Tissue- and ethnicity-independent hypervariable DNA methylation states show evidence of establishment in the early human embryo

We analysed DNA methylation data from 30 datasets comprising 3474 individuals, 19 tissues and 8 ethnicities at CpGs covered by the Illumina450K array. We identified 4143 hypervariable CpGs ('hvCpGs') with methylation in the top 5% most variable sites across multiple tissues and ethnicities. hvCpG methylation was influenced but not determined by genetic variation, and was not linked to probe reliability, epigenetic drift, age, sex or cell heterogeneity effects. hvCpG methylation tended to covary across tissues derived from different germ-layers and hvCpGs were enriched for proximity to ERV1 and ERVK retrovirus elements. hvCpGs were also enriched for loci previously associated with periconceptional environment, parent-of-origin-specific methylation, and distinctive methylation signatures in monozygotic twins. Together, these properties position hvCpGs as strong candidates for studying how stochastic and/or environmentally influenced DNA methylation states which are established in the early embryo and maintained stably thereafter can influence life-long health and disease.

The addition of metronomic chemotherapy does not improve outcome for canine splenic haemangiosarcoma

OBJECTIVES

To determine whether the addition of metronomic chemotherapy improved outcome for dogs with splenic haemangiosarcoma treated with splenectomy and adjuvant maximum tolerated dose chemotherapy.

MATERIALS AND METHODS

Medical records were examined retrospectively for dogs with splenic haemangiosarcoma that had undergone splenectomy followed by anthracycline-based chemotherapy. Thirty-nine dogs underwent splenectomy followed by maximum tolerated dose chemotherapy with an anthracycline, cyclophosphamide, or both (Group 1). Twenty-two dogs underwent splenectomy followed by adjuvant maximum tolerated dose chemotherapy with an anthracycline, cyclophosphamide, or both, plus metronomic chemotherapy (Group 2). Dogs in both groups were further separated into those treated with either maximum tolerated dose anthracycline or maximum tolerated dose anthracycline and cyclophosphamide.

RESULTS

Median progression-free survival was 165 days and median overall survival time was 180 days in Group 1. Median progression-free survival was 185 days and median overall survival time was 212 days in Group 2. In both groups, the overall survival was shorter in dogs that had received maximum tolerated dose cyclophosphamide.

CLINICAL SIGNIFICANCE

The addition of metronomic to maximum tolerated dose chemotherapy protocols does not appear to improve outcome in dogs with splenic haemangiosarcoma treated with splenectomy and maximum tolerated dose chemotherapy.

Abstract P6-03-03: Not presented

This abstract was not presented at the symposium.

Geographical differences in survival of dogs with non-Hodgkin lymphoma treated with a CHOP based chemotherapy protocol

BACKGROUND

In humans geographical differences in the incidence and presentation of various cancers have been reported. However, much of this information has not been collected in veterinary oncology.

AIM

The purpose of this study was to determine if a geographic difference in progression free survival exists for dogs with lymphoma treated within the US.

MATERIALS AND METHODS

Medical records of 775 cases of canine lymphoma from 3 US regions (west, south and north), treated with CHOP chemotherapy, were retrospectively evaluated. Cases were collected from referral institutions and were required to have received at least one doxorubicin treatment and have follow up information regarding time to progression.

RESULTS

Significant differences in sex (p = 0.05), weight (p = 0.049), stage (p < 0.001), immunophenotype (p = <0.001), and number of doxorubicin doses (p = 0.001) were seen between regions. Upon univariate analysis, progression free survival (PFS) differed by region (p = 0.006), stage (p = 0.009), sub-stage (p = 0.0005), and immunophenotype (p = 0.001). A multivariable Cox regression model showed that dogs in the western region had a significantly shorter PFS when compared to the south and east.

CONCLUSION

PFS was significantly affected by stage, sub-stage and phenotype.

Abstract P5-03-03: A blood-based proteomic Videssa® breast assay performs comparably in women with dense and non-dense breasts

Breast density is associated with reduced imaging sensitivity and specificity for breast cancer (BC). Women with dense breasts are at a four- to six-fold increased risk of developing BC. A biochemical approach that is not affected by density would provide an additional tool to health-care professionals who are managing women with dense breasts and suspicious imaging findings. Videssa® Breast, a combinatorial proteomic biomarker assay, comprised of Serum Protein Biomarkers (SPBs) and Tumor –Associated Autoantibodies (TAAbs) integrated with clinical characteristic data to produce one diagnostic score that reliably detects BC was recently developed as an adjunctive tool to imaging. The goal of this study was to determine whether the diagnostic performance of Videssa® Breast was impacted by breast density.

