A multi-organ map of the human immune system across age, sex and ethnicity.

Understanding tissue biology's heterogeneity is crucial for advancing precision medicine. Despite the centrality of the immune system in tissue homeostasis, a detailed and comprehensive map of immune cell distribution and interactions across human tissues and demographics remains elusive. To fill this gap, we harmonised data from 12,981 single-cell RNA sequencing samples and curated 29 million cells from 45 anatomical sites to create a comprehensive compositional and transcriptional healthy map of the healthy immune system. We used this resource and a novel multilevel modelling approach to track immune ageing and test differences across sex and ethnicity. We uncovered conserved and tissue-specific immune-ageing programs, resolved sex-dependent differential ageing and identified ethnic diversity in clinically critical immune checkpoints. This study provides a quantitative baseline of the immune system, facilitating advances in precision medicine. By sharing our immune map, we hope to catalyse further breakthroughs in cancer, infectious disease, immunology and precision medicine.

Diet type and changes in food cravings following weight loss: findings from the POUNDS LOST Trial.

Few well-controlled trials have evaluated the effects that macronutrient composition has on changes in food cravings during weight loss treatment. The present study, which was part of the Preventing Overweight Using Novel Dietary Strategies (POUNDS LOST) trial, investigated whether the fat and protein content of four different diets affected changes in specific food cravings in overweight and obese adults. A sample of 811 adults were recruited across two clinical sites, and each participant was randomly assigned to one of four macronutrient prescriptions: 1) low fat (20% of energy), average protein (15% of energy); 2) moderate fat (40%), average protein (15%); 3) low fat (20%), high protein (25%); 4) moderate fat (40%), high protein (25%). With few exceptions, the type of diet that participants were assigned did not differentially affect changes in specific food cravings. Participants assigned to the high-fat diets, however, had reduced cravings for carbohydrates at month 12 (p<0.05) and fruits and vegetables at month 24. Also, participants assigned to high-protein diets had increased cravings for sweets at month 6 and month 12 (ps<0.05). Participants in all four dietary conditions reported significant reductions in food cravings for specific types of foods (i.e., high fat foods, fast food fats, sweets, and carbohydrates/starches; all ps<0.05). Cravings for fruits and vegetables, however, were increased at month 24 (p<0.05). Calorically restricted diets (regardless of their macronutrient composition) yielded significant reductions in cravings for fats, sweets, and starches whereas cravings for fruits and vegetables were increased.

Interpreting genetics of gene expression: integrative architecture in Bioconductor.

Several influential studies of genotypic determinants of gene expression in humans have now been published based on various populations including HapMap cohorts. The magnitude of the analytic task (transcriptome vs. SNP-genome) is a hindrance to dissemination of efficient, thorough, and auditable inference methods for this project. We describe the structure and use of Bioconductor facilities for inference in genetics of gene expression, with simultaneous application to multiple HapMap cohorts. Tools distributed for this purpose are readily adapted for the structure and analysis of privately-generated data in expression genetics.

Polymorphic variation in surfactant protein B is associated with COPD exacerbations.

Exacerbations of chronic obstructive pulmonary disease (COPD) reduce quality of life and increase mortality. Genetic variation might explain the substantial variability seen in exacerbation frequency among COPD subjects with similar lung function. Polymorphisms in five candidate genes, previously associated with COPD susceptibility, were analysed in order to determine whether they demonstrated association with COPD exacerbations. A total of 88 single nucleotide polymorphisms (SNPs) in the genes microsomal epoxide hydrolase (EPHX1), transforming growth factor, beta-1 (TGFB1), serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2 (SERPINE2), glutathione S-transferase pi (GSTP1) and surfactant protein B (SFTPB) were genotyped in 389 non-Hispanic white participants in the National Emphysema Treatment Trial. Exacerbations were defined as COPD-related emergency room visits or hospitalisations using the Centers for Medicare and Medicaid Services claims data. One or more exacerbations were experienced by 216 (56%) subjects during the study period. An SFTPB promoter polymorphism, rs3024791, was associated with COPD exacerbations. Logistic regression models, analysing a binary outcome of presence or absence of exacerbations, confirmed the association of rs3024791 with COPD exacerbations. Negative binomial regression models demonstrated association of multiple SFTPB SNPs (rs2118177, rs2304566, rs1130866 and rs3024791) with exacerbation rates. Polymorphisms in EPHX1, GSTP1, TGFB1 and SERPINE2 did not demonstrate association with COPD exacerbations. In conclusion, genetic variation in surfactant protein B is associated with chronic obstructive pulmonary disease susceptibility and exacerbation frequency.

