Limited Genomics Training Among Physicians Remains a Barrier to Genomics-Based Implementation of Precision Medicine.

The field of precision medicine has undergone significant growth over the past 10 years. Despite increasing applications of clinical genetic and genomic testing, studies consistently report limited knowledge of genetics and genomics among healthcare providers. This study explored barriers to the implementation of precision medicine by surveying physicians working in a large academic medical center. We assessed prior training in genetics, use of genetic testing in the clinic, desire for additional resources in genetics and genomic medicine and perceived barriers to successful integration of precision medicine. Only 20% of respondents reported moderate or extensive training in genetics. Physicians with limited or no training in genetics were less likely to have ordered a genetic test for any purpose. Furthermore, 41% of physicians responded that their lack of training identifying appropriate genetic tests and how to interpret genetic testing results was the most significant barrier to ordering genetic testing for their patients. These findings suggest that future efforts to realize the promise of precision medicine should focus on the integration of training programs for non-genetics trained healthcare providers.

Argentina's National Program for Control of Breast Cancer: Time 1, Patient Navigation, and Patient Cancer Education Experience.

Argentina has the second highest mortality rate for breast cancer (BC) in South America. The age-standardized incidence of BC in Argentina is 73 per 100,000. Despite the availability of early detection services, 30% of BCs are diagnosed at advanced disease stages. The National Cancer Institute (NCI) of Argentina and the National Program for Control of Breast Cancer (NPCBC) focus on two main objectives: guaranteeing adequate and timely BC treatment and reducing BC mortality in Argentina. These objectives are addressed by maintaining three core concepts: quality control, disease monitoring, and wide coverage of available early detection and treatment services. The NPCBC is currently implementing the "Time 1 Survey Study." Time 1 is defined as the time from the first appearance of BC signs or symptoms to the first consult within the public healthcare system. This timeframe is important in Argentina because it is outside of the health timeframes and data parameters monitored by the national cancer data registry system. The Time 1 Survey study has the potential to serve as an informational tool for BC patient navigation efforts in Argentina because it can be used to identify and characterize the barriers and delays that women face during Time 1. Lessons and experiences included in this study could be translated to other Latin American and middle-income countries for developing cancer control programs that can lead to improving treatment and reducing mortality through patient navigation and cancer education efforts for the public, health professionals, and patients.

The Development of a Novel, Standards-Based Core Curriculum for Community Facing, Clinic-Based Community Health Workers.

Introduction: Historically, CHW trainings have been developed to support community-based CHWs. When CHWs have been trained to engage with patients, typically such trainings have been for short term grant funded projects, focusing on a specific health intervention and not for long term, ongoing engagement of CHWs employed in clinical settings. To the best of our knowledge, this is the first such effort to describe the development of a standards-based training curriculum for clinic-based CHWs using a novel conceptual framework. Methods: Our conceptual approach for curricular development has several innovative features including: (1) a foundational consultation process with CHW national experts to inform curricular development approach, process and content; (2) utilization of the CHW Consensus Project (C3 Project) to provide curricular standards and guide learning objectives; (3) integration of three key stakeholder group perspectives (patients, healthcare teams, and healthcare systems); (4) use of popular education principles, aiming to foster a collaborative learning process; (5) integration of adult learning principles which build on learners' experiences, culminating in a modified apprenticeship model and (6) collaboration with clinical partners throughout planning and development of the curriculum. Results: The resulting standards-based curriculum is comprised of 10 modules, which span three areas of focus: (1) Establishing a professional CHW identity and competencies; (2) Outlining the context, processes and key actors in health care settings with whom CHWs will engage; and (3) Identifying the main forces that shape health and health care outcomes of patients/families and communities. Discussion: We highlight four lessons from our curriculum development process that may help other such efforts. First, curricular development should utilize CHW standards, existing training materials, and community-focused principles to inform curricular content and learning outcomes. Second, curricula should support training delivery using experience-based, participatory approaches, consistent with adult education and popular education principles. Third, training development for clinical settings should also draw from clinical CHW experiences and input. Fourth, curricula should support training for key stakeholders and champions in clinical organizations to improve organizational readiness for integrating CHWs into healthcare teams and health systems. Our results contribute to growing research on effective CHW training methods for clinical settings.

