Risk factors affecting polygenic score performance across diverse cohorts

Apart from ancestry, personal or environmental covariates may contribute to differences in polygenic score (PGS) performance. We analyzed effects of covariate stratification and interaction on body mass index (BMI) PGS (PGS BMI ) across four cohorts of European (N=491,111) and African (N=21,612) ancestry. Stratifying on binary covariates and quintiles for continuous covariates, 18/62 covariates had significant and replicable R 2 differences among strata. Covariates with the largest differences included age, sex, blood lipids, physical activity, and alcohol consumption, with R 2 being nearly double between best and worst performing quintiles for certain covariates. 28 covariates had significant PGS BMI -covariate interaction effects, modifying PGS BMI effects by nearly 20% per standard deviation change. We observed overlap between covariates that had significant R 2 differences among strata and interaction effects - across all covariates, their main effects on BMI were correlated with their maximum R 2 differences and interaction effects (0.56 and 0.58, respectively), suggesting high-PGS BMI individuals have highest R 2 and increase in PGS effect. Using quantile regression, we show the effect of PGS BMI increases as BMI itself increases, and that these differences in effects are directly related to differences in R 2 when stratifying by different covariates. Given significant and replicable evidence for context-specific PGS BMI performance and effects, we investigated ways to increase model performance taking into account non-linear effects. Machine learning models (neural networks) increased relative model R 2 (mean 23%) across datasets. Finally, creating PGS BMI directly from GxAge GWAS effects increased relative R 2 by 7.8%. These results demonstrate that certain covariates, especially those most associated with BMI, significantly affect both PGS BMI performance and effects across diverse cohorts and ancestries, and we provide avenues to improve model performance that consider these effects.

Penn Healthy Diet survey: pilot validation and scoring

Though diet quality is widely recognised as linked to risk of chronic disease, health systems have been challenged to find a user-friendly, efficient way to obtain information about diet. The Penn Healthy Diet (PHD) survey was designed to fill this void. The purposes of this pilot project were to assess the patient experience with the PHD, to validate the accuracy of the PHD against related items in a diet recall and to explore scoring algorithms with relationship to the Healthy Eating Index (HEI)-2015 computed from the recall data. A convenience sample of participants in the Penn Health BioBank was surveyed with the PHD, the Automated Self-Administered 24-hour recall (ASA24) and experience questions. Kappa scores and Spearman correlations were used to compare related questions in the PHD to the ASA24. Numerical scoring, regression tree and weighted regressions were computed for scoring. Participants assessed the PHD as easy to use and were willing to repeat the survey at least annually. The three scoring algorithms were strongly associated with HEI-2015 scores using National Health and Nutrition Examination Survey 2017-2018 data from which the PHD was developed and moderately associated with the pilot replication data. The PHD is acceptable to participants and at least moderately correlated with the HEI-2015. Further validation in a larger sample will enable the selection of the strongest scoring approach.

Lymphocyte Count Derived Polygenic Score and Interindividual Variability in CD4 T-cell Recovery in Response to Antiretroviral Therapy

Access to safe and effective antiretroviral therapy (ART) is a cornerstone in the global response to the HIV pandemic. Among people living with HIV, there is considerable interindividual variability in absolute CD4 T-cell recovery following initiation of virally suppressive ART. The contribution of host genetics to this variability is not well understood. We explored the contribution of a polygenic score which was derived from large, publicly available summary statistics for absolute lymphocyte count from individuals in the general population (PGSlymph) due to a lack of publicly available summary statistics for CD4 T-cell count. We explored associations with baseline CD4 T-cell count prior to ART initiation (n=4959) and change from baseline to week 48 on ART (n=3274) among treatment-naïve participants in prospective, randomized ART studies of the AIDS Clinical Trials Group. We separately examined an African-ancestry-derived and a European-ancestry-derived PGSlymph, and evaluated their performance across all participants, and also in the African and European ancestral groups separately. Multivariate models that included PGSlymph, baseline plasma HIV-1 RNA, age, sex, and 15 principal components (PCs) of genetic similarity explained ∼26-27% of variability in baseline CD4 T-cell count, but PGSlymph accounted for <1% of this variability. Models that also included baseline CD4 T-cell count explained ∼7-9% of variability in CD4 T-cell count increase on ART, but PGSlymph accounted for <1% of this variability. In univariate analyses, PGSlymph was not significantly associated with baseline or change in CD4 T-cell count. Among individuals of African ancestry, the African PGSlymph term in the multivariate model was significantly associated with change in CD4 T-cell count while not significant in the univariate model. When applied to lymphocyte count in a general medical biobank population (Penn Medicine BioBank), PGSlymph explained ∼6-10% of variability in multivariate models (including age, sex, and PCs) but only ∼1% in univariate models. In summary, a lymphocyte count PGS derived from the general population was not consistently associated with CD4 T-cell recovery on ART. Nonetheless, adjusting for clinical covariates is quite important when estimating such polygenic effects.

How to Run the Pharmacogenomics Clinical Annotation Tool (PharmCAT)

Pharmacogenomics (PGx) investigates the genetic influence on drug response and is an integral part of precision medicine. While PGx testing is becoming more common in clinical practice and may be reimbursed by Medicare/Medicaid and commercial insurance, interpreting PGx testing results for clinical decision support is still a challenge. The Pharmacogenomics Clinical Annotation Tool (PharmCAT) has been designed to tackle the need for transparent, automatic interpretations of patient genetic data. PharmCAT incorporates a patient's genotypes, annotates PGx information (allele, genotype, and phenotype), and generates a report with PGx guideline recommendations from the Clinical Pharmacogenetics Implementation Consortium (CPIC) and/or the Dutch Pharmacogenetics Working Group (DPWG). PharmCAT has introduced new features in the last 2 years, including a variant call format (VCF) Preprocessor, the inclusion of DPWG guidelines, and functionalities for PGx research. For example, researchers can use the VCF Preprocessor to prepare biobank-scale data for PharmCAT. In addition, PharmCAT enables the assessment of novel partial and combination alleles that are composed of known PGx variants and can call CYP2D6 genotypes based on single and deletions in the input VCF file. This tutorial provides materials and detailed step-by-step instructions for how to use PharmCAT in a versatile way that can be tailored to users' individual needs.

Evaluating the frequency and the impact of pharmacogenetic alleles in an ancestrally diverse Biobank population

BACKGROUND

Pharmacogenomics (PGx) aims to utilize a patient's genetic data to enable safer and more effective prescribing of medications. The Clinical Pharmacogenetics Implementation Consortium (CPIC) provides guidelines with strong evidence for 24 genes that affect 72 medications. Despite strong evidence linking PGx alleles to drug response, there is a large gap in the implementation and return of actionable pharmacogenetic findings to patients in standard clinical practice. In this study, we evaluated opportunities for genetically guided medication prescribing in a diverse health system and determined the frequencies of actionable PGx alleles in an ancestrally diverse biobank population.

