Quality Assurance of UMLS Semantic Type Assignments Using SNOMED CT Hierarchies

BACKGROUND

The Unified Medical Language System (UMLS) is one of the largest biomedical terminological systems, with over 2.5 million concepts in its Metathesaurus repository. The UMLS's Semantic Network (SN) with its collection of 133 high-level semantic types serves as an abstraction layer on top of the Metathesaurus. In particular, the SN elaborates an aspect of the Metathesaurus's concepts via the assignment of one or more types to each concept. Due to the scope and complexity of the Metathesaurus, errors are all but inevitable in this semantic-type assignment process.

OBJECTIVES

To develop a semi-automated methodology to help assure the quality of semantic-type assignments within the UMLS.

METHODS

The methodology uses a cross-validation strategy involving SNOMED CT's hierarchies in combination with UMLS semantic types. Semantically uniform, disjoint concept groups are generated programmatically by partitioning the collection of all concepts in the same SNOMED CT hierarchy according to their respective semantic-type assignments in the UMLS. Domain experts are then called upon to review the concepts in any group having a small number of concepts. It is our hypothesis that a semantic-type assignment combination applicable only to a very small number of concepts in a SNOMED CT hierarchy is an indicator of potential problems.

RESULTS

The methodology was applied to the UMLS 2013AA release along with the SNOMED CT from January 2013. An overall error rate of 33% was found for concepts proposed by the quality-assurance methodology. Supporting our hypothesis, that number was four times higher than the error rate found in control samples.

CONCLUSION

The results show that the quality-assurance methodology can aid in effective and efficient identification of UMLS semantic-type assignment errors.

Interleukin 12B rs3212227 T > G polymorphism was associated with an increased risk of gastric cardiac adenocarcinoma in a Chinese population

Gastric cardiac adenocarcinoma (GCA) is one of common malignant tumors in the world. Multiple genes that play critical roles in inflammatory pathways probably are associated with GCA risk. We conducted a hospital-based case-control study to evaluate the genetic effects of functional single nucleotide polymorphisms (SNPs): interleukin 9 (IL9) rs31563 C > T, IL9 rs31564 G > T, IL10 rs1800872 T > G, IL12A rs2243115 T > G, IL12B rs3212227 T > G, and IL13 rs1800925 C > T on the development of GCA. Two hundred and forty-three GCA cases and 476 controls were recruited. Their genotypes were determined using a custom-by-design 48-Plex SNPscan kit. IL12B rs3212227 T > G polymorphism was associated with the increased risk of GCA. However, there was no significant association between the other five SNPs and GCA risk. Stratified analyses indicated that the risk of GCA associated with the IL12B rs3212227 T > G polymorphism was evident among female patients and patients who never smoked or consumed alcoholic drinks. These findings indicated that functional polymorphism IL12B rs3212227 T > G might correlate with GCA risk. However, our results were obtained with a limited sample size; the power of our analysis was low. Larger studies are required to confirm the current findings.

Aggression is associated with aerobic glycolysis in the honey bee brain(1)

Aerobic glycolysis involves increased glycolysis and decreased oxidative catabolism of glucose even in the presence of an ample oxygen supply. Aerobic glycolysis, a common metabolic pattern in cancer cells, was recently discovered in both the healthy and diseased human brain, but its functional significance is not understood. This metabolic pattern in the brain is surprising because it results in decreased efficiency of adenosine triphosphate (ATP) production in a tissue with high energetic demands. We report that highly aggressive honey bees (Apis mellifera) show a brain transcriptomic and metabolic state consistent with aerobic glycolysis, i.e. increased glycolysis in combination with decreased oxidative phosphorylation. Furthermore, exposure to alarm pheromone, which provokes aggression, causes a metabolic shift to aerobic glycolysis in the bee brain. We hypothesize that this metabolic state, which is associated with altered neurotransmitter levels, increased glycolytically derived ATP and a reduced cellular redox state, may lead to increased neuronal excitability and oxidative stress in the brain. Our analysis provides evidence for a robust, distinct and persistent brain metabolic response to aggression-inducing social cues. This finding for the first time associates aerobic glycolysis with naturally occurring behavioral plasticity, which has important implications for understanding both healthy and diseased brain function.