Serum levels of L1-ORF1p and airflow limitation.

In a population-based study, higher circulating levels of L1-ORF1p were associated with lower lung function levels and increased risk for airflow limitation among former smokers http://bit.ly/2ZEIjNv.

Precision prevention: A focused response to shifting paradigms in healthcare.

IMPACT STATEMENT: The study of LINE-1 retroelements and their role in the pathogenesis of diseases of the lung such as COPD and lung cancer may provide valuable diagnostic and therapeutic tools to identify pre-emptively individuals at risk of pulmonary disease progression. Limited information is presently available on the role of LINE-1 in the regulation of disease phenotypes and the development of novel therapeutics designed to curtail LINE-1-mediated pathogenesis. Successful implementation of precision prevention strategies may help to spare those impacted by obstructive pulmonary disease from continued deterioration, while realizing significant cost savings and improved quality of healthcare.

Driving the precision medicine highway: community health workers and patient navigators.

The general public is currently bombarded with direct-to-consumer advertising, real time "medical" guidance through the internet, access to digital devices that capture health information, and science-based adds that promote foods, cosmetics, and dietary supplements. Unfortunately, much of this information relies on terminology and concepts not well-understood by consumers, particularly those with lower levels of health and genomic literacy. Such constraints align with the limitations of the American public to obtain and process the basic medical information needed to make appropriate healthcare decisions. Low levels of health and genomic literacy render the American public ill-equipped to make informed decisions, use and interpret genomic information, or appreciate the benefits afforded by genomics-based technologies. We propose that coordinated expansion of the roles of community health workers and patient navigators within the precision medicine space can be effectively used to disseminate the knowledge required for the public to benefit from precision medicine advances in healthcare. A well-organized and trained community health worker and patient navigator workforce will provide a voice for the disadvantaged, especially among recent immigrants likely to be experiencing social isolation, language barriers, and economic deprivation. Armed with this knowledge, community health workers and patient navigators can advance the precision medicine agenda and empower disadvantaged communities to take advantage of major advances in the precision medicine era.

Genetics and epigenetics of pediatric leukemia in the era of precision medicine.

Pediatric leukemia represents a heterogeneous group of diseases characterized by germline and somatic mutations that manifest within the context of disturbances in the epigenetic machinery and genetic regulation. Advances in genomic medicine have allowed finer resolution of genetic and epigenetic strategies that can be effectively used to risk-stratify patients and identify novel targets for therapy. This review discusses the genetic and epigenetic mechanisms of leukemogenesis, particularly as it relates to acute lymphocytic leukemias, the mechanisms of epigenetic control of leukemogenesis, namely DNA methylation, histone modifications, microRNAs, and LINE-1 retroelements, and highlights opportunities for precision medicine therapeutics in further guiding disease management. Future efforts to broaden the integration of advances in genomic and epigenomic science into the practice of pediatric oncology will not only identify novel therapeutic strategies to improve clinical outcomes but also improve the quality of life for this unique patient population. Recent findings in precision therapeutics of acute lymphocytic leukemias over the past three years, along with some provocative areas of epigenetics research, are reviewed here.

LINE-1 couples EMT programming with acquisition of oncogenic phenotypes in human bronchial epithelial cells.

Although several lines of evidence have established the central role of epithelial-to-mesenchymal-transition (EMT) in malignant progression of non-small cell lung cancers (NSCLCs), the molecular events connecting EMT to malignancy remain poorly understood. This study presents evidence that Long Interspersed Nuclear Element-1 (LINE-1) retrotransposon couples EMT programming with malignancy in human bronchial epithelial cells (BEAS-2B). This conclusion is supported by studies showing that: 1) activation of EMT programming by TGF-ß1 increases LINE-1 mRNAs and protein; 2) the lung carcinogen benzo(a)pyrene coregulates TGF-ß1 and LINE-1 mRNAs, with LINE-1 positioned downstream of TGF-ß1 signaling; and, 3) forced expression of LINE-1 in BEAS-2B cells recapitulates EMT programming and induces malignant phenotypes and tumorigenesis in vivo. These findings identify a TGFß1-LINE-1 axis as a critical effector pathway that can be targeted for the development of precision therapies during malignant progression of intractable NSCLCs.