METHODS

A retrospective analysis of the Penn Medicine electronic health records (EHRs), which includes ~ 3.3 million patients between 2012 and 2020, provides a snapshot of the trends in prescriptions for drugs with genotype-based prescribing guidelines ('CPIC level A or B') in the Penn Medicine health system. The Penn Medicine BioBank (PMBB) consists of a diverse group of 43,359 participants whose EHRs are linked to genome-wide SNP array and whole exome sequencing (WES) data. We used the Pharmacogenomics Clinical Annotation Tool (PharmCAT), to annotate PGx alleles from PMBB variant call format (VCF) files and identify samples with actionable PGx alleles.

RESULTS

We identified ~ 316.000 unique patients that were prescribed at least 2 drugs with CPIC Level A or B guidelines. Genetic analysis in PMBB identified that 98.9% of participants carry one or more PGx actionable alleles where treatment modification would be recommended. After linking the genetic data with prescription data from the EHR, 14.2% of participants (n = 6157) were prescribed medications that could be impacted by their genotype (as indicated by their PharmCAT report). For example, 856 participants received clopidogrel who carried CYP2C19 reduced function alleles, placing them at increased risk for major adverse cardiovascular events. When we stratified by genetic ancestry, we found disparities in PGx allele frequencies and clinical burden. Clopidogrel users of Asian ancestry in PMBB had significantly higher rates of CYP2C19 actionable alleles than European ancestry users of clopidrogrel (p < 0.0001, OR = 3.68).

CONCLUSIONS

Clinically actionable PGx alleles are highly prevalent in our health system and many patients were prescribed medications that could be affected by PGx alleles. These results illustrate the potential utility of preemptive genotyping for tailoring of medications and implementation of PGx into routine clinical care.

SARS-CoV-2 Seropositivity and Seroconversion in Patients Undergoing Active Cancer-Directed Therapy

PURPOSE

Multiple studies have demonstrated the negative impact of cancer care delays during the COVID-19 pandemic, and transmission mitigation techniques are imperative for continued cancer care delivery. We aimed to gauge the effectiveness of these measures at the University of Pennsylvania.

METHODS

We conducted a longitudinal study of SARS-CoV-2 antibody seropositivity and seroconversion in patients presenting to infusion centers for cancer-directed therapy between May 21, 2020, and October 8, 2020. Participants completed questionnaires and had up to five serial blood collections.

RESULTS

Of 124 enrolled patients, only two (1.6%) had detectable SARS-CoV-2 antibodies on initial blood draw, and no initially seronegative patients developed newly detectable antibodies on subsequent blood draw(s), corresponding to a seroconversion rate of 0% (95% CI, 0.0 TO 4.1%) over 14.8 person-years of follow up, with a median of 13 health care visits per patient.

CONCLUSION

These results suggest that patients with cancer receiving in-person care at a facility with aggressive mitigation efforts have an extremely low likelihood of COVID-19 infection.

A unified framework identifies new links between plasma lipids and diseases from electronic medical records across large-scale cohorts

Plasma lipids are known heritable risk factors for cardiovascular disease, but increasing evidence also supports shared genetics with diseases of other organ systems. We devised a comprehensive three-phase framework to identify new lipid-associated genes and study the relationships among lipids, genotypes, gene expression and hundreds of complex human diseases from the Electronic Medical Records and Genomics (347 traits) and the UK Biobank (549 traits). Aside from 67 new lipid-associated genes with strong replication, we found evidence for pleiotropic SNPs/genes between lipids and diseases across the phenome. These include discordant pleiotropy in the HLA region between lipids and multiple sclerosis and putative causal paths between triglycerides and gout, among several others. Our findings give insights into the genetic basis of the relationship between plasma lipids and diseases on a phenome-wide scale and can provide context for future prevention and treatment strategies.

SARS-CoV-2 seropositivity and seroconversion in patients undergoing active cancer-directed therapy

Multiple studies have demonstrated the negative impact of cancer care delays during the COVID-19 pandemic, and transmission mitigation techniques are imperative for continued cancer care delivery. To gauge the effectiveness of these measures at the University of Pennsylvania, we conducted a longitudinal study of SARS-CoV-2 antibody seropositivity and seroconversion in patients presenting to infusion centers for cancer-directed therapy between 5/21/2020 and 10/8/2020. Participants completed questionnaires and had up to five serial blood collections. Of 124 enrolled patients, only two (1.6%) had detectable SARS-CoV-2 antibodies on initial blood draw, and no initially seronegative patients developed newly detectable antibodies on subsequent blood draw(s), corresponding to a seroconversion rate of 0% (95%CI 0.0-4.1%) over 14.8 person-years of follow up, with a median of 13 healthcare visits per patient. These results suggest that cancer patients receiving in-person care at a facility with aggressive mitigation efforts have an extremely low likelihood of COVID-19 infection.

A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans

We performed a hypothesis-generating phenome-wide association study (PheWAS) to identify and characterize cross-phenotype associations, where one SNP is associated with two or more phenotypes, between thousands of genetic variants assayed on the Metabochip and hundreds of phenotypes in 5,897 African Americans as part of the Population Architecture using Genomics and Epidemiology (PAGE) I study. The PAGE I study was a National Human Genome Research Institute-funded collaboration of four study sites accessing diverse epidemiologic studies genotyped on the Metabochip, a custom genotyping chip that has dense coverage of regions in the genome previously associated with cardio-metabolic traits and outcomes in mostly European-descent populations. Here we focus on identifying novel phenome-genome relationships, where SNPs are associated with more than one phenotype. To do this, we performed a PheWAS, testing each SNP on the Metabochip for an association with up to 273 phenotypes in the participating PAGE I study sites. We identified 133 putative pleiotropic variants, defined as SNPs associated at an empirically derived p-value threshold of p<0.01 in two or more PAGE study sites for two or more phenotype classes. We further annotated these PheWAS-identified variants using publicly available functional data and local genetic ancestry. Amongst our novel findings is SPARC rs4958487, associated with increased glucose levels and hypertension. SPARC has been implicated in the pathogenesis of diabetes and is also known to have a potential role in fibrosis, a common consequence of multiple conditions including hypertension. The SPARC example and others highlight the potential that PheWAS approaches have in improving our understanding of complex disease architecture by identifying novel relationships between genetic variants and an array of common human phenotypes.