Provista-001 enrolled 351 participants under the age of 50 years with no prior history of breast biopsy, and Provista-002 cohort one enrolled 210 participants under the age of 50 years with no history of breast biopsy within six months; all participants were assessed as BI-RADS 3 or 4. Breast density status was retrospectively obtained for participants; the four American College of Radiology breast density categories (a, b, c, and d) used for clinical reporting were applied. Serum was collected and tested with Videssa® Breast. Women were categorized into Dense, which included categories c and d, and Non-dense, which included categories a and b, groups.

To understand the performance of Videssa® Breast in women with dense breasts, the clinical sensitivity, specificity, NPV and PPV were evaluated in the dense and non-dense groups from the comprehensive Provista-001 and Provista-002 set (n=545). Of these 545, breast density information was available for 454; 62.6% (n=284) were categorized as having dense breasts and 37.4% (n=170) were categorized as having non-dense breasts. The sensitivity of Videssa® Breast in the non-dense and dense groups was 92.3% and 88.9%, respectively, and the specificity in the non-dense and dense groups was 86.6% and 81.2%, respectively. No significant differences were observed in the sensitivity (p=1.0) or specificity (p=0.1783) of Videssa® Breast in detecting BC in participants with non-dense breasts compared to those with dense breasts. The NPV in both groups exceeded 99%; the PPV was similar across groups.

In summary, this study demonstrates that Videssa® Breast has comparable performance in women with dense and non-dense breasts. Videssa® Breast demonstrates high sensitivity and specificity for detecting BC (Grades I through III), irrespective of density status. Videssa® breast provides an additional tool for health-care providers when women with dense breasts present with challenging imaging findings. In addition, Videssa® breast provides assurance to a woman with dense breasts that she does not have BC, potentially reducing further anxiety in this higher risk patient population.

Citation Format: Silver M, Tran Q, Gordon K, Benson KL, Henderson MC, Letsios E, Mulpuri R, Reese DE. A blood-based proteomic Videssa® breast assay performs comparably in women with dense and non-dense breasts [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P5-03-03.

Abstract P5-02-02: The final study report on the performance of Klarify™. Assessment of full data set from NCT01839045 a 6-month liquid biopsy panel run in women under the age of 50 that were initially assessed as a high risk population

The precise diagnosis of breast lesions represents a significant problem in women under the age of 50, especially given the high prevalence of confounding factors such as dense breast. No new approaches have been developed to augment standard of care in the more precise detection of breast cancer. The combination of breast imaging with a robust protein signature that would detect biochemical cues of breast cancer offers a potentially attractive approach to detection regardless of the quality of the radiographic evidence. We have recently tested a protein signature (KARIFY BREAST™) composed of immune-regulatory cytokines, growth factors and tumor-associated autoantibodies (TAAbs). Here, we confirm the hypothesis that this protein signature, combined with standard of care can increase the precision of the diagnosis of breast cancer in women under the age of 50. We have tested this method in a prospective study of 351 women at 8 centers across the US in a randomized and blinded manner. Presented is both data from the initial blood draw and results of the six-month follow up blood draw. The achievement of 93% sensitivity and greater than a 80 percent specificity was demonstrated.

Methods: Provista-001 enrolled 351 patients from 9 sites across the US and will follow patients for 6 months prior to first blood draw under IRB approval. Upon enrollment, patients were randomized to either training or validation groups. Clinical truth was set at equal to or greater than 80% sensitivity/specificity. Serum protein biomarkers and autoantibodies identified in prior proteomic screens were measured prior to biopsy. Individual biomarker (25 serum protein biomarkers (SPB) and TAAbs) concentrations were measured , together with specific patient data were evaluated using various logistic regression models. Additionally, 200 patients were used as a training set to develop and refine new models, which were then validated in the remaining 151 subjects. Clinical findings were compared to biopsy (largely BIRADS 4) or were followed for 6 months and re-assessed (BIRADS 3).

