessment, increasing cognitive impairment, presence of a primary caregiver, male sex, absence of economic barriers, use of at least 9 medications, and various indicators of positive health status (e.g., stability in health, absence of chronic health and neurological conditions, and no recent hospitalization). The percentage of clients receiving ChEIs increased with cognitive impairment scores but declined slightly at the highest level of impairment, whereas the percentage receiving memantine increased with cognitive impairment level. The number and percentage of dementia clients receiving any pharmacotherapy increased during the study interval. CONCLUSIONS: We observed a relatively high prevalence of dementia-specific pharmacotherapy among Ontario long-stay home care clients as well as significant variation in utilization patterns by select sociodemographic, functional, and clinical characteristics, and over time. While physicians generally followed recommended guidelines regarding appropriate dementia pharmacotherapy, continued efforts to monitor practice patterns are required among vulnerable older adults across care settings.

Examining correlates of different cigarette access behaviours among Canadian youth: data from the Canadian Youth Smoking Survey (2006).

Understanding factors associated with youth cigarette access behaviours can provide insight into the development of more effective means of preventing youth from accessing cigarettes. This cross-sectional study used self-reported data collected from 41,886 students in grades 9 to 12 who participated in the 2006-07 Youth Smoking Survey to examine the student- and school-level characteristics that differentiate youth smokers who usually access cigarettes from a social source versus buying their own from retailers. Multi-level regression analyses revealed significant between-school variability in the odds of a smoking student reporting that they usually buy their own cigarettes. Important student-level characteristics associated with how youth usually access their cigarettes included binge drinking and being asked for age or photo identification when purchasing cigarettes from a retailer. Future studies should further explore the school- and student-level characteristics associated with youth cigarette access behaviour.

Factors associated with different cigarette access behaviours among underage smoking youth who usually smoke contraband (native) cigarettes.

OBJECTIVES: Given that little is known about how youth access contraband cigarettes, the current study seeks to examine factors associated with how underage smoking youth report usually accessing contraband cigarettes. METHODS: This study used nationally representative data collected from 41,886 students (grades 9 to 12) as part of the 2006-07 Canadian Youth Smoking Survey (YSS). Using data from current smokers who report that their usual brand of cigarettes is contraband, three logistic regression models were used to examine factors associated with buying cigarettes from a store, getting cigarettes from a family member, or getting cigarettes from friends or strangers. RESULTS: In 2006, 7.9% (n = 1 3,300) of Canadian youth who were current smokers reported that their usual brand of cigarettes was contraband. Among these youth, the majority reported that they usually get their cigarettes from a friend or stranger (54.8%), whereas 26.4% report usually getting them from a family member and 18.8% usually buying their own from a store. Boys were more likely to buy contraband cigarettes from a store, whereas youth with a parent who smokes contraband cigarettes were substantially more likely to get contraband cigarettes from a family member and youth with friends who smoke contraband cigarettes were substantially more likely to get contraband cigarettes from a friend or stranger. CONCLUSION: Ongoing surveillance of contraband cigarette use among youth and how youth access contraband cigarettes is required for guiding future tobacco control policy and programming activities.

Inscribing the perimeter of the PagP hydrocarbon ruler by site-specific chemical alkylation.

The Escherichia coli outer membrane phospholipid:lipid A palmitoyltransferase PagP selects palmitate chains using its ß-barrel-interior hydrocarbon ruler and interrogates phospholipid donors by gating them laterally through an aperture known as the crenel. Lipid A palmitoylation provides antimicrobial peptide resistance and modulates inflammation signaled through the host TLR4/MD2 pathway. Gly88 substitutions can raise the PagP hydrocarbon ruler floor to correspondingly shorten the selected acyl chain. To explore the limits of hydrocarbon ruler acyl chain selectivity, we have modified the single Gly88Cys sulfhydryl group with linear alkyl units and identified C10 as the shortest acyl chain to be efficiently utilized. Gly88Cys-S-ethyl, S-n-propyl, and S-n-butyl PagP were all highly specific for C12, C11, and C10 acyl chains, respectively, and longer aliphatic or aminoalkyl substitutions could not extend acyl chain selectivity any further. The donor chain length limit of C10 coincides with the phosphatidylcholine transition from displaying bilayer to micellar properties in water, but the detergent inhibitor lauryldimethylamine N-oxide also gradually became ineffective in a micellar assay as the selected acyl chains were shortened to C10. The Gly88Cys-S-ethyl and norleucine substitutions exhibited superior C12 acyl chain specificity compared to that of Gly88Met PagP, thus revealing detection by the hydrocarbon ruler of the Met side chain tolerance for terminal methyl group gauche conformers. Although norleucine substitution was benign, selenomethionine substitution at Met72 was highly destabilizing to PagP. Within the hydrophobic and van der Waals-contacted environment of the PagP hydrocarbon ruler, side chain flexibility, combined with localized thioether-aromatic dispersion attraction, likely influences the specificity of acyl chain selection.