Collective feature selection to identify crucial epistatic variants

Background

Machine learning methods have gained popularity and practicality in identifying linear and non-linear effects of variants associated with complex disease/traits. Detection of epistatic interactions still remains a challenge due to the large number of features and relatively small sample size as input, thus leading to the so-called "short fat data" problem. The efficiency of machine learning methods can be increased by limiting the number of input features. Thus, it is very important to perform variable selection before searching for epistasis. Many methods have been evaluated and proposed to perform feature selection, but no single method works best in all scenarios. We demonstrate this by conducting two separate simulation analyses to evaluate the proposed collective feature selection approach.

Results

Through our simulation study we propose a collective feature selection approach to select features that are in the "union" of the best performing methods. We explored various parametric, non-parametric, and data mining approaches to perform feature selection. We choose our top performing methods to select the union of the resulting variables based on a user-defined percentage of variants selected from each method to take to downstream analysis. Our simulation analysis shows that non-parametric data mining approaches, such as MDR, may work best under one simulation criteria for the high effect size (penetrance) datasets, while non-parametric methods designed for feature selection, such as Ranger and Gradient boosting, work best under other simulation criteria. Thus, using a collective approach proves to be more beneficial for selecting variables with epistatic effects also in low effect size datasets and different genetic architectures. Following this, we applied our proposed collective feature selection approach to select the top 1% of variables to identify potential interacting variables associated with Body Mass Index (BMI) in ~ 44,000 samples obtained from Geisinger's MyCode Community Health Initiative (on behalf of DiscovEHR collaboration).

Conclusions

In this study, we were able to show that selecting variables using a collective feature selection approach could help in selecting true positive epistatic variables more frequently than applying any single method for feature selection via simulation studies. We were able to demonstrate the effectiveness of collective feature selection along with a comparison of many methods in our simulation analysis. We also applied our method to identify non-linear networks associated with obesity.

A simulation study investigating power estimates in phenome-wide association studies

Background

Phenome-wide association studies (PheWAS) are a high-throughput approach to evaluate comprehensive associations between genetic variants and a wide range of phenotypic measures. PheWAS has varying sample sizes for quantitative traits, and variable numbers of cases and controls for binary traits across the many phenotypes of interest, which can affect the statistical power to detect associations. The motivation of this study is to investigate the various parameters which affect the estimation of statistical power in PheWAS, including sample size, case-control ratio, minor allele frequency, and disease penetrance.

Results

We performed a PheWAS simulation study, where we investigated variations in statistical power based on different parameters, such as overall sample size, number of cases, case-control ratio, minor allele frequency, and disease penetrance. The simulation was performed on both binary and quantitative phenotypic measures. Our simulation on binary traits suggests that the number of cases has more impact on statistical power than the case to control ratio; also, we found that a sample size of 200 cases or more maintains the statistical power to identify associations for common variants. For quantitative traits, a sample size of 1000 or more individuals performed best in the power calculations. We focused on common genetic variants (MAF > 0.01) in this study; however, in future studies, we will be extending this effort to perform similar simulations on rare variants.

Conclusions

This study provides a series of PheWAS simulation analyses that can be used to estimate statistical power for some potential scenarios. These results can be used to provide guidelines for appropriate study design for future PheWAS analyses.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2135-0) contains supplementary material, which is available to authorized users.

Discovery and replication of SNP-SNP interactions for quantitative lipid traits in over 60,000 individuals

BACKGROUND

The genetic etiology of human lipid quantitative traits is not fully elucidated, and interactions between variants may play a role. We performed a gene-centric interaction study for four different lipid traits: low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), total cholesterol (TC), and triglycerides (TG).

RESULTS

Our analysis consisted of a discovery phase using a merged dataset of five different cohorts (n = 12,853 to n = 16,849 depending on lipid phenotype) and a replication phase with ten independent cohorts totaling up to 36,938 additional samples. Filters are often applied before interaction testing to correct for the burden of testing all pairwise interactions. We used two different filters: 1. A filter that tested only single nucleotide polymorphisms (SNPs) with a main effect of p < 0.001 in a previous association study. 2. A filter that only tested interactions identified by Biofilter 2.0. Pairwise models that reached an interaction significance level of p < 0.001 in the discovery dataset were tested for replication. We identified thirteen SNP-SNP models that were significant in more than one replication cohort after accounting for multiple testing.

CONCLUSIONS

These results may reveal novel insights into the genetic etiology of lipid levels. Furthermore, we developed a pipeline to perform a computationally efficient interaction analysis with multi-cohort replication.

ID: 109: PARKIN MEDIATES ENDOTHELIAL PRO-INFLAMMATORY RESPONSES IN ACUTE LUNG INJURY

Introduction

Acute lung injury (ALI) and its more severe form, the Acute Respiratory Distress Syndrome (ARDS), are serious conditions resulting from direct or indirect lung injury that occur in critically ill patients and are associated with an unacceptable mortality of up to 40%. A key biological event in the pathogenesis of ALI/ARDS is the dysfunction of the lung endothelium (EC), which is triggered by a variety of inflammatory insults leading to damaged EC, vascular leak, and excessive inflammation. Recently, we demonstrated that an Abl family tyrosine kinase inhibitor, imatinib, protects against LPS-induced endothelial dysfunction by inhibiting c-Abl kinase through mechanisms that remain largely unknown. In the present study, we identified parkin, a novel c-Abl substrate, as a critical mediator of endothelial dysfunction in ALI.

Methods

In vitro Human pulmonary artery endothelial cells (EC) were transfected with siRNA for parkin and then challenged with LPS (1 µg/ml, 3 hrs). Inflammatory mediators were determined in cell lysates and supernatants by Western blotting and ELISA respectively. In vivo C57BL/6 (WT) and parkin deficient (PARK2 KO) male mice (8–12 wks, n=5–8) were subjected to LPS (intratracheally, 1 mg/kg) or PBS (controls), and allowed to recover prior to harvest 18 hrs later. Leakage of proteins into the alveolar space was assessed by measuring the protein levels in the bronchoalveolar lavage (BAL). To assess lung inflammation, neutrophil cell counts, myeloperoxidase (MPO) activity, and IL-6 levels were determined in BAL.

Results

In human lung EC, down-regulation of parkin by siRNA reduces LPS-induced VCAM-1 expression (adhesion molecule involved in neutrophil adhesion to EC) (by 35%, p<0.05), IL-8 (neutrophil chemoattractant) (by 59%, p<0.01), and IL-6 (inflammatory cytokine) release (by 79%, p<0.01). PARK2 KO mice exhibit less ALI after LPS compared to WT. In PARK2 KO, BAL protein levels were reduced by 27% (p=0.0024) compared to WT mice. LPS-induced neutrophil recruitment into the alveoli of PARK2 KO was attenuated by 47% compared to WT (p=0.0019). BAL MPO activity (marker of neutrophil activation) and BAL IL-6 levels were also significantly lower in PARK2 KO by 52% (p=0.03) and 28% (p=0.0061) respectively.

