Facilitating Cancer Epidemiologic Efforts in Cleveland via Creation of Longitudinal De-Duplicated Patient Data Sets

BACKGROUND

Cleveland, Ohio, is home to three major hospital systems serving approximately 80% of the Northeast Ohio population. The Cleveland Clinic, University Hospitals Health System, and MetroHealth are direct competitors for primary and specialty care, and patient overlap between these systems is high. Fragmentation of health data that exist in silos at these health systems produces an overestimation of disease burden due to double and sometimes triple counting of patients. As a result, longitudinal population-based studies across the Cleveland patient population are impeded unless accurate and actionable clinically derived health data sets can be created.

METHODS

The Cleveland Institute for Computational Biology has developed the De-Duplicate and De-Identify Research Engine (DeDeRE) that, without any exchange of personal health identifiers (PHI) between health systems, will effectively de-duplicate the patients between one or more health entities.

RESULTS

The immediate utility of this software for cancer epidemiology is the increased accuracy in measuring cancer burden and the potential to perform longitudinal studies with de-duplicated, de-identified data sets.

CONCLUSIONS

The DeDeRE software developed and tested here accomplishes its goals without exposing PHIs using a state-of-the-art, trusted privacy preservation network enabled by a hash-based matching algorithm.

IMPACT

This paper will guide the reader through the functions currently developed in DeDeRE and how a healthcare organization (HCO) employing the release version of this technology can begin sharing data with one or more additional HCOs in a collaborative and noncompetitive manner to create a regional population health resource for cancer researchers.See all articles in this CEBP Focus section, "Modernizing Population Science."

Effects of different starch sources on glucose and fat metabolism in broiler chickens

1. The aim of the present study was to investigate the effects of different starch sources (corn, wheat, and rice) on the blood glucose level, glycogen content of liver and muscle, expression of GSK-3β and FAS mRNA, abdominal fat weight and abdominal fat deposition in broiler chickens. 2. A total of 360, one-day-old AA (Arbor Acres) broiler chickens were randomly assigned to three treatment groups, each with six replicates, consisting of 20 chickens per replicate, and fed either a corn-, wheat- or rice-based diet for 21 days. The chickens were then subdivided into groups A and B, and the chickens in these two subgroups were processed or sampled for 28 days, respectively. 3. The results indicated that post-prandial time significantly affected the glucose concentration, glycogen content in the liver and breast muscle and expression of GSK-3β and FAS mRNAs (P < 0.05). The expression of the GSK-3β gene in the chicken liver of the corn-based diet group was higher (P < 0.05) than that in the wheat-based diet group, and the expression of the FAS gene in the corn-based diet group was lower (P < 0.05) than that in the wheat-based and rice-based diet groups. Abdominal fat weight and deposition in the corn-based diet group were lower than those of the wheat-based and rice-based diet groups, but these differences were not significant (P > 0.05). 4. The results suggested that the efficiency of glucose absorption in animals might have an effect on the fat deposition efficiency in the liver and that diets with different starch sources might affect fat deposition in chickens.

Adipochemokines induced by ultraviolet irradiation contribute to impaired fat metabolism in subcutaneous fat cells

BACKGROUND

Adipose tissue is now appreciated as the pivotal regulator of metabolic and endocrine functions. Subcutaneous (SC) fat, in contrast to visceral fat, may protect against metabolic syndrome and systemic inflammation. We demonstrated that chronic as well as acute ultraviolet (UV) irradiation to the skin induces loss of underlying SC fat. UV-irradiated SC fat may produce chemokines or cytokines that modulate lipid homeostasis and secretion of adipokines.

OBJECTIVES

To elucidate UV-induced specific adipochemokines implicated in UV-induced modulation of SC fat.

METHODS

Primary cultured adipocytes were treated with conditioned medium from UV- or sham-irradiated skin cells. Young and older healthy participants provided SC fat from sun-exposed and sun-protected skin. Sun-protected skin from other participants was irradiated with UV. Differentially expressed adipochemokines were screened by cytokine array, and confirmed in vitro and in vivo. The functions of select adipochemokines involved in lipid metabolism were examined via short interfering RNA-mediated knockdown of cognate receptors.