Aedes aegypti breeding ecology in Guerrero: cross-sectional study of mosquito breeding sites from the baseline for the Camino Verde trial in Mexico.

BACKGROUND: Understanding the breeding patterns of Aedes aegypti in households and the factors associated with infestation are important for implementing vector control. The baseline survey of a cluster randomised controlled trial of community mobilisation for dengue prevention in Mexico and Nicaragua collected information about the containers that are the main breeding sites, identified possible actions to reduce breeding, and examined factors associated with household infestation. This paper describes findings from the Mexican arm of the baseline survey. METHODS: In 2010 field teams conducted household surveys and entomological inspections in 11,995 households from 90 representative communities in the three coastal regions of Guerrero State, Mexico. We characterized Ae. aegypti breeding sites and examined the effect of two preventive measures: temephos application in water containers, and keeping the containers covered. We examined associations with household infestation, using bivariate and multivariate analysis adjusted for clustering effects. RESULTS: We conducted entomological inspections in 11,995 households. Among 45,353 water containers examined, 6.5% (2958/45,353) were positive for larvae and/or pupae. Concrete tanks (pilas) and barrels (tambos) together accounted for 74% of pupal productivity. Both covering water containers and inserting temephos were independently associated with a lower risk of presence of larvae or pupae, with the effect of covering (OR 0.22; 95% CIca 0.15-0.27) stronger than that of temephos (OR 0.66; 95% CIca 0.53-0.84). Having more than four water containers was associated with household infestation in both rural areas (OR 1.42; 95% CIca 1.17-1.72) and urban areas (1.81; 1.47-2.25), as was low education of the household head (rural: 1.27; 1.11-1.46, and urban: 1.39; 1.17-1.66). Additional factors in rural areas were: household head without paid work (1.31; 1.08-1.59); being in the Acapulco region (1.91; 1.06-3.44); and using anti-mosquito products (1.27; 1.09-1.47). In urban areas only, presence of temephos was associated with a lower risk of household infestation (0.44; 0.32-0.60). CONCLUSION: Concrete tanks and barrels accounted for the majority of pupal productivity. Covering water containers could be an effective means of Ae. aegypti vector control, with a bigger effect than using temephos. These findings were useful in planning and implementing the Camino Verde trial intervention in Mexico.

Germline Mutations in PALB2, BRCA1, and RAD51C, Which Regulate DNA Recombination Repair, in Patients With Gastric Cancer.

Up to 10% of cases of gastric cancer are familial, but so far, only mutations in CDH1 have been associated with gastric cancer risk. To identify genetic variants that affect risk for gastric cancer, we collected blood samples from 28 patients with hereditary diffuse gastric cancer (HDGC) not associated with mutations in CDH1 and performed whole-exome sequence analysis. We then analyzed sequences of candidate genes in 333 independent HDGC and non-HDGC cases. We identified 11 cases with mutations in PALB2, BRCA1, or RAD51C genes, which regulate homologous DNA recombination. We found these mutations in 2 of 31 patients with HDGC (6.5%) and 9 of 331 patients with sporadic gastric cancer (2.8%). Most of these mutations had been previously associated with other types of tumors and partially co-segregated with gastric cancer in our study. Tumors that developed in patients with these mutations had a mutation signature associated with somatic homologous recombination deficiency. Our findings indicate that defects in homologous recombination increase risk for gastric cancer.

The aryl hydrocarbon receptor agonist benzo(a)pyrene reactivates LINE-1 in HepG2 cells through canonical TGF-ß1 signaling: implications in hepatocellular carcinogenesis.