Conclusion

These results suggest that endothelial parkin mediates EC activation and neutrophil adhesion/migration after LPS, and therefore it may represent a new potential therapeutic target in ALI/ARDS.

ID: 128: FTY720 S-PHOSPHONATE DOES NOT ACTIVATE GRK2-MEDIATED S1PR1 PHOSPHORYLATION AND DEGRADATION

Rationale

A significant and sustained increase in vascular permeability is a hallmark of acute inflammatory diseases such as acute lung injury (ALI), but effective therapies for preserving or reconstituting the vascular barrier are lacking. Prior work has demonstrated that FTY720 S-phosphonate (Tysiponate/Tys), an analog of sphingosine 1-phosphate (S1P) and FTY720, has more potent pulmonary barrier protective effects than these agents in vitro and in the LPS- and bleomycin-induced models of mouse ALI. Moreover, Tys preserves expression of the barrier promoting S1P1 receptor (S1PR1), whereas S1P and FTY720 induce its ubiquitination and degradation. In this report, we further characterize the mechanism of preservation of S1PR1 expression by Tys in cultured human pulmonary endothelial cells (EC).

Results

P-FTY720 significantly induced the association of S1PR1 and GRK2 and increased the p-serine content of S1PR1, which are critical for S1PR1 internalization and degradation, but Tys failed to do so. In contrast, both p-FTY720 and Tys induced significant tyrosine phosphorylation of S1PR1. Tys also preserves expression of S1PR2 and S1PR3. Although prior work reported that E3 ubiquitin-protein ligase WWP2 is critical for ubiquitination and degradation of S1PR1, neither p-FTY720 nor Tys changed its association with S1PR1 in human lung EC. Moreover, ubiquitin activating enzyme E1 inhibitor significantly inhibited S1PR1 degradation induced by p-FTY or S1P. Pharmacological inhibition of PKA, PKG, PKC, GSK3, PI3K, ERK, Src, or c-Abl activity, as well as inhibition of calcium flux, all fail to inhibit p-FTY720-induced S1PR1 degradation.

Conclusion

Unlike p-FTY720, Tys fails to activate the GRK2-mediated ubiquitination pathway and thus preserves S1PR1 expression. These results provide additional mechanistic insights into the barrier-regulatory effects of this potential ALI therapy.

ID: 124: ABL FAMILY KINASES MEDIATE LUNG VASCULAR PERMEABILITY AND INFLAMMATION IN ACUTE LUNG INJURY

Rationale

Acute respiratory distress syndrome (ARDS) is a life-threatening disease process in which overwhelming inflammation causes disruption of the pulmonary endothelial cell (EC) barrier, leading to leakage of fluid and inflammatory cells from the blood stream into the airspaces. Current research aims to identify agents that could both decrease inflammation and increase pulmonary vascular barrier integrity. Recently published work suggests that imatinib, an FDA-approved Abl family kinase inhibitor, may attenuate vascular leak and inflammation; however the mechanism underlying these effects is not completely understood. In the present study we explored the effects of LPS on the expression of the Abl family kinases, c-Abl and Arg, as well as the effects of Abl family kinases on LPS-induced vascular permeability and inflammation.

Methods

In silico analyses of the promoter regions of Abl1 (encodes c-Abl) and Abl2 (encodes Arg) were analyzed for potential responsive elements using the online programs Genomatix, TFsearch, and Jaspar. Cultured human pulmonary artery ECs were challenged with LPS (100 ng/mL, 24 hrs), harvested using RNeasy kit and reverse transcribed to cDNA. RT-PCR was performed to assess alterations in the expression of Abl1 and Abl2 after LPS challenge. In separate studies, siRNA was used to selectively silence either c-Abl or Arg and inter-endothelial gap formation was assessed by measuring FITC-dextran binding to a biotinylated avidin substrate. Complementary immunofluorescence studies were carried out to assess effects on adherens junction distributions. Western blotting was used to assess the effects of c-Abl and Arg silencing on NFkB phosphorylation.

Results

In silico analyses revealed that c-Abl contains two antioxidant responsive elements, whereas Arg contains two mechanical stress responsive elements. LPS treatment caused an increase in the mRNA expression of c-Abl (1.5 fold, p<0.05), without effecting Arg expression. Silencing c-Abl, but not Arg, attenuated LPS induced NFkB phosphorylation. However, silencing Arg, but not c-Abl attenuated inter-endothelial gap formation (41%, p<0.05) and adherens junction dissociation (figure 1).

Conclusions

The Abl family kinases c-Abl and Arg play complementary but distinct roles in mediating vascular permeability and inflammation following LPS challenge. The promoter of Abl1 (c-Abl) contains antioxidant response elements and LPS causes an increase in c-Abl expression. Additionally, LPS increases the mRNA expression of c-Abl, but not Arg. C-Abl contributes to LPS-induced NFκB signaling; whereas Arg contributes to inter-endothelial gap formation and adherens junction stability. Inhibition of both of these kinases may be of benefit in patients with ARDS.

ID: 131: ACTIN RELATED PROTEIN 2/3 COMPLEX REGULATES ACTIN MEMBRANE STRUCTURES TO DETERMINE ENDOTHELIAL BARRIER FUNCTION

Rationale

Disruption of the pulmonary endothelial barrier is a hallmark feature of sepsis and acute lung injury/ARDS. Cytoskeletal structures such as the peripheral protrusive structures lamellipodia and filopodia are hypothesized to be important determinants of endothelial barrier function. The actin related protein 2/3 complex (Arp 2/3) is a key regulator of branched actin polymerization and may play a role in the determination and recovery of endothelial cell (EC) barrier integrity. In the current study, we make detailed observations of actin structures and membrane formations in the presence of a specific Arp 2/3 inhibitor. In addition, we study the subcellular co-localization of Arp 2/3 and cortactin, another known protein regulator of peripheral actin dynamics.

Methods

Cultured human lung microvascular endothelial cells (HLMVEC) were subjected to pre-treatment with the specific Arp 2/3 inhibitor (CK-666 50 µM) or vehicle (DMSO) x 1 hour. Cells were then treated with barrier enhancing sphingosine-1-phosphate (S1P 1 µM) or barrier disruptive thrombin (1 U/ml) and fixed at various time points (2–90 min) for subsequent imaging. Cells were permeabilized and treated with far-red phalloidin to stain actin, an anti-cortactin-GFP mAb as well as DAPI and imaged by confocal microscopy. Peripheral actin formations and associated membrane lamellipodia and filopodia were then measured and characterized. Additionally, the co-localization of Arp 2/3 and cortactin was determined.