RESULTS

Specific adipochemokines, including C-X-C motif chemokine (CXCL) family members such as CXCL5/ENA-78, and C-C motif chemokine (CCL) family members such as CCL20/MIP-3α and CCL5/RANTES, were greatly induced in SC fat by UV exposure. They could impair triglyceride synthesis via downregulation of lipogenic enzymes and sterol regulatory element-binding protein-1 through their respective cognate receptors, CXC chemokine receptor type (CXC-R)2, C-C chemokine receptor type (CCR)-6, and CCR-5. In addition, UV irradiation induced infiltration of adipose tissue macrophages responsible for the secretion of several chemokines into SC fat.

CONCLUSIONS

These UV-induced adipochemokines may be implicated in the reduction of lipogenesis in SC fat, leading to impairment of fat homeostasis and associated comorbidities such as obesity.

Polymorphisms of Flanking Region of the ASB15 Gene and Their Associations with Performance Traits in Chicken

Research on the identity of genes and their relationship with traits of economic importance in chickens could assist in the selection of poultry. In this study, an F₂ resource population of Gushi chickens crossed with Anka broilers was used to detect single-nucleotide polymorphisms (SNPs) in the flanking region of the ASB15 gene by DNA sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). One SNP of -1271 C>T in 5' flanking region of the chicken ASB15 gene and two SNPs of the 10618 A>G and 10716 G>A in 3' flanking region were identified. Furthermore, the 10618 A>G and 10716 G>A in 3' flanking region were in complete linkage. Association analysis results showed that -1271 C>T was not associated with performance traits, while the 10618 A>G and 10716 G>A were significantly associated with BW2, 4, 6, 8, 10, 12, SL12, CD8, CW4, 8, 12, BSL4, 8, 12, and SEW, EW, WW, BMW, LW, CW, SFT. Our results suggest that the ASB15 gene profoundly affects chicken performance traits.

Predicting Barrett's Esophagus in Families: An Esophagus Translational Research Network (BETRNet) Model Fitting Clinical Data to a Familial Paradigm

BACKGROUND

Barrett's esophagus is often asymptomatic and only a small portion of Barrett's esophagus patients are currently diagnosed and under surveillance. Therefore, it is important to develop risk prediction models to identify high-risk individuals with Barrett's esophagus. Familial aggregation of Barrett's esophagus and esophageal adenocarcinoma, and the increased risk of esophageal adenocarcinoma for individuals with a family history, raise the necessity of including genetic factors in the prediction model. Methods to determine risk prediction models using both risk covariates and ascertained family data are not well developed.

METHODS

We developed a Barrett's Esophagus Translational Research Network (BETRNet) risk prediction model from 787 singly ascertained Barrett's esophagus pedigrees and 92 multiplex Barrett's esophagus pedigrees, fitting a multivariate logistic model that incorporates family history and clinical risk factors. The eight risk factors, age, sex, education level, parental status, smoking, heartburn frequency, regurgitation frequency, and use of acid suppressant, were included in the model. The prediction accuracy was evaluated on the training dataset and an independent validation dataset of 643 multiplex Barrett's esophagus pedigrees.

RESULTS

Our results indicate family information helps to predict Barrett's esophagus risk, and predicting in families improves both prediction calibration and discrimination accuracy.

CONCLUSIONS

Our model can predict Barrett's esophagus risk for anyone with family members known to have, or not have, had Barrett's esophagus. It can predict risk for unrelated individuals without knowing any relatives' information.

IMPACT

Our prediction model will shed light on effectively identifying high-risk individuals for Barrett's esophagus screening and surveillance, consequently allowing intervention at an early stage, and reducing mortality from esophageal adenocarcinoma. Cancer Epidemiol Biomarkers Prev; 25(5); 727-35. ©2016 AACR.