Long interspersed nuclear element-1 (L1) is a genetic element that mobilizes throughout the mammalian genome via retrotransposition and damages host DNA via mutational insertions, chromosomal rearrangements, and reprogramming of gene expression. The cellular mechanisms responsible for aberrant L1 expression during cancer pathogenesis are unclear. Previously, we have shown that L1 reactivation in several human cell lines is dependent upon the activation of aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor member of the PAS superfamily of proteins. We also showed that ectopic expression of L1 reprograms the HepG2 genome leading to epithelial-to-mesenchymal transition (EMT). Here we present evidence that reactivation of L1 and modulation of EMT in HepG2 cells by the AhR ligand benzo(a)pyrene (BaP) is effected through the canonical TGF-ß1 signaling pathway. BaP increased TGF-ß1 mRNA, SMAD2 phosphorylation and decreased expression of E-Cadherin. The functional relevance of these interactions and the involvement of TGFBR1/ALK5 and SMAD2/3 were confirmed by siRNA interference. Furthermore, expression of L1-encoded ORF1p was positively correlated with the activation of TGF-ß1 signaling in human hepatocarcinoma samples at various stages of malignant progression. These results indicate that ligand-mediated AhR activation regulates L1 via canonical TGF-ß1 signaling and raise important questions about the molecular etiology of human hepatocarcinomas.

LINE-1 silencing by retinoblastoma proteins is effected through the nucleosomal and remodeling deacetylase multiprotein complex.

BACKGROUND: Long Interspersed Nuclear Element-1 (L1) is an oncogenic mammalian retroelement silenced early in development via tightly controlled epigenetic mechanisms. We have previously shown that the regulatory region of human and murine L1s interact with retinoblastoma (RB) proteins to effect retroelement silencing. The present studies were conducted to identify the corepressor complex responsible for RB-mediated silencing of L1. METHODS: Chromatin immunoprecipitation and silencing RNA technology were used to identify the repressor complex that silences L1 in human and murine cells. RESULTS: Components of the Nucleosomal and Remodeling Deacetylase (NuRD) multiprotein complex specifically enriched the L1 5'-untranslated DNA sequence in human and murine cells. Genetic ablation of RB proteins in murine cells destabilized interactions within the NuRD macromolecular complex and mediated nuclear rearrangement of Mi2-ß, an ATP-dependent helicase subunit with nucleosome remodeling activity. Depletion of Mi2-ß, RbAP46 and HDAC2 reduced the repressor activity of the NuRD complex and reactivated a synthetic L1 reporter in human cells. Epigenetic reactivation of L1 in RB-null cells by DNA damage was markedly enhanced compared to wild type cells. CONCLUSIONS: RB proteins stabilize interactions of the NuRD corepressor complex within the L1 promoter to effect L1 silencing. L1 retroelements may serve as a scaffold on which RB builds heterochromatic regions that regulate chromatin function.

Health status, perceptions and needs of Hispanics in rural Shelbyville, Kentucky.

This cross-sectional study was completed to characterize the health status, perceptions and needs of Hispanics in Shelbyville, KY, USA. Community Health Workers interviewed 668 Hispanic residents in Shelbyville, KY, USA. Data were collected from 2009 to 2010 and analyzed from 2011 until present. Hispanic immigrants from Mexico and other Central American countries completed the survey. The most common self-reported diseases were allergies, asthma, diabetes, lung disease and cardiovascular disease. High blood pressure and diabetes were the two most common diagnoses among insured, older females. Health education, disease prevention and nutrition were the top health concerns among participants. Deficits in health care infrastructure for this largely transient community may compromise their ability to meet health care needs and concerns. Similar issues may be faced by other disadvantaged Hispanic communities in the continental US and likely to be influenced by anticipated provisions of the Patient Protection and Affordable Care Act.

Culturally-Tailored Education Programs to Address Health Literacy Deficits and Pervasive Health Disparities among Hispanics in Rural Shelbyville, Kentucky.