SGDI: system for genomic data integration.

This paper describes a framework for collecting, annotating, and archiving high-throughput assays from multiple experiments conducted on one or more series of samples. Specific applications include support for large-scale surveys of related transcriptional profiling studies, for investigations of the genetics of gene expression and for joint analysis of copy number variation and mRNA abundance. Our approach consists of data capture and modeling processes rooted in R/Bioconductor, sample annotation and sequence constituent ontology management based in R, secure data archiving in PostgreSQL, and browser-based workspace creation and management rooted in Zope. This effort has generated a completely transparent, extensible, and customizable interface to large archives of high-throughput assays. Sources and prototype interfaces are accessible at www.sgdi.org/software.

Deregulated expression of fat and muscle genes in B-cell chronic lymphocytic leukemia with high lipoprotein lipase expression.

Lipoprotein lipase (LPL) is a prognostic marker in B-cell chronic lymphocytic leukemia (B-CLL) related to immunoglobulin V(H) gene (IgV(H))mutational status. We determined gene expression profiles using Affymetrix U133A GeneChips in two groups of B-CLLs selected for either high ('LPL+', n=10) or low ('LPL-', n=10) LPL mRNA expression. Selected genes were verified by real-time PCR in an extended patient cohort (n=42). A total of 111 genes discriminated LPL+ from LPL- B-CLLs. Of these, the top three genes associated with time to first treatment were Septin10, DMD and Gravin (P

Distribution of four capsular serotypes of Enterococcus faecalis among clinical isolates from different geographical origins and infection sites.

BACKGROUND: Enterococci possess capsular polysaccharide antigens that are the targets of opsonic antibodies. These antibodies are potential candidates for development as immunotherapy. MATERIAL AND METHODS: The present study analyzes the distribution of four capsular serotypes within a collection of 157 isolates of Enterococcus faecalis from four countries with different sites of clinical infection. RESULTS: By using a capsular polysaccharide-specific ELISA, 42% of the isolates were grouped into one of four serogroups, and another 9% showed cross-reactivity between two serotype-specific sera. Heterogeneity of serotype distribution by both geographical origin and infection site was observed. CONCLUSION: Half of the strain collection could be typed with four serotype-specific sera. No serotype from a given country or infection site clearly predominated.

Familial aggregation of FEF(25-75) and FEF(25-75)/FVC in families with severe, early onset COPD.

BACKGROUND: The Boston Early-Onset COPD study showed that current or ex-smoking first degree relatives of severe early onset COPD probands have significantly lower forced expiratory volume in 1 second (FEV(1)) and FEV(1)/forced vital capacity (FVC) values than current or ex-smoking control subjects, which suggests the existence of genetic risk factors for the development of COPD in response to cigarette smoking. We hypothesised that first degree relatives of early onset COPD probands may also have lower values of spirometric parameters such as forced expiratory flow at the mid-portion of forced vital capacity (FEF(25-75)) and FEF(25-75)/FVC. METHODS: Using generalised estimating equations, FEF(25-75) and FEF(25-75)/FVC were analysed in 333 first degree relatives of probands with severe early onset COPD and 83 population based controls; analyses were also performed on data stratified by smoking status. Narrow sense heritability estimates were calculated using a variance component approach. RESULTS: Significantly lower FEF(25-75) and FEF(25-75)/FVC were observed in smoking (FEF(25-75): beta -0.788 l/s (95% CI -1.118 to -0.457), FEF(25-75)/FVC: beta -20.4% (95% CI -29.3 to -11.6, p<0.0001 for both phenotypes) and non-smoking (FEF(25-75): beta -0.357 l/s (95% CI -0.673 to -0.041, p = 0.0271), FEF(25-75)/FVC: beta -9.5% (95% CI -17.1 to -1.9, p = 0.0145)) first degree relatives of early onset COPD probands. Narrow sense heritability estimates for FEF(25-75) (h(2) = 0.38) and FEF(25-75)/FVC (h(2) = 0.45) were similar to those for FEV(1) and FEV(1)/FVC. CONCLUSION: Lower values of FEF(25-75) and FEF(25-75)/FVC in non-smoking first degree relatives of early onset COPD probands than in controls suggest a genetic susceptibility to develop obstructive lung disease, independent of smoking, which is magnified by exposure to deleterious environments as suggested by the further decrements in FEF(25-75) and FEF(25-75)/FVC seen in smoking first degree relatives. FEF(25-75) and FEF(25-75)/FVC have high heritability and are important intermediate phenotypes for inclusion in genetic epidemiological studies of COPD.