Secretory clusterin is upregulated in rats with pulmonary arterial hypertension induced by systemic-to-pulmonary shunts and exerts important roles in pulmonary artery smooth muscle cells

AIM

Phenotype modification of pulmonary artery smooth muscle cells (PASMCs) (excessive proliferation, migration and impaired apoptosis) plays central roles in pulmonary vascular remodelling of pulmonary arterial hypertension (PAH); however, the potential mechanism and contributing factors involved in the phenotype alteration in PASMCs are still not completely elucidated. This study attempted to investigate the expression pattern of secretory clusterin (sCLU), a prosurvival protein, in systemic-to-pulmonary shunt-induced PAH rats and the potential roles of sCLU in pulmonary vascular remodelling.

METHODS

An original rat model of systemic-to-pulmonary shunt-induced PAH was established by combined surgery as we previously reported. Lung tissues were harvested at specific time points for real-time polymerase chain reaction, Western blot and immunohistochemisty analysis; meanwhile, plasma was collected for enzyme-linked immunosorbent assay. Cell culture experiments were performed using cultured human PASMCs (HPASMCs).

RESULTS

Expression of sCLU was significantly increased in lungs exposed to systemic-to-pulmonary shunt. Moreover, plasma sCLU levels were markedly elevated with the progression of PAH in rats and also presented a positive correlation with pulmonary hemodynamic indices. In vitro cell culture assay indicated that sCLU expression and secretion increased with the phenotype modification of HPASMCs; furthermore, sCLU promoted HPASMCs proliferation, migration and apoptosis resistance, at least in part, via Erk1/2 and Akt signalling pathways.

CONCLUSION

These results demonstrate that sCLU is functionally an important phenotype modulator of PASMCs, and its upregulation in lung tissues may exert a deteriorative role in pulmonary vascular remodelling.

Immune response of γδT cells in Schistosome japonicum-infected C57BL/6 mouse liver

Systematic evaluation of the role of γδT cells during the Schistosoma japonicum infection has not been reported, despite the fact that γδT cells contribute to many infectious diseases in innate immunity. Therefore, the aim of this study was to observe the properties of γδT cells in the liver of C57BL/6 mice infected by S. japonicum. In this report, using immuno-fluorescent histological analysis, γδT cells were found around hepatic granulomatous. Moreover, the flow cytometry results revealed that the percentage of hepatic γδT cells increased significantly after S. japonicum infection. More interestingly, a subset of CD3(-)γδTCR(+) cells were found and markedly increased after infection. Furthermore, expression of activation markers (CD25 and CD69) and cytokine profiles were detected in these hepatic CD3(+)γδTCR(+) and CD3(-)γδTCR(+) cells. The significantly higher level of CD69, IL-4 and IL-17 were observed in CD3(+)γδTCR(+) cells after infection, suggesting that CD3(+)γδTCR(+) cells instead of CD3(-)γδTCR(+) cells might play a predominant role during the infection. Finally, our results indicated that the expression of NKG2D on CD3(+)γδTCR(+) cells was higher than that on CD3(-)γδTCR(+) cells. Collectively, γδT cells could play an important role in the liver of C57BL/6 mouse during japonicum infection.

Methylenetetrahydrofolate reductase C667T polymorphism is associated with increased risk of coronary artery disease in a Chinese population

Coronary artery disease (CAD) is a complex disease resulting from a combination of environmental and genetic factors. We hypothesized that polymorphisms in methylenetetrahydrofolate reductase (MTHFR) rs1801133 C/T, matrix metalloproteinases (MMPs)-2, tumour necrosis factor (TNF)-α, macrophage migration inhibitory factor (MIF) rs755622 G/C and cyclin D1 (CCND1) rs678653 G/C contribute to CAD susceptibility. We examined the association between the five polymorphisms and the risk of CAD in a Chinese population of 435 CAD patients and 480 controls. Genotyping was performed using matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI/TOF MS). When the MTHFR rs1801133 CC homozygote genotype was used as the reference group, the TT or CT/TT genotypes were associated with a significantly increased risk for CAD. The CT heterozygote genotype was not associated with the risk for CAD. Logistic regression analyses revealed that MMP-2 rs243865 C/T, TNF-α rs1800629 A/G, MIF rs755622 G/C and CCND1 rs678653 G/C polymorphisms were not associated with the risk of CAD. These findings suggest that the MTHFR rs1801133 C/T polymorphism is associated with CAD development. Future larger studies with other ethnic populations are required to confirm current findings.