A novel 31-bp indel in the paired box 7 (PAX7) gene is associated with chicken performance traits

1. A novel 31-bp indel polymorphism in intron 3 of the chicken paired box 7 (PAX7) gene was identified and genotyped in an F2 resource population of Gushi chicken crossed with Anka broiler to analyse its associations with chicken growth, carcass and meat quality traits. 2. Results showed that the 31-bp indel was significantly associated with body weight at 4, 6, 8, 10, 12 weeks of age and body size indices including shank length, shank girth, body slanting length at 8 and 12 weeks of age. Significant associations were found for carcass weight, semi-evisceration weight, evisceration weight, breast muscle fibre diameter, leg muscle fibre diameter, breast muscle fibre density, while no significant association with leg muscle fibre density was observed. 3. It was concluded that the 31-bp indel in intron 3 of the PAX7 gene was associated with chicken growth, carcass and meat quality traits where the 31-bp deletion had a negative effect on chicken growth and carcass traits and positive effect on meat quality traits.

Adjacent SNPs in the transcriptional regulatory region of the FADS2 gene associated with fatty acid and growth traits in chickens

Delta-6 fatty acid desaturases are rate-limiting desaturases involved in metabolic processes of fatty acids, and they are encoded by the FADS2 gene. In the current study, an F2 resource population of Gushi chickens crossed with Anak broilers was used to investigate the genetic effects of the chicken FADS2. Two adjacent single nucleotide polymorphisms (SNPs) (g.4290C>G and g.4291C>A) were identified in the transcriptional regulatory region of the FADS2 gene by means of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and created restriction site-PCR-RFLP. Associations between the two SNPs with chicken fatty acid contents and growth traits were determined using linkage disequilibrium, haplotype construction, and association analysis. The two SNPs and their haplotype combinations were significantly associated with linoleic acid (C18:2), α-linolenic acid (C18:3), arachidonic acid (C20:4), body weight (BW)2, BW4, BW6, shank girth (SG)4, and breast bone length 4 (P<0.05). These results suggested that the SNPs of the FADS2 gene affected the content of essential fatty acid in muscle, and played a role in the early-stage growth rate of chickens.

Deposition rule of yolk cholesterol in two different breeds of laying hens

The objective of this study was to investigate the deposition rule of yolk cholesterol in Lushi Green-shelled and Silky Fowl layers. A total of 90 layers of each breed were selected at an age of 15 to 51 weeks. Productive performance was recorded on a weekly basis, whereas yolk cholesterol was determined at 4-week intervals from 21 to 51 weeks of age. The average yolk cholesterol content of Silky Fowl layers during the laying period was higher than that of Lushi Green-shelled layers (58.16 and 49.67%, P > 0.05). Yolk cholesterol content decreased at 21 to 31 weeks of the laying period, whereas a non-significant increasing trend was observed during 31 to 51 weeks of laying period. In conclusion, yolk cholesterol content is not only dependent on the age of hen but also the breed of layers.

Association study of polymorphisms inside the miR-1657 seed region with chicken growth and meat traits

1. Polymorphisms occurring in the seed region of microRNAs (miRNAs) could influence their target gene and lead to phenotypic variation. The purpose of the research was to explore the genetic effects of the rs14934924 (G > A) mutation resident in the conserved seed region of miR-1657 on growth and meat traits of the Gushi-Anka F2 resource population. 2. The NdeI polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method and association analysis were used to analyse the polymorphism. 3. The mutation was associated with body weight at 8 weeks of age, shank girth at 12 weeks of age, breast bone length at 12 weeks of age, pelvis breadth at 4 weeks of age and subcutaneous fat thickness (P < 0·05) and was associated with body weight at 4, 6, 10 and 12 weeks of age (P < 0·01). 4. Our results will be a useful resource for a subsequent study in miRNA function, and provide a basis for molecular techniques in chicken breeding.