OBJECTIVES: This investigation was conducted to evaluate the impact of culturally-tailored education on health knowledge among Hispanic residents of rural, Shelbyville, KY. DESIGN: The program identified specific pathways to address health literacy deficits and disparities identified through a community-wide health assessment completed in 2010. RESULTS: A total of 43 Hispanic males who shared deficiencies in community-wide health infrastructure were enrolled in the program. The curriculum included an introductory session followed by five, subject-specific, sessions offered on a weekly basis from February to April 2011. Pre/post-test assessments showed marked improvement in knowledge base for all participants after each session, most notably related to cardiovascular disease, diabetes and metabolic syndrome. The group reconvened in January 2012 for follow-up instruction on cardiovascular disease and diabetes, as well as global assessment of knowledge retention over a nine-month period. Comparisons of pre/post testing in cardiovascular disease and diabetes, as well as global health-related knowledge showed significant gains for all parameters. CONCLUSIONS: Health education programs that embrace perceptions of the community of their own health, and that integrate knowledge into culturally-sensitive education, significantly improved health knowledge among Hispanic residents in rural Kentucky. Such gains may translate into sustainable improvements in health literacy and help reduce health disparities.

Assessment of tools for marker-assisted selection in a marine commercial species: significant association between MSTN-1 gene polymorphism and growth traits.

Growth is a priority trait from the point of view of genetic improvement. Molecular markers linked to quantitative trait loci (QTL) have been regarded as useful for marker-assisted selection in complex traits as growth. Polymorphisms have been studied in five candidate genes influencing growth in gilthead seabream (Sparus aurata): the growth hormone (GH), insulin-like growth factor-1 (IGF-1), myostatin (MSTN-1), prolactin (PRL), and somatolactin (SL) genes. Specimens evaluated were from a commercial broodstock comprising 131 breeders (from which 36 males and 44 females contributed to the progeny). In all samples eleven gene fragments, covering more than 13,000 bp, generated by PCR-RFLP, were analyzed; tests were made for significant associations between these markers and growth traits. ANOVA results showed a significant association between MSTN-1 gene polymorphism and growth traits. Pairwise tests revealed several RFLPs in the MSTN-1 gene with significant heterogeneity of genotypes among size groups. PRL and MSTN-1 genes presented linkage disequilibrium. The MSTN-1 gene was mapped in the centromeric region of a medium-size acrocentric chromosome pair.

In vivo expression of Helicobacter pylori virulence genes in patients with gastritis, ulcer, and gastric cancer.

The best-studied Helicobacter pylori virulence factor associated with development of peptic ulcer disease or gastric cancer (GC) rather than asymptomatic nonatrophic gastritis (NAG) is the cag pathogenicity island (cagPAI), which encodes a type IV secretion system (T4SS) that injects the CagA oncoprotein into host epithelial cells. Here we used real-time reverse transcription-PCR (RT-PCR) to measure the in vivo expression of genes on the cagPAI and of other virulence genes in patients with NAG, duodenal ulcer (DU), or GC. In vivo expression of H. pylori virulence genes was greater overall in gastric biopsy specimens of patients with GC than in those of patients with NAG or DU. However, since in vitro expression of cagA was not greater in H. pylori strains from patients with GC than in those from patients with NAG or DU, increased expression in GC in vivo is likely a result of environmental conditions in the gastric mucosa, though it may in turn cause more severe pathology. Increased expression of virulence genes in GC may represent a stress response to elevated pH or other environmental conditions in the stomach of patients with GC, which may be less hospitable to H. pylori colonization than the acidic environment in patients with NAG or DU.

Helicobacter pylori genotyping from American indigenous groups shows novel Amerindian vacA and cagA alleles and Asian, African and European admixture.

It is valuable to extend genotyping studies of Helicobacter pylori to strains from indigenous communities across the world to better define adaption, evolution, and associated diseases. We aimed to genetically characterize both human individuals and their infecting H. pylori from indigenous communities of Mexico, and to compare them with those from other human groups. We studied individuals from three indigenous groups, Tarahumaras from the North, Huichols from the West and Nahuas from the center of Mexico. Volunteers were sampled at their community site, DNA was isolated from white blood cells and mtDNA, Y-chromosome, and STR alleles were studied. H. pylori was cultured from gastric juice, and DNA extracted for genotyping of virulence and housekeeping genes. We found Amerindian mtDNA haplogroups (A, B, C, and D), Y-chromosome DYS19T, and Amerindian STRs alleles frequent in the three groups, confirming Amerindian ancestry in these Mexican groups. Concerning H.pylori cagA phylogenetic analyses, although most isolates were of the Western type, a new Amerindian cluster neither Western nor Asian, was formed by some indigenous Mexican, Colombian, Peruvian and Venezuelan isolates. Similarly, vacA phylogenetic analyses showed the existence of a novel Amerindian type in isolates from Alaska, Mexico and Colombia. With hspA strains from Mexico and other American groups clustered within the three major groups, Asian, African or European. Genotyping of housekeeping genes confirmed that Mexican strains formed a novel Asian-related Amerindian group together with strains from remote Amazon Aborigines. This study shows that Mexican indigenous people with Amerindian markers are colonized with H. pylori showing admixture of Asian, European and African strains in genes known to interact with the gastric mucosa. We present evidence of novel Amerindian cagA and vacA alleles in indigenous groups of North and South America.