Growth velocity assessment in paediatric AIDS: smoothing, penalized quantile regression and the definition of growth failure.

The analysis of growth records in paediatric anti-HIV clinical trials plays an important role in trial evaluation. Growth failure may be a manifestation of progressive disease or treatment toxicity, and is commonly specified as a major trial outcome event indicating poor treatment performance. Despite new therapeutic advances against HIV proliferation in infected patients, accurate monitoring and interpretation of somatic growth in paediatric AIDS remains clinically important, in light of uncertainties regarding relationship between viral load reductions and achievement of favourable somatic growth profiles. Our aim in this paper is to construct a criterion for growth failure that discriminates patients whose risk of death subsequent to growth failure is elevated to a clinically significant degree. To construct the criterion, individual growth curves and velocities are modelled using loess smoothing, penalized likelihood quantile regressions are fit to model age-specific growth velocity distributions for gender-stratified cohorts, and proportional hazards model selection is conducted to identify features of velocity series that are informative on the survival distribution. The resulting growth-failure criterion is expected to be useful for disease staging in resource-limited medical environments where T-cell counts and viral load measures are unavailable.

Tandem repeat deletion in the alpha C protein of group B streptococcus is recA independent.

Group B streptococci (GBS) contain a family of protective surface proteins characterized by variable numbers of repeating units within the proteins. The prototype alpha C protein of GBS from the type Ia/C strain A909 contains a series of nine identical 246-bp tandem repeat units. We have previously shown that deletions in the tandem repeat region of the alpha C protein affect both the immunogenicity and protective efficacy of the protein in animal models, and these deletions may serve as a virulence mechanism in GBS. The molecular mechanism of tandem repeat deletion is unknown. To determine whether RecA-mediated homologous recombination is involved in this process, we identified, cloned, and sequenced the recA gene homologue from GBS. A strain of GBS with recA deleted, A909DeltarecA, was constructed by insertional inactivation in the recA locus. A909DeltarecA demonstrated significant sensitivity to UV light, and the 50% lethal dose of the mutant strain in a mouse intraperitoneal model of sepsis was 20-fold higher than that of the parent strain. The spontaneous rate of tandem repeat deletion in the alpha C protein in vitro, as well as in our mouse model of immune infection, was studied using A909DeltarecA. We report that tandem repeat deletion in the alpha C protein does occur in the absence of a functional recA gene both in vitro and in vivo, indicating that tandem repeat deletion in GBS occurs by a recA-independent recombinatorial pathway.

Polysaccharide biosynthesis locus required for virulence of Bacteroides fragilis.

Bacteroides fragilis, though only a minor component of the human intestinal commensal flora, is the anaerobe most frequently isolated from intra-abdominal abscesses. B. fragilis 9343 expresses at least three capsular polysaccharides-polysaccharide A (PS A), PS B, and PS C. Purified PS A and PS B have been tested in animal models and are both able to induce the formation of intra-abdominal abscesses. Mutants unable to synthesize PS B or PS C still facilitate abscess formation at levels comparable to those of wild-type 9343. To determine the contribution of PS A to abscess formation in the context of the intact organism, the PS A biosynthesis region was cloned, sequenced, and deleted from 9343 to produce a PS A-negative mutant. Animal experiments demonstrate that the abscess-inducing capability of 9343 is severely attenuated when the organism cannot synthesize PS A, despite continued synthesis of the other capsular polysaccharides. The PS A of 9343 contains an unusual free amino sugar that is essential for abscess formation by this polymer. PCR analysis of the PS A biosynthesis loci of 50 B. fragilis isolates indicates that regions flanking each side of this locus are conserved in all strains. The downstream conserved region includes two terminal PS A biosynthesis genes that homology-based analyses predict are involved in the synthesis and transfer of the free amino sugar of PS A. Conservation of these genes suggests that this sugar is present in the PS A of all serotypes and may explain the abscessogenic nature of B. fragilis.