Results

Arp 2/3 inhibition markedly reduced lamellipodia formation in response to S1P (1 µM) over a range of time points (2–30 min). Lamellipodia depth was decreased in Arp 2/3 inhibited cells compared to control both at baseline (1.825 +/− 0.407 µM) vs. (2.545 +/− 0.459 µM) and following 30 min treatment with 1 µM S1P (1.534 +/− 0.365 µM) vs. (2.090 +/− 0.356 µM). Similarly, filopodia were shorter following Arp 2/3 inhibition (2.392 +/− 0.393 µM) vs. control (2.753 +/− 0.274 µM). Robust colocalization of Arp 2/3 and cortactin was observed very early (2–5 min) following S1P (1 µM) treatment in vehicle treated cells but was attenuated in the presence of the Arp 2/3 inhibitor. Following thrombin treatment (1 U/ml), peripheral lamellipodia were observed during the barrier recovery phase (30–60 min) but were markedly reduced following Arp 2/3 inhibition along with the persistence of intercellular gaps.

Conclusion

These results further demonstrate the importance of the Arp 2/3 complex in pulmonary endothelial barrier integrity and recovery. These experiments also serve to relate the concept of altered peripheral actin and membrane dynamics leading to changes in EC barrier function.

Pathway analysis by randomization incorporating structure-PARIS: an update

MOTIVATION

We present an update to the pathway enrichment analysis tool 'Pathway Analysis by Randomization Incorporating Structure (PARIS)' that determines aggregated association signals generated from genome-wide association study results. Pathway-based analyses highlight biological pathways associated with phenotypes. PARIS uses a unique permutation strategy to evaluate the genomic structure of interrogated pathways, through permutation testing of genomic features, thus eliminating many of the over-testing concerns arising with other pathway analysis approaches.

RESULTS

We have updated PARIS to incorporate expanded pathway definitions through the incorporation of new expert knowledge from multiple database sources, through customized user provided pathways, and other improvements in user flexibility and functionality.

AVAILABILITY AND IMPLEMENTATION

PARIS is freely available to all users at https://ritchielab.psu.edu/software/paris-download

CONTACT

jnc43@case.edu

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

INTEGRATING CLINICAL LABORATORY MEASURES AND ICD-9 CODE DIAGNOSES IN PHENOME-WIDE ASSOCIATION STUDIES

Electronic health records (EHR) provide a comprehensive resource for discovery, allowing unprecedented exploration of the impact of genetic architecture on health and disease. The data of EHRs also allow for exploration of the complex interactions between health measures across health and disease. The discoveries arising from EHR based research provide important information for the identification of genetic variation for clinical decision-making. Due to the breadth of information collected within the EHR, a challenge for discovery using EHR based data is the development of high-throughput tools that expose important areas of further research, from genetic variants to phenotypes. Phenome-Wide Association studies (PheWAS) provide a way to explore the association between genetic variants and comprehensive phenotypic measurements, generating new hypotheses and also exposing the complex relationships between genetic architecture and outcomes, including pleiotropy. EHR based PheWAS have mainly evaluated associations with case/control status from International Classification of Disease, Ninth Edition (ICD-9) codes. While these studies have highlighted discovery through PheWAS, the rich resource of clinical lab measures collected within the EHR can be better utilized for high-throughput PheWAS analyses and discovery. To better use these resources and enrich PheWAS association results we have developed a sound methodology for extracting a wide range of clinical lab measures from EHR data. We have extracted a first set of 21 clinical lab measures from the de-identified EHR of participants of the Geisinger MyCodeTM biorepository, and calculated the median of these lab measures for 12,039 subjects. Next we evaluated the association between these 21 clinical lab median values and 635,525 genetic variants, performing a genome-wide association study (GWAS) for each of 21 clinical lab measures. We then calculated the association between SNPs from these GWAS passing our Bonferroni defined p-value cutoff and 165 ICD-9 codes. Through the GWAS we found a series of results replicating known associations, and also some potentially novel associations with less studied clinical lab measures. We found the majority of the PheWAS ICD-9 diagnoses highly related to the clinical lab measures associated with same SNPs. Moving forward, we will be evaluating further phenotypes and expanding the methodology for successful extraction of clinical lab measurements for research and PheWAS use. These developments are important for expanding the PheWAS approach for improved EHR based discovery.

The Impact of Three Genospecies of Borrelia on Expression of Genes Associated with Chemokines and Their Receptors in Normal Human Dermal Fibroblasts in Vitro

An important role in pathomechanism of Lyme disease is played by the ability of spirochetes to spread within tissues, and to adhere (to platelets, erythrocytes and vascular epithelium). The principal factors regulating that process are chemokines, cytokines and adhesion particles. The aim of this study was to select genes related to the chemokines and their receptors, differentiating the type of infection in the system model, i.e. a culture of normal human diploid fibroblasts infected with three different spirochete genospecies: B. afzelii, B. garinii and B. burgdorferii sensu stricto, by comparing the infected fibroblast culture with that of the control fibroblast. The differences in the expression of genes selected on the basis of a scientific database Affymetrix were analysed by comparing transcriptomes from the four cultures of fibroblasts, using the oligonucleotide microarrays HG_U133A. In the result of infection of fibroblast cultivation with a specific Borrelia genospecies, a variable expression of the chemokines and their receptors, specific for one genospecies was observed. The fibroblast infected with B. afzelii expressed CCL4, CCL1, CCL2 and CCR10; with B. garinii - CXCL12, IL6, CCR3 and CXCR5; and with B. burgorferii sensu stricto - CCL5, CCR1, CCL3, CCL16, CXCR6, IL8, CXCR7 and CXCR3.

Visualizing genomic information across chromosomes with PhenoGram

Background

With the abundance of information and analysis results being collected for genetic loci, user-friendly and flexible data visualization approaches can inform and improve the analysis and dissemination of these data. A chromosomal ideogram is an idealized graphic representation of chromosomes. Ideograms can be combined with overlaid points, lines, and/or shapes, to provide summary information from studies of various kinds, such as genome-wide association studies or phenome-wide association studies, coupled with genomic location information. To facilitate visualizing varied data in multiple ways using ideograms, we have developed a flexible software tool called PhenoGram which exists as a web-based tool and also a command-line program.

Results

With PhenoGram researchers can create chomosomal ideograms annotated with lines in color at specific base-pair locations, or colored base-pair to base-pair regions, with or without other annotation. PhenoGram allows for annotation of chromosomal locations and/or regions with shapes in different colors, gene identifiers, or other text. PhenoGram also allows for creation of plots showing expanded chromosomal locations, providing a way to show results for specific chromosomal regions in greater detail. We have now used PhenoGram to produce a variety of different plots, and provide these as examples herein. These plots include visualization of the genomic coverage of SNPs from a genotyping array, highlighting the chromosomal coverage of imputed SNPs, copy-number variation region coverage, as well as plots similar to the NHGRI GWA Catalog of genome-wide association results.