The novel algorithm utilizing patient data, SPBs and TAAb concentrations and regression models were able to distinguish benign from breast cancer lesions in a statistically significant manner. Importantly, the SPBs alone were unable to adequately distinguish benign lesions, consistent with prior work. However, the addition of TAAbs markedly increased both the sensitivity (93%) and specificity (80.3%) of the assay in this group of women. The use of the algorithm in conjunction with imaging detected more lesions than imaging alone.

Our findings suggest that when used in combination, the protein signature developed here and breast imaging provides a more precise detection methodology than either alone. This is particularly important in women under the age of 50 where detection is difficult. The follow-up data at six months (BIRADS 3) have yielded additional data in this understudied group of women. Such as the apparent lack of effect of breast density on early detection when using the algorithm.

Citation Format: Reese DE, Lourenco A, Mulpuri R, Borman S, Benson K, Alpers J, Silver M. The final study report on the performance of Klarify™. Assessment of full data set from NCT01839045 a 6-month liquid biopsy panel run in women under the age of 50 that were initially assessed as a high risk population. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-02-02.

Vitamin D binding protein genotype is associated with plasma 25OHD concentration in West African children

Vitamin D is well known for its role in promoting skeletal health. Vitamin D status is determined conventionally by circulating 25-dihydroxyvitamin D (25OHD) concentration. There is evidence indicating that circulating 25OHD concentration is affected by variation in Gc, the gene encoding the vitamin D binding protein (DBP). The composite genotype of two single nucleotide polymorphisms (rs7041 and rs4588) results in different DBP isotypes (Gc1f, Gc1s and Gc2). The protein configurational differences among DBP isotypes affect DBP substrate binding affinity. The aims of this study were to determine 1) Gc variant frequencies in a population from an isolated rural region of The Gambia, West Africa (n=3129) with year-round opportunity for cutaneous vitamin D synthesis and 2) the effects of Gc variants on 25OHD concentration (n=237) in a genetically representative sub-group of children (mean (SD) age: 11.9 (4.8) years). The distribution of Gc variants was Gc1f: 0.86, Gc1s: 0.11 and Gc2: 0.03. The mean (SD) concentration of 25OHD was 59.6 (12.9) nmol/L and was significantly higher in those homozygous for Gc1f compared to other Gc variants (60.7 (13.1) vs. 56.6 (12.1) nmol/L, P=0.03). Plasma 25OHD and 1,25(OH)2D concentration was significantly associated with parathyroid hormone in Gc1f-1f but not in the other Gc variants combined. This study demonstrates that different Gc variants are associated with different 25OHD concentrations in a rural Gambian population. Gc1f-1f, thought to have the highest affinity for 25OHD, had the highest 25OHD concentration compared with lower affinity Gc variants. The considerable difference in Gc1f frequency observed in Gambians compared with other non-West African populations and associated differences in plasma 25OHD concentration, may have implications for the way in which vitamin D status should be interpreted across different ancestral groups.

Ertapenem-Resistant Enterobacteriaceae Risk Factors for Acquisition and Outcomes

Background and Objective.

Carbapenem resistance among Enterobacteriaceae is of concern because of increasing prevalence and limited therapeutic options. Limited research has been focused on understanding ertapenem resistance as a more sensitive marker for resistance to other carbapenems. We sought to determine risk factors for acquisition of ertapenem-resistant, meropenem-susceptible, or intermediate Enterobacteriaceae and to assess associated patient outcomes.

Design.

Retrospective case-control study among adult hospitalized inpatients.

Setting.

A 902-bed quaternary care urban hospital.

Results.

Sixty-two cases of ertapenem-resistant Enterobacteriaceae were identified from March 14, 2006, through October 31, 2007, and 62 unmatched control patients were randomly selected from other inpatients with cultures positive for ertapenem-susceptible Enterobacteriaceae. Thirty-seven (60%) of case patient isolates were Enterobacter cloacae, 20 (32%) were Klebsiella pneumoniae, and 5 (8%) were other species of Enterobacteriaceae. Risk factors for ertapenem-resistant Enterobacteriaceae infection included intensive care unit stay (odds ratio [OR], 4.6 [95% confidence interval {CI}, 2.0–10.3]), vancomycin-resistant Enterococcus colonization (OR, 7.1 [95% CI, 2.4–21.4]), prior central venous catheter use (OR, 10.0 [95% CI, 3.0–33.1]), prior receipt of mechanical ventilation (OR, 5.8 [95% CI, 2.1–16.2]), exposure to any antibiotic during the 30 days prior to a positive culture result (OR, 18.5 [95% CI, 4.9–69.9]), use of a β-lactam during the 30 days prior to a positive culture result (OR, 6.9 [95% CI, 3.0–16.0], and use of a carbapenem during the 30 days prior to a positive culture result (OR, 18.2 [95% CI, 2.6–130.0]). For the 62 case patients, 30-day outcomes from the time of positive culture result were 24 discharges (39%), 10 deaths (16%), and 28 continued hospitalizations (44%). The final end point of the hospitalization was discharge for 44 patients (71%) and death for 18 patients (29%).