Bayesian inference on protective antibody levels using case-control data.

In the study of immune responses to infectious pathogens, the minimum protective antibody concentration (MPAC) is a quantity of great interest. We use case-control data to estimate the posterior distribution of the conditional risk of disease given a lower bound on antibody concentration in an at-risk subject. The concentration bound beyond which there is high credibility that infection risk is zero or nearly so is a candidate for the MPAC. A very simple Gibbs sampling procedure that permits inference on the risk of disease given antibody level is presented. In problems involving small numbers of patients, the procedure is shown to have favorable accuracy and robustness to choice/misspecification of priors. Frequentist evaluation indicates good coverage probabilities of credibility intervals for antibody-dependent risk, and rules for estimation of the MPAC are illustrated with epidemiological data.

Exposure to cockroach allergen in the home is associated with incident doctor-diagnosed asthma and recurrent wheezing.

BACKGROUND: Indoor inhaled allergens have been repeatedly demonstrated to worsen asthma in sensitized individuals, but their role in incident asthma is more controversial. OBJECTIVE: We investigated the relationship between exposure to allergens (dust mite, cat, and cockroach) measured in the home and incident doctor-diagnosed asthma and recurrent wheezing in children born to parents with asthma, allergies, or both. METHODS: From an ongoing longitudinal family and birth cohort study, we identified 222 siblings (median age, 2.87 years) of the index children. Allergen levels in the home were measured from dust samples obtained at the beginning of the study. Incident doctor-diagnosed asthma and recurrent wheezing were determined from questionnaires administered at 14 months and 22 months after the initial questionnaire. RESULTS: Thirteen (5.9%) children were reported to have incident asthma, twenty (9.0%) children had recurrent asthmatic wheezing, and 18 (8.1%) had recurrent wheezing without asthma. Compared with children living in homes with Bla g 1 or 2 levels of less than 0.05 U/g, children exposed to Bla g 1 or 2 levels of 0.05 to less than 2 U/g had a relative risk for incident asthma of 8.27 (95% confidence interval, 1.04-66.04), whereas children exposed to Bla g 1 or 2 levels of 2 U/g or greater had a relative risk for incident asthma of 35.87 (95% confidence interval, 4.49-286.62). Cockroach allergen exposure was likewise a significant predictor for recurrent asthmatic wheezing. Neither dust mite nor cat allergen levels were significantly associated with either outcome. These findings remained after control for several covariates. CONCLUSION: Exposure to cockroach allergen early in life may contribute to the development of asthma in susceptible children.

Analysis of longitudinally observed irregularly timed multivariate outcomes: regression with focus on cross-component correlation.

Components of repeatedly observed multivariate outcomes (for example, the two components of blood pressure measures (SBP(it), DBP(it)), obtained on subject i at arbitrarily spaced times t) are often analysed separately. We present a unified approach to regression analysis of such irregularly timed multivariate longitudinal data, with particular attention to assessment of the magnitude and durability of cross-component correlation. Maximum likelihood estimates are presented for component-specific regression parameters and autocorrelation and cross-correlation functions. The component-specific autocorrelation function has the 'damped exponential' form [see text], which generalizes the AR(1), MA(1) and random intercept models for univariate longitudinal outcomes. The cross-component correlation function (CCCF) has an analogous form, allowing damped-exponential decay of cross-component correlation as time between repeated measures elapses. Finite sample performance is assessed through simulation studies. The methods are illustrated through blood pressure modelling and construction of multivariate prediction regions.

Use of capsular polysaccharide-tetanus toxoid conjugate vaccine for type II group B Streptococcus in healthy women.