Conclusions

PhenoGram is a versatile, user-friendly software tool fostering the exploration and sharing of genomic information. Through visualization of data, researchers can both explore and share complex results, facilitating a greater understanding of these data.

Phenome-wide association study (PheWAS) for detection of pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network

Using a phenome-wide association study (PheWAS) approach, we comprehensively tested genetic variants for association with phenotypes available for 70,061 study participants in the Population Architecture using Genomics and Epidemiology (PAGE) network. Our aim was to better characterize the genetic architecture of complex traits and identify novel pleiotropic relationships. This PheWAS drew on five population-based studies representing four major racial/ethnic groups (European Americans (EA), African Americans (AA), Hispanics/Mexican-Americans, and Asian/Pacific Islanders) in PAGE, each site with measurements for multiple traits, associated laboratory measures, and intermediate biomarkers. A total of 83 single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) were genotyped across two or more PAGE study sites. Comprehensive tests of association, stratified by race/ethnicity, were performed, encompassing 4,706 phenotypes mapped to 105 phenotype-classes, and association results were compared across study sites. A total of 111 PheWAS results had significant associations for two or more PAGE study sites with consistent direction of effect with a significance threshold of p<0.01 for the same racial/ethnic group, SNP, and phenotype-class. Among results identified for SNPs previously associated with phenotypes such as lipid traits, type 2 diabetes, and body mass index, 52 replicated previously published genotype-phenotype associations, 26 represented phenotypes closely related to previously known genotype-phenotype associations, and 33 represented potentially novel genotype-phenotype associations with pleiotropic effects. The majority of the potentially novel results were for single PheWAS phenotype-classes, for example, for CDKN2A/B rs1333049 (previously associated with type 2 diabetes in EA) a PheWAS association was identified for hemoglobin levels in AA. Of note, however, GALNT2 rs2144300 (previously associated with high-density lipoprotein cholesterol levels in EA) had multiple potentially novel PheWAS associations, with hypertension related phenotypes in AA and with serum calcium levels and coronary artery disease phenotypes in EA. PheWAS identifies associations for hypothesis generation and exploration of the genetic architecture of complex traits.

A cross-validation procedure for general pedigrees and matched odds ratio fitness metric implemented for the multifactor dimensionality reduction pedigree disequilibrium test

As genetic epidemiology looks beyond mapping single disease susceptibility loci, interest in detecting epistatic interactions between genes has grown. The dimensionality and comparisons required to search the epistatic space and the inference for a significant result pose challenges for testing epistatic disease models. The multifactor dimensionality reduction-pedigree disequilibrium test (MDR-PDT) was developed to test for multilocus models in pedigree data. In the present study we rigorously tested MDR-PDT with new cross-validation (CV) (both 5- and 10-fold) and omnibus model selection algorithms by simulating a range of heritabilities, odds ratios, minor allele frequencies, sample sizes, and numbers of interacting loci. Power was evaluated using 100, 500, and 1,000 families, with minor allele frequencies 0.2 and 0.4 and broad-sense heritabilities of 0.005, 0.01, 0.03, 0.05, and 0.1 for 2- and 3-locus purely epistatic penetrance models. We also compared the prediction error (PE) measure of effect with a predicted matched odds ratio (MOR) for final model selection and testing. We report that the CV procedure is valid with the permutation test, MDR-PDT performs similarly with 5- and 10-fold CV, and that the MOR is more powerful than PE as the fitness metric for MDR-PDT.

Differences in staining of the unicellular algae Chlorococcales as a function of algaenan content

Algal strains belonging to the Chlorococcales (Chlorophyceae) show significant differences in the extent of staining with the commonly used dye, crystalline violet. This seems to depend on the cell wall composition and on the occurrence of the acetolysis-resistant biopolymer algaenan in the algal cells.Eighteen algal strains were investigated using 24 h staining with 0.2% crystalline violet and it was confirmed that algal strains which did not contain algaenan and had a trilaminar structure in the cell wall showed strong staining ability, while non-algaenan strains were stained very weakly, if at all. The simple method presented here may be helpful to distinguish both kinds of algal strains.

Exploring the performance of Multifactor Dimensionality Reduction in large scale SNP studies and in the presence of genetic heterogeneity among epistatic disease models

BACKGROUND/AIMS

In genetic studies of complex disease a consideration for the investigator is detection of joint effects. The Multifactor Dimensionality Reduction (MDR) algorithm searches for these effects with an exhaustive approach. Previously unknown aspects of MDR performance were the power to detect interactive effects given large numbers of non-model loci or varying degrees of heterogeneity among multiple epistatic disease models.

METHODS

To address the performance with many non-model loci, datasets of 500 cases and 500 controls with 100 to 10,000 SNPs were simulated for two-locus models, and one hundred 500-case/500-control datasets with 100 and 500 SNPs were simulated for three-locus models. Multiple levels of locus heterogeneity were simulated in several sample sizes.

RESULTS

These results show MDR is robust to locus heterogeneity when the definition of power is not as conservative as in previous simulation studies where all model loci were required to be found by the method. The results also indicate that MDR performance is related more strongly to broad-sense heritability than sample size and is not greatly affected by non-model loci.

CONCLUSIONS

A study in which a population with high heritability estimates is sampled predisposes the MDR study to success more than a larger ascertainment in a population with smaller estimates.

Regulation of gene expression by action potentials: dependence on complexity in cellular information processing

Nervous system development and plasticity are regulated by neural impulse activity, but it is not well understood how the pattern of action potential firing could regulate the expression of genes responsible for long-term adaptive responses in the nervous system. Studies on mouse sensory neurons in cell cultures equipped with stimulating electrodes show that specific genes can be regulated by different patterns of action potentials, and that the temporal dynamics of intracellular signalling cascades are critical in decoding and integrating information contained in the pattern of neural impulse activity. Functional consequences include effects on neurite outgrowth, cell adhesion, synaptic plasticity and axon-glial interactions. Signalling pathways involving Ca2+, CaM KII, MAPK and CREB are particularly important in coupling action potential firing to the transcriptional regulation of both neurons and glia, and in the conversion of short-term to long-term memory. Action potentials activate multiple convergent and divergent pathways, and the complex network properties of intracellular signalling and transcriptional regulatory mechanisms contribute to spike frequency decoding.