A mutant Ahr allele protects the embryonic kidney from hydrocarbon-induced deficits in fetal programming.

BACKGROUND: The use of experimental model systems has expedited the elucidation of pathogenetic mechanisms of renal developmental disease in humans and the identification of genes that orchestrate developmental programming during nephrogenesis. OBJECTIVES: We conducted studies to evaluate the role of AHR polymorphisms in the disruption of renal developmental programming by benzo(a)pyrene (BaP). METHODS: We used metanephric cultures of C57BL/6J (C57) mice expressing the Ahr(b-1) allele and B6.D2N-Ahr(d)/J (D2N) mice expressing a mutant allele deficient in ligand binding (Ahr(d)) to investigate molecular mechanisms of renal development. Deficits in fetal programming were evaluated in the offspring of pregnant mice treated with BaP during nephrogenesis. RESULTS: Hydrocarbon challenge of metanephri from C57 mice altered Wilms' tumor suppressor gene (Wt1) mRNA splice variant ratios and reduced mRNAs of the Wt1 transcriptional targets syndecan-1 (Sdc1) paired box gene 2 (Pax2), epidermal growth factor receptor (Egfr), and retinoic acid receptor, alpha (Rarα). These changes correlated with down-regulation of effectors of differentiation [secreted frizzled-related sequence protein 1 (Sfrp1), insulin-like growth factor 1 receptor (Igf1r), wingless-related MMTV-integration site 4 (Wnt4), Lim homeobox protein 1 (Lhx1), E-cadherin]. In contrast, metanephri from D2N mice were spared hydrocarbon-induced changes in Wt1 splice variant ratios and deficits of differentiation. We observed similar patterns of dysmorphogenesis and progressive loss of renal function at postnatal weeks 7 and 52 in the offspring of pregnant C57 but not D2N mice gavaged with 0.1 or 0.5 mg/kg BaP on gestation days 10-13. CONCLUSIONS: These findings support a functional link between AHR and WT1 in the regulation of renal morphogenesis and raise important questions about the contribution of human AHR polymorphisms to the fetal origins of adult-onset kidney disease.

Strategies to vaccinate against cancer of the cervix: feasibility of a school-based HPV vaccination program in Peru.

Operational research using a mixed method, cross-sectional, case-study approach assessed the feasibility and health system impact of large-scale implementation of human papillomavirus (HPV) vaccination into routine vaccine delivery by the Ministry of Health in Peru. The strategy was school-based vaccination of fifth grade girls in 527 primary schools in Piura region. Our evaluation showed that school-based HPV vaccination is feasible without major changes in existing health systems. This was reflected in the opinions of health personnel, the lack of impact on other vaccine coverage, and the high HPV vaccine coverage documented in routine records and by an independent community-based survey.

Vacuna contra el VPH en el Perú: Resúmen de la experiencia y evaluación del proyecto piloto de la vacuna contra el VPH en el Perú / HPV vaccine in Peru: Summary of experience and evaluation of the pilot of the HPV vaccine in Peru

La presente publicación describe la evaluación de los principales efectos y resultados del Proyecto Piloto de la vacuna contra el Virus de Papiloma Humano (VPH) en dos de sus tipos: Tipo 16 y tipo 18, que son responsables de casi el 70% de los casos de cáncer uterino