Chronic urticaria in Chinese population: a hospital-based multicenter epidemiological study

BACKGROUND

The epidemiologic profiles of chronic urticaria (CU) vary considerably among regions, and few such data are available from China.

METHODS

We performed a multicenter open questionnaire investigation about the clinical and laboratory features of CU, defined as recurrent wheals with/without angioedema lasting for ≥6 weeks, among 3027 patients.

RESULTS

Female preponderance was observed (female/male ratio, 1.46 : 1). The mean age at diagnosis was 34.7 ± 13.8 years, and the mean disease duration was 18.5 ± 46.1 months (range, 1.5-127 months). Patients were classified as having chronic spontaneous urticaria (CSU, 61.0% of patients), physical urticaria (PU, 26.2%), or other urticaria types (OU, 2.3%). Nocturnal attacks were reported by 60% of cases. The Urticaria Activity Score (UAS) in patients with CSU was 3.8 ± 1.4. The mean Dermatology Life Quality Index was 7.3 ± 3.4 (range 0-30). Induction or exacerbation of wheals with alcohol drinking was reported by 55.7% of patients. Chronic hepatitis B was less prevalent in our CU patients compared with the general Chinese population (2.7% vs 7%). Positive autologous serum skin tests (ASSTs) were observed in 66.9% of patients. Patients with positive ASST had higher UAS, greater angioedema frequencies, longer disease durations, and poorer QoL compared with patients with negative ASST (P < 0.05).

CONCLUSION

In this Chinese population, CU usually affected youth, and CSU was the most common subtype. Autoreactivity and alcohol consumption were the top two triggers for CU, whereas latent infectious and chronic inflammatory diseases were not as common as in previous reports.

In vitro selection of allosteric ribozymes that sense the bacterial second messenger c-di-GMP

Recently, a number of study have shown the ligand-dependent allosteric ribozymes can be harnessed as biosensors, high-throughput screening, and agents for the control of gene expression in vivo, called artificial riboswitches. In this chapter, we describe how in vitro selection can be used to create an allosteric ribozyme that senses bacterial second messenger cyclic-di-GMP (c-di-GMP). A hammerhead ribozyme was joined to a natural c-di-GMP class I riboswitch aptamer via communication modules. Both c-di-GMP-activating and -inhibiting ribozyme can be obtained by this approach.

Interleukin 17A rs4711998 A>G polymorphism was associated with a decreased risk of esophageal cancer in a Chinese population

Esophageal cancer is the eighth most common cancer and sixth leading cause of cancer-associated death worldwide. Besides environmental risk factors, genetic factors might play an important role in the esophageal cancer carcinogenesis. We conducted a hospital-based case-control study to evaluate the genetic effects of functional single nucleotide polymorphisms (SNPs) in the interleukin 17A (IL17A) gene on the development of esophageal cancer. A total of 380 esophageal squamous cell carcinoma (ESCC) cases and 380 controls were recruited for this study. The genotypes were determined using a custom-by-design 48-Plex SNPscan Kit. IL17A rs4711998 A>G polymorphism was associated with the decreased risk of ESCC. When the IL17A rs4711998 AA homozygote genotype was used as the reference group, the AG genotype was associated with a significantly decreased risk for ESCC (AG vs. AA: adjusted odds ratio 0.72, 95% confidential interval 0.53-0.98, P = 0.039). However, there was no significant association between the other five SNPs and ESCC risk. Stratified analyses indicated that a significantly decreased risk of ESCC associated with the IL17A rs4711998 A>G polymorphism was evident among younger patients and patients who never smoking or drinking. These findings indicated that functional polymorphism IL17A rs4711998 A>G might contribute to ESCC susceptibility. However, our results were obtained with a limited sample size; the power of our analysis was low. Future larger studies with more rigorous study designs of other ethnic populations are required to confirm current findings.