Differential regulation of alternatively spliced endothelial cell myosin light chain kinase isoforms by p60(Src)

The Ca(2+)/calmodulin-dependent endothelial cell myosin light chain kinase (MLCK) triggers actomyosin contraction essential for vascular barrier regulation and leukocyte diapedesis. Two high molecular weight MLCK splice variants, EC MLCK-1 and EC MLCK-2 (210-214 kDa), in human endothelium are identical except for a deleted single exon in MLCK-2 encoding a 69-amino acid stretch (amino acids 436-505) that contains potentially important consensus sites for phosphorylation by p60(Src) kinase (Lazar, V., and Garcia, J. G. (1999) Genomics 57, 256-267). We have now found that both recombinant EC MLCK splice variants exhibit comparable enzymatic activities but a 2-fold reduction of V(max), and a 2-fold increase in K(0.5 CaM) when compared with the SM MLCK isoform, whereas K(m) was similar in the three isoforms. However, only EC MLCK-1 is readily phosphorylated by purified p60(Src) in vitro, resulting in a 2- to 3-fold increase in EC MLCK-1 enzymatic activity (compared with EC MLCK-2 and SM MLCK). This increased activity of phospho-MLCK-1 was observed over a broad range of submaximal [Ca(2+)] levels with comparable EC(50) [Ca(2+)] for both phosphorylated and unphosphorylated EC MLCK-1. The sites of tyrosine phosphorylation catalyzed by p60(Src) are Tyr(464) and Tyr(471) within the 69-residue stretch deleted in the MLCK-2 splice variant. These results demonstrate for the first time that p60(Src)-mediated tyrosine phosphorylation represents an important mechanism for splice variant-specific regulation of nonmuscle MLCK and vascular cell function.

Limited tryptic hydrolysis of pea legumin: molecular mass and conformational stability of legumin-T

The investigation of hydrodynamic and thermodynamic properties and the determination of the molecular mass of legumin-T, the product of limited tryptic hydrolysis of the 11-S-globulin from pea seeds, was carried out to ascertain the structural relationship to globulin-T's from other legumin-like proteins. The obtained legumin-T preparation has a molecular mass M(W)=260+/-10 kDa and M(S,D)=270+/-20 kDa. The secondary structure of legumin-T is characterised by a high percentage of beta-sheet conformation, comparable to that of native legumin and a reduced percentage of helical conformation. The conformational stability of legumin-T evaluated by equilibrium unfolding in the presence of guanidinium chloride was only slightly reduced in comparison to the native legumin, whereas the calorimetrically determined denaturation enthalpy and Gibbs energy of denaturation were found to be increased for legumin-T. These physicochemical properties are very similar to those of faba bean legumin-T.

Changes in interfacial behaviour, emulsifying and foaming properties of faba bean legumin after modification with dimethylsuberimidate

The effect of a rising rigidity and surface hydrophobicity of the 11S storage protein from faba beans--legumin--induced by chemical modification with dimethylsuberimidate (DMS) on some surface functional properties was studied. Short-time adsorption kinetics using a droplet-volume tensiometer, pressure transformation and desorption behaviour of monolayer using a film balance, and emulsifying and foaming properties were determined to characterize surface activity and interfacial film forming behaviour. Tensio-active properties at the air-water interface, i.e. decay in surface tension and pressure transformation in monolayer, were improved by modification. However, a decrease in emulsifying activity, foam capacity and foam expansion after modification of the legumin points to an overall deterioration of energy-induced film forming behaviour. The results support the view that surface activity is generally governed more by molecular flexibility than by surface hydrophobicity.

Phosphorylation of the 12S globulin from rapeseed (Brassica napus L.) by phosphorous oxychloride: chemical and conformational aspects

The effect of progressive phosphorylation by phosphorous oxychloride upon the conformation of the 300 kDa storage protein (cruciferin) from rapeseed has been studied using chemical analysis, SDS-PAGE, HPLC, analytical ultracentrifugation, viscometry, fluorescence spectroscopy, and hydrophobicity measurement. The amount of phosphorous in the protein increased with the excess of phosphorous oxychloride and the pH of reaction. The bulk of phosphorus was only loosely bound to the protein and was removed by washing with cold perchloric acid. The more stably bound phosphorus groups after reaction at pH 8 were found to be nearly equally attached to amino and hydroxyl groups, whereas phosphorylation at pH 10-11 led to predominant O-phosphorylation as detected by studying the acid- and alkali-lability of the protein-phosphorous bonds. A 50 kDa component appeared as a product of covalent cross-linking of the constituent alpha- and beta-polypeptide chains. A 2.5S fraction appeared as the main product of dissociation, which takes place after a critical step of modification. The higher the extent of phosphorylation, the larger was the percentage of higher molecular weight products, the percentage of which was most significant after modification under strongly alkaline conditions. They may be attributed both to products of chemical cross-linking and to noncovalently linked aggregates formed by interactions of partially unfolded derivatives exhibiting an increased surface hydrophobicity.

Genetic variation within and among populations of Arabidopsis thaliana

We investigated levels of nucleotide polymorphism within and among populations of the highly self-fertilizing Brassicaceous species, Arabidopsis thaliana. Four-cutter RFLP data were collected at one mitochondrial and three nuclear loci from 115 isolines representing 11 worldwide population collections, as well as from seven commonly used ecotypes. The collections include multiple populations from North America and Eurasia, as well as two pairs of collections from locally proximate sites, and thus allow a hierarchical geographic analysis of polymorphism. We found no variation at the mitochondrial locus Nad5 and very low levels of intrapopulation nucleotide diversity at Adh, Dhs1, and Gpa1. Interpopulation nucleotide diversity was also consistently low among the loci, averaging 0.0014. gst, a measure of population differentiation, was estimated to be 0.643. Interestingly, we found no association between geographical distance between populations and genetic distance. Most haplotypes have a worldwide distribution, suggesting a recent expansion of the species or long-distance gene flow. The low level of polymorphism found in this study is consistent with theoretical models of neutral mutations and background selection in highly self-fertilizing species.

Dosimetric comparison of bolus and continuous injections of CC49 monoclonal antibody in a colon cancer xenograft model

BACKGROUND

Improved understanding of dose and effective dose calculations may contribute to the optimization of fractionated radioimmunotherapy.

METHODS

Comparison three-dimensional tumor dosimetry was performed on athymic nude mice bearing established LS174T human colon carcinoma xenografts. Mice were given bolus intraperitoneal injections of 300 microCi 131I-labeled CC49 monoclonal antibody once (Day 0) or three times (Days 0, 3, and 7) or continuous intraperitoneal infusion with miniosmotic pumps over 7 days. Serial section autoradiography was used to reconstruct tumor activity density distributions for Days 3, 4, 7, 10, and 11 (single injection); Days 3, 4, 7, 8, and 11 (3 injections); and Days 4, 7, 10, and 13 (pump). At least three tumors were reconstructed at each time point. Uptakes in blood and tumor were measured up to 14 days (single injection), 11 days (3 injections), or 16 days (pump) after injection.