Transforming growth factor-beta can suppress tumorigenesis through effects on the putative cancer stem or early progenitor cell and committed progeny in a breast cancer xenograft model.

The transforming growth factor-beta (TGF-beta) pathway has tumor-suppressor activity in many epithelial tissues. Because TGF-beta is a potent inhibitor of epithelial cell proliferation, it has been widely assumed that this property underlies the tumor-suppressor effect. Here, we have used a xenograft model of breast cancer to show that endogenous TGF-beta has the potential to suppress tumorigenesis through a novel mechanism, involving effects at two distinct levels in the hierarchy of cellular progeny that make up the epithelial component of the tumor. First, TGF-beta reduces the size of the putative cancer stem or early progenitor cell population, and second it promotes differentiation of a more committed, but highly proliferative, progenitor cell population to an intrinsically less proliferative state. We further show that reduced expression of the type II TGF-beta receptor correlates with loss of luminal differentiation in a clinical breast cancer cohort, suggesting that this mechanism may be clinically relevant. At a molecular level, the induction of differentiation by TGF-beta involves down-regulation of Id1, and forced overexpression of Id1 can promote tumorigenesis despite persistence of the antiproliferative effect of TGF-beta. These data suggest new roles for the TGF-beta pathway in regulating tumor cell dynamics that are independent of direct effects on proliferation.

TGF-beta switches from tumor suppressor to prometastatic factor in a model of breast cancer progression.

The TGF-beta signaling network plays a complex role in carcinogenesis because it has the potential to act as either a tumor suppressor or a pro-oncogenic pathway. Currently, it is not known whether TGF-beta can switch from tumor suppressor to pro-oncogenic factor during the course of carcinogenic progression in a single cell lineage with a defined initiating oncogenic event or whether the specific nature of the response is determined by cell type and molecular etiology. To address this question, we have introduced a dominant negative type II TGF-beta receptor into a series of genetically related human breast-derived cell lines representing different stages in the progression process. We show that decreased TGF-beta responsiveness alone cannot initiate tumorigenesis but that it can cooperate with an initiating oncogenic lesion to make a premalignant breast cell tumorigenic and a low-grade tumorigenic cell line histologically and proliferatively more aggressive. In a high-grade tumorigenic cell line, however, reduced TGF-beta responsiveness has no effect on primary tumorigenesis but significantly decreases metastasis. Our results demonstrate a causal role for loss of TGF-beta responsiveness in promoting breast cancer progression up to the stage of advanced, histologically aggressive, but nonmetastatic disease and suggest that at that point TGF-beta switches from tumor suppressor to prometastatic factor.

Genomic characterization and regulation of CYP3a13: role of xenobiotics and nuclear receptors.

We report that CYP3a13 gene, located on mouse chromosome 5, spans 27.5 Kb and contains 13 exons. The transcription start site is 35 bp upstream of the coding region and results in a 109 bp 5' untranslated region. CYP3a13 promoter shows putative binding sites for retinoid X receptor, pregnane X receptor, and estrogen receptor. CYP3a13 shows a broad tissue distribution with predominant expression in liver. Although CYP3a13 shares 92% nucleotide identity with the female-specific rat CYP3A9, its expression does not exhibit sexual dimorphism. Ligand activation of peroxisomal proliferator-activated receptor-gamma and retinoid X receptor inhibit expression of CYP3a13 at the transcription level in a tissue-specific manner. Another novel finding is hepatic induction of CYP3a13 by dexamethasone occurring only in pregnane X receptor null mice. We also report that pregnane X receptor is essential to maintain robust in vivo basal levels of CYP3a13 in contrast to CYP3a11. CYP3a13 protein expressed in vitro can metabolize clinically active drugs ethylmorphine and erythromycin, as well as benzphetamine. We conclude that CYP3a13 is regulated differentially by various nuclear receptors. In humans this may lead to altered drug metabolism, as many of the newly synthesized ligands/drugs targeted toward these nuclear receptors could influence CYP3A gene expression.