An estimated 15% of invasive group B streptococcal (GBS) disease is caused by type II capsular polysaccharide (II CPS). In developing a pentavalent vaccine for the prevention of GBS infections, individual GBS CPSs have been coupled to tetanus toxoid (TT) to prepare vaccines with enhanced immunogenicity. Type II GBS (GBS II) vaccine was created by direct, covalent coupling of II CPS to TT by reductive amination. In 2 clinical trials, 75 healthy nonpregnant women 18-45 years old were randomized to receive II CPS-TT (II-TT) conjugate (dose range, 3.6-57 microg of CPS component) or uncoupled II CPS vaccine. Both vaccines were well tolerated. II CPS-specific IgG serum concentrations (as well as IgM and IgA) peaked 2 weeks after immunization, being significantly higher in recipients of conjugated vaccine than in recipients of uncoupled CPS. Immunological responses to conjugate were dose dependent and correlated with opsonophagocytosis in vitro. These results support inclusion of II-TT conjugate when preparing a multivalent GBS vaccine.

Effect of molecular size on the ability of zwitterionic polysaccharides to stimulate cellular immunity.

The large-molecular-sized zwitterionic capsular polysaccharide of the anaerobe Bacteroides fragilis NCTC 9343, designated polysaccharide (PS) A, stimulates T cell proliferation in vitro and induces T cell-dependent protection against abscess formation in vivo. In the present study, we utilized a modification of a recently developed ozonolytic method for depolymerizing polysaccharides to examine the influence of the molecular size of PS A on cell-mediated immunity. Ozonolysis successfully depolymerized PS A into structurally intact fragments. PS A with average molecular sizes of 129.0 (native), 77.8, 46.9, and 17.1 kDa stimulated CD4+-cell proliferation in vitro to the same degree, whereas the 5.0-kDa fragment was much less stimulatory than the control 129.0-kDa PS A. Rats treated with 129.0-kDa, 46.9-kDa, and 17.1-kDa PS A molecules, but not those treated with the 5.0-kDa molecule, were protected against intraabdominal abscesses induced by challenge with viable B. fragilis. These results demonstrate that a zwitterionic polysaccharide as small as 22 repeating units (88 monosaccharides) elicits a T cell-dependent immune response. These findings clearly distinguish zwitterionic T cell-dependent polysaccharides from T cell-independent polysaccharides and give evidence of the existence of a novel mechanism for a polysaccharide-induced immune response.

Bronchodilator responsiveness and serum total IgE levels in families of probands with severe early-onset COPD.

Bronchodilator responsiveness has been associated with a subsequent accelerated decline in forced expiratory volume in one second (FEV1). Therefore, bronchodilator responsiveness and total serum immunoglobulin E(IgE) levels were assessed in 184 adult first-degree relatives of probands with severe early-onset chronic obstructive pulmonary disease (COPD) and a control group. Greater bronchodilator responsiveness was found among current smokers or exsmokers who were first-degree relatives of early-onset COPD probands than in currently or exsmoking controls, expressed as increase in FEV1 as a percentage of baseline (5.8+/-8.1 versus 2.9+/-5.1%, p<0.01), absolute increase in FEV1 from baseline (120+/-130 versus 60+/-110 mL, p<0.05), and increase in FEV1 as a percentage of the predicted value (3.6:4.1 versus 2.2+/-3.9%, p<0.05). However, elevated total serum IgE levels were not found in first-degree relatives of early-onset COPD probands compared with control subjects. The increased bronchodilator responsiveness among currently smoking/exsmoking first-degree relatives of early-onset COPD probands suggests that these individuals may have enhanced susceptibility to the detrimental effects of cigarette smoking.

Race, socioeconomic factors, and area of residence are associated with asthma prevalence.