Conclusions.

Ertapenem-resistant Enterobacteriaceae are important nosocomial pathogens. Multiple mechanisms of resistance maybe in operation. Additional study of ertapenem resistance is needed.

State funding for health information technology and selected ambulatory healthcare quality measures

BACKGROUND

Previous studies on the effects of health information technology (health IT) on ambulatory quality have had mixed results. New York State has invested heavily in health IT throughout the State, creating a unique opportunity to assess effects on health care quality across multiple communities.

OBJECTIVE

To determine any association between primary care providers' receipt of funding from New York State's Healthcare Efficiency and Affordability Law for New Yorkers Program (HEAL NY) and ambulatory quality of care.

METHODS

A statewide, longitudinal cohort study of primary care physicians in New York State was conducted. Data regarding which primary care physicians received funding through the HEAL NY program (Phase 5 or Phase 10) in 2008 or 2009 were obtained from the New York State Department of Health. Health care quality in 2010 was measured using claims data that had been aggregated across 7 commercial health plans across the state. Physicians were divided into 2 groups, based on receipt of HEAL funding (yes/no). Any association was measured between study group and each of 7 quality measures, all of which appear in the Stage 1 federal Meaningful Use program. Negative binomial regression was used, adjusting for provider gender and specialty.

RESULTS

The study included 3,988 primary care providers, of whom 863 (22%) had received HEAL NY funding. The HEAL-funded physicians provided higher quality of care on 5 of the 7 measures: breast cancer screening, eye exams in patients with diabetes, nephropathy screening in patients with diabetes, influenza vaccination and pneumococcal vaccination (p<0.0001 for all adjusted comparisons). The HEAL-funded group provided higher quality of care by an absolute 2 to 6 percentage points per measure for those 5 measures.

CONCLUSION

Primary care physicians who received state funding for health IT provided higher quality of care than those who did not receive such funding.

Sonic hedgehog gene therapy increases the ability of the dystrophic skeletal muscle to regenerate after injury

The Hedgehog (Hh) pathway is a crucial regulator of muscle development during embryogenesis. We have previously demonstrated that Sonic hedgehog (Shh) regulates postnatal myogenesis in the adult skeletal muscle both directly, by acting on muscle satellite cells, and indirectly, by promoting the production of growth factors from interstitial fibroblasts. Here, we show that in mdx mice, the murine equivalent of Duchenne muscular dystrophy in humans, progression of the dystrophic pathology corresponds to progressive inhibition of the Hh signaling pathway in the skeletal muscle. We also show that the upregulation of the Hh pathway in response to injury and during regeneration is significantly impaired in mdx muscle. Shh treatment increases the proliferative potential of satellite cells isolated from the muscles of mdx mice. This treatment also increases the production of proregenerative factors, such as insulin-like growth factor-1 and vascular endothelial growth factor, from fibroblasts isolated from the muscle of mdx mice. In vivo, overexpression of the Hh pathway using a plasmid encoding the human Shh gene promotes successful regeneration after injury in terms of increased number of proliferating myogenic cells and newly formed myofibers, as well as enhanced vascularization and decreased fibrosis.

Flagella and pili of iron-oxidizing thiobacilli isolated from a uranium mine in northern ontario, Canada

Five strains of Thiobacillus ferrooxidans, which included three recent isolates from a uranium mine, possessed flagella. Three of the strains had several pili per cell. The dimensions, fine structure, and orientation of the flagella were different. Both polar and peritrichous flagella were observed, indicating strain-dependent ultrastructural variation in acidophilic thiobacilli. Neither flagella nor pili were detected in eight other strains of T. ferrooxidans and two strains of Thiobacillus acidophilus by electron microscopy, although all of the cultures contained motile cells.