Identification and abundance of miRNA in chicken hypothalamus tissue determined by Solexa sequencing

We used Solexa sequencing technology to identify and determine the abundance of miRNAs and compared the characteristics and expression patterns of miRNA of 1-day-old and 36-week-old chicken hypothalamuses. We obtained 17,825,753 and 10,928,745 high-quality reads from 36-week-old and 1-day-old chickens, respectively. Three hundred and seventy-one conserved miRNAs were expressed in both libraries. Among the conserved miRNAs, 22 miRNAs were up-regulated and 157 miRNAs were down-regulated in the 36-week-old chicken hypothalamus tissues. The abundance of sRNAs between 1-day-old and 36-week-old chickens differed considerably. KEGG pathway analysis suggested that the target genes of highly expressed miRNAs in the chicken hypothalamus are associated with metabolism and development. This information on differential expression of miRNAs in the hypothalamus of 1-day-old and 36-week-old chickens will help us understand the molecular mechanisms of metabolism and development.

Two novel SNPs of the 3-hydroxy-3-methylglutaryl coenzyme A reductase gene associated with growth and meat quality traits in the chicken

The enzyme 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR) is rate-limiting for metabolism of cholesterol; it plays an important role in endogenous cholesterol biosynthesis. We used DNA sequencing technology and created restriction site PCR-RFLP to detect HMGCR SNPs in an F(2) resource population of Gushi chicken and Anka broilers. We found a G/T mutation (Gln/His) in exon 17 and a T/C mutation (Pro/Pro) in exon 18. Based on association analysis of these HMGCR polymorphisms in 864 Gushi/Anka F(2) hybrids, these two mutations have significant effects on growth, carcass, meat quality, and lipid concentration.

Identification of differentially expressed genes induced by energy restriction using annealing control primer system from the liver and adipose tissues of broilers

Female Arbor Acre broilers were divided into 2 groups at 18 d of age. One group of chickens had free access to feed (AL), and the other group of chickens had 30% energy restriction (ER). Adipose and hepatic RNA samples were collected at 48 d of age. We employed an accurate reverse-transcription (RT) PCR method that involves annealing control primers to identify the differentially expressed genes (DEG) between ER and AL groups. Using 20 annealing control primers, 43 differentially expressed bands (40 downregulated and 3 upregulated in the ER group) were detected from the hepatic tissue, whereas no differentially expressed bands were detected from the adipose tissue. It seems that energy restriction could induce more DEG in hepatic tissue than that in adipose tissue and could result in more gene-expression downregulation in hepatic tissue. Eight DEG (6 known and 2 unknown genes) were gained from hepatic tissue and confirmed by RT-PCR, which were all supported by released expressed sequence tag sequences. Their expressions were all downregulated by energy restriction in hepatic tissues. Six known genes are RPL7, RPLP1, FBXL12, ND1, ANTXR2, and SLC22A18, respectively, which seem to play essential roles in the protein translation, energy metabolism, and tumor inhibition. The alterations of gene expression in 3 selected genes, including ND1 (P < 0.01), FBXL12 (P < 0.01), and RPLP1 (P < 0.05), were supported by real-time quantitative RT-PCR reaction. Our data provide new insights on the metabolic state of broilers changed by energy restriction.

Study and clinical application of a porcine biomembrane for the repair of dural defects

A biomembrane was developed from pig peritoneum treated with 0.65% glutaraldehyde. This was evaluated for use as a dural substitute in an animal model and in a patient population. After being treated with the glutaraldehyde solution, the biomembrane lost its antigenicity while its collagen underwent an irreversible cross-linking reaction, causing it to become a stable nonviable polymer resistant to absorption by the host. The biomembrane was used experimentally in 43 procedures on 20 dogs and was applied clinically in 614 patients. The results demonstrated that it is an acceptable material for the repair of dural defects, with the following advantages: 1) it is nontoxic to the body and brain tissues, with minimal tissue reaction; 2) its biophysical properties facilitate watertight closure with sutures; 3) its distensibility makes it suitable for decompressive surgical dural repair; and 4) its visceral surface is extremely smooth, causing virtually no adhesions with the brain tissue while the outer surface readily heals with the subcutaneous tissue.