A voxel-based morphometry study of anosmic patients

OBJECTIVE

The aim of our study was to compare volume change in grey matter (GM) and white matter (WM) in a group of subjects with anosmia and a healthy control group. We tried to find a regular pattern of atrophy within and between GM and WM and to determine whether any particular areas are more sensitive to olfactory injury.

METHODS

There were 19 anosmic patients and 20 age- and sex-matched control subjects. We acquired MR images on a 3-T scanner and performed voxel-based morphometry using the VBM8 toolbox and SPM8 in a MATLAB® (MathWorks®, Natick, MA) environment.

RESULTS

Patients with anosmia showed a significant decrease in GM volume, mainly in the anterior cingulate cortex, middle temporal gyrus, superior temporal gyrus, fusiform gyrus, supramarginal gyrus, superior frontal gyrus, middle frontal gyrus, middle occipital gyrus, anterior insular cortex and cerebellum. In addition, we observed volume decreases in smaller areas such as the piriform cortex, the inferior temporal gyrus, the precuneus and the subcallosal gyrus. All WM areas with atrophy were near those GM areas that experienced volume loss. There was more volume atrophy in GM areas corresponding to WM areas with more volume loss. Atrophy increased with disease duration.

CONCLUSION

There is simultaneous atrophy in GM and WM, and the degree of atrophy is greater with longer disease duration. Different GM and WM areas have different sensitivities to olfactory injury.

ADVANCES IN KNOWLEDGE

This study examines the atrophy pattern in and between GM and WM-a subject that has not been widely researched previously.

Necro-inflammatory response of pancreatic acinar cells in the pathogenesis of acute alcoholic pancreatitis

The role of pancreatic acinar cells in initiating necro-inflammatory responses during the early onset of alcoholic acute pancreatitis (AP) has not been fully evaluated. We investigated the ability of acinar cells to generate pro- and anti-inflammatory mediators, including inflammasome-associated IL-18/caspase-1, and evaluated acinar cell necrosis in an animal model of AP and human samples. Rats were fed either an ethanol-containing or control diet for 14 weeks and killed 3 or 24 h after a single lipopolysaccharide (LPS) injection. Inflammasome components and necro-inflammation were evaluated in acinar cells by immunofluorescence (IF), histology, and biochemical approaches. Alcohol exposure enhanced acinar cell-specific production of TNFα, IL-6, MCP-1 and IL-10, as early as 3 h after LPS, whereas IL-18 and caspase-1 were evident 24 h later. Alcohol enhanced LPS-induced TNFα expression, whereas blockade of LPS signaling diminished TNFα production in vitro, indicating that the response of pancreatic acinar cells to LPS is similar to that of immune cells. Similar results were observed from acinar cells in samples from patients with acute/recurrent pancreatitis. Although morphologic examination of sub-clinical AP showed no visible signs of necrosis, early loss of pancreatic HMGB1 and increased systemic levels of HMGB1 and LDH were observed, indicating that this strong systemic inflammatory response is associated with little pancreatic necrosis. These results suggest that TLR-4-positive acinar cells respond to LPS by activating the inflammasome and producing pro- and anti-inflammatory mediators during the development of mild, sub-clinical AP, and that these effects are exacerbated by alcohol injury.

Small, highly active DNAs that hydrolyze DNA

DNA phosphoester bonds are exceedingly resistant to hydrolysis in the absence of chemical or enzymatic catalysts. This property is particularly important for organisms with large genomes, as resistance to hydrolytic degradation permits the long-term storage of genetic information. Here we report the creation and analysis of two classes of engineered deoxyribozymes that selectively and rapidly hydrolyze DNA. Members of class I deoxyribozymes carry a catalytic core composed of only 15 conserved nucleotides and attain an observed rate constant (k(obs)) of ~1 min(-1) when incubated near neutral pH in the presence of Zn(2+). Natural DNA sequences conforming to the class I consensus sequence and structure were found that undergo hydrolysis under selection conditions (2 mM Zn(2+), pH 7), which demonstrates that the inherent structure of certain DNA regions might promote catalytic reactions, leading to genomic instability.