RESULTS

Average dose values calculated from total activity uptake data only (assuming no energy loss external to the tumor) yielded 102 Gy (single injection), 158 Gy (three injections), and 47 Gy (pump). Average doses using three-dimensional dose calculations were 88 Gy, 139 Gy, and 40 Gy, respectively. The nonuniformity of dose deposition affects treatment outcome, because cell loss is an exponential function of dose. Using the linear quadratic model with fractional cell survival to define an effective dose, D(eff) were calculated to be 20 Gy, 23 Gy, and 14 Gy, respectively. Cell proliferation affects outcome for variable dose-rate treatments. With cell proliferation parameters set to reproduce single-fraction 60Co recurrence results, D(eff) (for local control endpoint) were 8.9 Gy, 12.8 Gy, and 3.9 Gy, respectively. Three bolus injections compared with a single bolus injection were relatively less efficient in tumor uptake. However, three bolus injections resulted in a more uniform dose rate over a longer period, resulting in a 50% improvement in D(eff). The slower dose delivery for pump infusion resulted in a significantly lower D(eff), although dose-rate distributions were more uniform compared with the single bolus injection.

CONCLUSIONS

Improvement in dose-rate nonuniformities was observed for fractionated and continuous radiolabeled monoclonal antibody injections. Fractionated injections produced superior dosimetric results compared with single bolus or continuous injections.

Structural and functional changes of faba bean legumin during super-limited tryptic hydrolysis

The influence of a super-limited tryptic hydrolysis on physicochemical and surface functional properties of faba bean legumin has been studied using size-exclusion HPLC, SDS-PAGE, UV and fluorescence spectroscopy, fluorescence probe techniques, surface tension measurements as well as determination of emulsifying activity index (EAI) and emulsion droplets diameter (D). The extent of legumin hydrolysis comprised the range between about 14 and 60 split peptide bonds per molecule resulting in a stepwise decrease of legumin molecular weight to 240 kDa (legumin-T) via discrete intermediates with characteristic subunit patterns. These changes are accompanied by an increase in the surface hydrophobicity and the exposure of aromatic chromophores. No differences were found in the surface tension between the variously hydrolyzed legumin samples. Best emulsifying properties (highest EAI and lowest D values) were attained after a rather low tryptic hydrolysis (about 30 split peptide bonds per mol). Further hydrolysis impaired the emulsifying parameter which were, however, higher (EAI) or lower (D) than those for native legumin.

Prostatic ductal system in rats: regional variation in localization of an androgen-repressed gene product, sulfated glycoprotein-2

The rat prostate is a complex ductal system with branches and subbranches extending from one end to another. Owing to the relative distance of various regions from the urethra, the entire length of the ductal system can be divided into three segments, i.e. the proximal, intermediate, and distal segments. The present study was carried out to examine the pattern of localization of sulfated glycoprotein-2 (SGP-2), a marker protein associated with programmed cell death, in various regions of the prostatic ductal system under normal conditions and during castration-induced regression. SGP-2 has been considered an androgen-repressed gene product in the rat prostate and has previously been known as castration-induced protein or TRPM-2. In the normal rat prostate, immunoreactive SGP-2 was localized in epithelial cells lining the proximal segment in which signs of programmed cell death were apparent. Cells lining the distal and intermediate segments were, however, devoid of SGP-2. This observed regional variation in SGP-2 localization did not support an earlier hypothesis which stated that SGP-2 was constitutively expressed by all prostatic epithelial cells in the normal rat prostate. After castration in adult rats, there was a shift in the location of cells containing SGP-2 from the proximal segment toward the distal segment. Therefore, there is a regional variation in the distribution of SGP-2 in the rat prostate both before and after castration in the host. These findings are likely to be associated with a regional variation in cellular responsiveness to androgen stimulation and androgen depletion in the prostatic ductal system. Results also support the view that SGP-2 localization is associated with an early manifestation of programmed cell death in the rat prostate.

High-performance liquid chromatographic method for the study of solvent effects on the peptidase and esterase activity of thermitase

The high-performance liquid chromatographic separation of enzymatic degradation products of a multi-functional peptide substrate under isocratic conditions is described. This technique was applied to the study of solvent effects on the peptidase and esterase activity of thermitase.

Long-lasting physiological effects of bath applied N-methyl-D-aspartate

The present experiments describe a long-lasting form of potentiation induced in field CA1 of rat hippocampal slices by bath application of N-methyl-D-aspartate (NMDA), in association with low magnesium concentrations, glycine and spermine. The potentiation effect consisted of a 50% increase in slope of field potentials and was stable for at least 80 min post treatment. It was not accompanied by detectable changes in antidromic responses and was completely blocked by an antagonist of NMDA receptor. The possible relationship of pharmacologically induced potentiation to long-term potentiation (LTP) is discussed.

Calmodulin stimulates the degradation of brain spectrin by calpain

Brain spectrin has been shown to be a preferential substrate of calcium-dependent proteases (Baudry, Bundman, Smith, and Lynch: Science 212:937-938, 1981) and a major calmodulin-binding protein (Kakiuchi, Sobue, and Fujita: FEBS Lett. 132:144-148, 1981). Since calmodulin, spectrin, and a proteolytically derived spectrin fragment are all components of isolated postsynaptic density preparations (Grab, Berzins, Cohen, and Siekevitz: J. Biol. Chem. 254:8690-8696, 1979; Carlin, Bartelt, and Siekevitz: J. Cell Biol. 96:443-448, 1983), we investigated the functional role of calmodulin binding to brain spectrin with respect to its susceptibility to digestion by proteases. We report that calmodulin's interaction with brain spectrin results in a marked acceleration of the rate of spectrin degradation by calcium-dependent proteases (calpains I and II), but not by chymotrypsin. The cleavage of erythrocyte spectrin (which lacks a high-affinity calmodulin binding site) by calpain I is unaffected by the presence of calmodulin. The stimulatory effect of calmodulin is blocked by trifluoperazine, a calmodulin antagonist, which by itself does not modify brain spectrin proteolysis by calcium-dependent proteases. These results suggest a novel role for calmodulin in neuronal function--namely, a synergistic interaction with calcium-dependent proteases in the regulation of cytoskeletal integrity.

Sex differences in the performance of school children

Marked and consistent differences in academic performance between boys and girls were found in a longitudinal study of young school-age children. Performance, measured by objective tests administered by a psychologist, was higher in girls in all grades (Grade I to Grade V). However, tests of intelligence, perceptual maturity and conceptual ability showed no sex-linked differences — the only tests favouring the girls were those of motor ability. To explain the better academic performance of female children, personality attributes were considered (C.P.I.). Statistically significant differences were found in three personality dimensions: girls were found to be obedient and dependent, sober-minded and quiet, practical and realistic. In contrast the boys were found to be assertive and independent, excitable and happy-go-lucky, sensitive and free thinking. The significance of these findings is discussed in terms of academic achievement and also in terms of culturally-determined sex-typing of young children.