Asthma prevalence in the United States has been reported to be higher in minority groups such as Blacks and Hispanics. Because a disproportionate number of individuals from such minority groups are of low socioeconomic status (SES), it is unclear how much of the racial/ethnic differences in asthma prevalence is related to low SES. We investigated the effect of SES on the relationship between race/ethnicity and asthma prevalence in a cohort of families with a history of asthma or allergies from the Boston, Massachusetts area. From 499 families, a cohort of 998 parents and 307 children was identified. We used total yearly family income (<$50,000 vs. > or = $50, 000), highest level of education (< or = high school vs. > or = college), and residence in high-poverty areas vs. low-poverty areas as measures of SES. Yearly family income <$50,000, < or = high school education, and residence in high poverty areas were all associated with increased risks for asthma in both cohorts. In the parental cohort, Blacks and Hispanics (OR = 2.1, 95% CI = 1.5, 2.8; and OR = 2.2, 95% CI = 1.5, 3.2, respectively) were at greater risk for asthma than Whites. In the cohort of children, Black and Hispanic children (OR = 2.9, 95% CI = 1.0, 8.0; and OR = 5.3, 95% CI = 1.6, 17.5, respectively) were also at increased risk for asthma. When the three measures of SES were included in the multivariable models, the risks associated with Blacks and Hispanics decreased in both cohorts: OR = 1.4, 95% CI = 0.9, 2.0; and OR = 1.6, 95% CI = 1.0, 2. 6, respectively, for the parents; and OR = 0.8, 95% CI = 0.2, 3.0; and 2.5, 95% CI = 0.5, 11.7, respectively, for the children. We conclude that a large proportion of the racial/ethnic differences in asthma prevalence in our study is explained by factors related to income, area of residence, and level of education.

Results of physical inspection before races and race-related characteristics and their association with musculoskeletal injuries in Thoroughbreds during races.

OBJECTIVE: To estimate the relative risk of injury among horses deemed to be at increased risk of injury on the basis of prerace physical inspection findings and to examine the association of injury during races with race-related characteristics. DESIGN: Cohort study. ANIMALS: 2,187 Thoroughbred horses that started 3,227 races in Kentucky. PROCEDURE: All race starts for which a horse was deemed to be at increased risk of injury on the basis of prerace physical inspection findings and a random sample of race starts for which horses were not deemed at increased risk of injury were included in the study. Findings of prerace physical inspection, race-related characteristics, and outcome of the race (race results and whether the horse incurred an injury) were recorded for each race start. Race starts in which a horse incurred an injury during a race were compared with race starts in which injuries were not incurred to identify factors associated with injury during races. RESULTS: Abnormality of the suspensory ligament of the forelimbs detected during prerace physical inspection, racetrack, class of race (claiming race < or = $25,000 vs other classes), and distance of race (< 7 furlongs vs other distances) were significantly associated with increased risk of injury. CONCLUSIONS AND CLINICAL RELEVANCE: Prerace physical inspection findings, particularly abnormalities of the suspensory ligament, may be used to identify horses at increased risk of injury during races. Rate of injury differed among racetracks, and horses in certain types of races (lower-priced claiming races and races of shorter distance) may be at increased risk of injury during races.

Abdominal adiposity and coronary heart disease in women.

CONTEXT: Obesity is a well-established risk factor for coronary heart disease (CHD), but whether regional fat distribution contributes independently to risk remains unclear. OBJECTIVE: To compare waist-hip ratio (WHR) and waist circumference in determining risk of CHD in women. DESIGN AND SETTING: Prospective cohort study among US female registered nurses participating in the Nurses' Health Study conducted between 1986, when the nurses completed a questionnaire, and follow-up in June 1994. PARTICIPANTS: A total of 44702 women aged 40 to 65 years who provided waist and hip circumferences and were free of prior CHD, stroke, or cancer in 1986. MAIN OUTCOME MEASURES: Incidence of CHD (nonfatal myocardial infarction or CHD death). RESULTS: During 8 years of follow-up 320 CHD events (251 myocardial infarctions and 69 CHD deaths) were documented. Higher WHR and greater waist circumference were independently associated with a significantly increased age-adjusted risk of CHD. After adjusting for body mass index (BMI) (defined as weight in kilograms divided by the square of height in meters) and other cardiac risk factors, women with a WHR of 0.88 or higher had a relative risk (RR) of 3.25 (95% confidence interval [CI], 1.78-5.95) for CHD compared with women with a WHR of less than 0.72. A waist circumference of 96.5 cm (38 in) or more was associated with an RR of 3.06 (95% CI, 1.54-6.10). The WHR and waist circumference were independently strongly associated with increased risk of CHD also among women with a BMI of 25 kg/m2 or less. After adjustment for reported hypertension, diabetes, and high cholesterol level, a WHR of 0.76 or higher or waist circumference of 76.2 cm (30 in) or more was associated with more than a 2-fold higher risk of CHD. CONCLUSIONS: The WHR and waist circumference are independently associated with risk of CHD in women.