RKIP inhibits the malignant phenotypes of gastric cancer cells

Raf kinase inhibitor protein (RKIP) is first identified as an interacting partner of Raf-1. RKIP expression is low or absent in several established cell lines derived from metastatic breast cancer, prostate cancer and melanoma cells. However, the functional role of RKIP in gastric cancer remains unclear. In this study, we employed human gastric cancer cell line SGC7901 as a model to reconstitute RKIP expression in gastric cancer cells. The growth curve and soft agar assay showed that RKIP inhibited the growth and clonogenicity of SGC7901 cells. Flow cytometry analysis showed that RKIP inhibited the cell cycle progression and induced the apoptosis of SGC7901 cells. Wound healing and transwell invasion assay showed that RKIP inhibited the migration and invasion of SGC7901 cells. Furthermore, we observed that RKIP inhibited the growth of SMGC7901 cells in xenografts in nude mice. Taken together, our in vitro and in vivo data demonstrate that RKIP modulates the proliferation, apoptosis, migration, invasion and tumorigenicity of SGC7901 cells. These results reveal the tumor suppressor role of RKIP in gastric cancer and suggest that RKIP may be new therapeutic target for gastric cancer.

Host susceptibility of citrus cultivars to Queensland fruit fly (Diptera: Tephritidae)

Citrus crops are considered to be relatively poor hosts for Queensland fruit fly, Bactrocera tryoni (Froggatt), as for other tephritid species. Australian citrus growers and crop consultants have reported observable differences in susceptibility of different citrus cultivars under commercial growing conditions. In this study we conducted laboratory tests and field surveys to determine susceptibility to B. tryoni of six citrus cultivars [(Eureka lemon (Citrus limon (L.) Osbeck); Navel and Valencia oranges (C. sinensis (L.) Osbeck); and Imperial, Ellendale, and Murcott mandarins (C. reticulata Blanco). The host susceptibility of these citrus cultivars was quantified by a Host Susceptibility Index, which is defined as the number of adult flies produced per gram of fruit infested at a calculated rate of one egg per gram of fruit. The HSI was ranked as Murcott (0.083) > Imperial (0.052) > Navel (0.026) - Ellendale (0.020) > Valencia (0.008) > Eureka (yellow) (0.002) > Eureka (green) (0). Results of the laboratory study were in agreement with the level of field infestation in the four citrus cultivars (Eureka lemon, Imperial, Ellendale, and Murcott mandarins) that were surveyed from commercial orchards under baiting treatments against fruit flies in the Central Burnett district of Queensland. Field surveys of citrus hosts from the habitats not subject to fruit fly management showed that the numbers of fruit flies produced per gram of fruit were much lower, compared with the more susceptible noncitrus hosts, such as guava (Psidium guajava L.), cherry guava (P. littorale Raddi), mulberry (Morus nigra L.), loquat (Eriobotrya japonica (Thunb.) Lindl.), and pear (Pyrus communis L.). Therefore, the major citrus crops commercially cultivated in Australia have a relatively low susceptibility to B. tryoni, with Eureka lemons being a particularly poor host for this tephritid fruit fly.

Safety evaluation of daidzein in laying hens: part II. Effects on calcium-related metabolism

Daidzein, an estrogen-like product, has become increasingly popular as a dietary supplement, particularly for postpeak-estrus animals seeking a safe natural alternative to play a role of estrogen. However, there is little available safety data of it for raisers and consumers. A subchronic laying hensafety study has been conducted to examine if the high-dose daidzein could affect calcium-related metabolism (eggshell quality and bone mineralization). Seven hundred and sixty-eight 56-week-old Hyline Brown were randomly assigned to 4 groups with 8 replicates of 24 birds each (192 laying hensper group) and 3weeks later fed diets supplemented with 0(control), 10, 50 and 100mg of daidzein/kg for 12week. Eggshell thickness, eggshell percentage, eggshell strength, eggshell Ca concentration was increased linearly with increasing dietary daidzein supplementation (P=0.001, P=0.007, P=0.002 and P=0.000, respectively). Serum Ca increased linearly with increasing dietarydaidzein supplementation (P=0.042), and serum P showed a significant quadratic response to dietarydaidzein supplementation (P=0.036). Bone ash and bone Ca were significantly influenced by dietarydaidzein supplementation (P<0.05). These findings indicate that daidzein hold no observed adverse effect on calcium metabolism, but also a safe and effective food additive for calcium metabolism in animals and humans.

Abstract P5-10-06: A functional role for miR-150 in breast cancer

Background: During mammary gland development, massive coordinated changes in protein expression govern the progression through pregnancy to lactation and involution. These dramatic changes are likely regulated in part at the translational level by changes in microRNAs (miRNAs). We profiled miRNA expression in mammary epithelial cells (MECs) isolated from mice at pregnancy day 14 (P14) or lactation day 2 (L2) and found that miR-150 is the most significantly downregulated miRNA between pregnancy and lactation. Interestingly, miR-150 was recently discovered to be decreased in mouse mammary tumors compared to normal mammary tissue in numerous transgenic models. However, a causal role for miR-150 has yet to be studied in human breast cancer and little is known about its functional role and relevant targets in the normal breast or breast cancer.

Hypothesis: We hypothesized that miR-150 may be a tumor suppressor whose loss in breast cancer cells is an important event that allows for expression of multiple pro-tumorigenic genes.

Methods: miR-150 levels in human breast cancers were evaluated in specimens of both ER+ and triple-negative breast cancer (TNBC) as compared to adjacent, non-involved normal breast epithelium by in situ hybridization. miR-150 levels were also measured by qRT-PCR in cell lines representative of multiple breast cancer subtypes. We stably restored miR-150 in TNBC cell lines by lentiviral infection and evaluated its effects on clonogenicity, growth in 3D culture, migration/invasion, and tumorigenicity. Expression of predicted miR-150 targets was assessed by immunoblot. Crossing of miR-150fl/fl mice with BLG-Cre or MMTV/NIC transgenic mice will be utilized to determine the effects of MEC-specific loss of this miRNA on mammary tumorigenesis.

Results: In clinical samples, in situ hybridization reveals that miR-150 levels are lower in both ER+ and TNBC tumor specimens compared to adjacent normal epithelium, with triple-negative tumors having the lowest expression. All breast cancer cell lines tested also have low miR-150 expression as compared to normal mammary epithelial tissue, with TNBC cell lines expressing the lowest levels. Exogenous expression of miR-150 in breast cancer cell lines caused a dramatic decrease in migration and invasion in vitro, and we are testing predicted miR-150 targets for their role in this phenotype. Experiments with transgenic models will determine if loss of miR-150 in mammary epithelial cells in the MMTV/NIC mouse model results in decreased latency or increased tumor formation and metastasis, or if miR-150 loss during pregnancy results in alterations in lactation, hyperplasia, or tumor formation.

Conclusions: TNBC specimens and cell lines have the lowest expression of miR-150, though decreased miR-150 expression compared to normal mammary epithelium is a common feature of breast cancers regardless of subtype. miR-150 expression dramatically inhibits breast cancer cell migration and invasion in vitro, and ongoing experiments will determine the relevant target genes.

Supported by Susan G. Komen Grant KG090415 and NIH NICHD P01 PAR-10-245 (Project 3) to JKR

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-10-06.

Identification of ligand analogues that control c-di-GMP riboswitches

Riboswitches for the bacterial second messenger c-di-GMP control the expression of genes involved in numerous cellular processes such as virulence, competence, biofilm formation, and flagella synthesis. Therefore, the two known c-di-GMP riboswitch classes represent promising targets for developing novel modulators of bacterial physiology. Here, we examine the binding characteristics of circular and linear c-di-GMP analogues for representatives of both class I and II c-di-GMP riboswitches derived from the pathogenic bacterium Vibrio choleae (class I) and Clostridium difficile (class II). Some compounds exhibit values for apparent dissociation constant (K(D)) below 1 μM and associate with riboswitch RNAs during transcription with a speed that is sufficient to influence riboswitch function. These findings are consistent with the published structural models for these riboswitches and suggest that large modifications at various positions on the ligand can be made to create novel compounds that target c-di-GMP riboswitches. Moreover, we demonstrate the potential of an engineered allosteric ribozyme for the rapid screening of chemical libraries for compounds that bind c-di-GMP riboswitches.