Complex association patterns for inflammatory mediators in induced sputum from subjects with asthma.

BACKGROUND: The release of various inflammatory mediators into the bronchial lumen is thought to reflect both the type and degree of airway inflammation, eosinophilic Th2, and Th9, or neutrophilic Th1, and Th17, in patients with asthma. AIMS: We investigated whether cytokines and chemokines differed in sputum from subjects with more severe compared with milder asthma and whether unbiased factor analysis of cytokine and chemokine groupings indicates specific inflammatory pathways. METHODS: Cell-free supernatants from induced sputum were obtained from subjects with a broad range of asthma severity (n = 158) and assessed using Milliplex® Cytokines/Chemokine kits I, II and III, measuring 75 individual proteins. Each cytokine, chemokine or growth factor concentration was examined for differences between asthma severity groups, for association with leucocyte counts, and by factor analysis. RESULTS: Severe asthma subjects had 9 increased and 4 decreased proteins compared to mild asthma subjects and fewer differences compared to moderate asthma. Twenty-six mediators were significantly associated with an increasing single leucocyte type: 16 with neutrophils (3 interleukins [IL], 3 CC chemokines, 4 CXC chemokines, 4 growth factors, TNF-α and CX3CL1/Fractalkine); 5 with lymphocytes (IL-7, IL-16, IL-23, IFN-α2 and CCL4/MIP1ß); IL-15 and CCL15/MIP1δ with macrophages; IL-5 with eosinophils; and IL-4 and TNFSF10/TRAIL with airway epithelial cells. Factor analysis grouped 43 cytokines, chemokines and growth factors which had no missing data onto the first 10 factors, containing mixes of Th1, Th2, Th9 and Th17 inflammatory and anti-inflammatory proteins. CONCLUSIONS: Sputum cytokines, chemokines and growth factors were increased in severe asthma, primarily with increased neutrophils. Factor analysis identified complex inflammatory protein interactions, suggesting airway inflammation in asthma is characterized by overlapping immune pathways. Thus, focus on a single specific inflammatory mediator or pathway may limit understanding the complexity of inflammation underlying airway changes in asthma and selection of appropriate therapy.

eQTL of bronchial epithelial cells and bronchial alveolar lavage deciphers GWAS-identified asthma genes.

BACKGROUND: Genome-wide association studies (GWASs) have identified various genes associated with asthma, yet, causal genes or single nucleotide polymorphisms (SNPs) remain elusive. We sought to dissect functional genes/SNPs for asthma by combining expression quantitative trait loci (eQTLs) and GWASs. METHODS: Cis-eQTL analyses of 34 asthma genes were performed in cells from human bronchial epithelial biopsy (BEC, n = 107) and from bronchial alveolar lavage (BAL, n = 94). RESULTS: For TSLP-WDR36 region, rs3806932 (G allele protective against eosinophilic esophagitis) and rs2416257 (A allele associated with lower eosinophil counts and protective against asthma) were correlated with decreased expression of TSLP in BAL (P = 7.9 × 10(-11) and 5.4 × 10(-4) , respectively) and BEC, but not WDR36. Surprisingly, rs1837253 (consistently associated with asthma) showed no correlation with TSLP expression levels. For ORMDL3-GSDMB region, rs8067378 (G allele protective against asthma) was correlated with decreased expression of GSDMB in BEC and BAL (P = 1.3 × 10(-4) and 0.04) but not ORMDL3. rs992969 in the promoter region of IL33 (A allele associated with higher eosinophil counts and risk for asthma) was correlated with increased expression of IL33 in BEC (P = 1.3 × 10(-6) ) but not in BAL. CONCLUSIONS: Our study illustrates cell-type-specific regulation of the expression of asthma-related genes documenting SNPs in TSLP, GSDMB, IL33, HLA-DQB1, C11orf30, DEXI, CDHR3, and ZBTB10 affect asthma risk through cis-regulation of its gene expression. Whenever possible, disease-relevant tissues should be used for transcription analysis. SNPs in TSLP may affect asthma risk through up-regulating TSLP mRNA expression or protein secretion. Further functional studies are warranted.

HLA-Dw2: a genetic marker for human immune response to short ragweed pollen allergen Ra5. II. Response after ragweed immunotherapy.

After artificial immunization (immunotherapy) with ragweed antigens, specific immunoglobulin G (IgG) antibody (Ab) response to Ra5 was significantly associated with HLA-Dw2 (P less than 0.0001). From a total of 61 treated patients, all 22 Dw2+ subjects made good IgG Ab responses to Ra5 by year 2 of therapy (21 by year 1), even though 8 of them had no detectable IgG Ab and 9 had no detectable IgE Ab before therapy. The prevalence of IgG Ab response among 39 Dw2- subjects was markedly lower; only 11 (28%) responded well after 1-9 yr of therapy. Both by univariate and multivariate statistical analysis, Dw2 was also found to be strongly associated with the quantity of IgG Ab produced. In particular, both the strength and significance of the association between Dw2 and log[IgG Ab] response to Ra5 increased over a 3-yr period of ragweed therapy (P = 10(-9) by year 3). Multiple regression analysis also revealed a weak association with HLA-B13, which became apparent only after year 2 of therapy. Genetic hypotheses for these findings are discussed. In particular, the possibility of a second Ir gene, Ir-Ra5', separate from HLA-Dw2 and possibly located elsewhere in the genome, is considered.

HLA-Dw2: a genetic marker for human immune response to short ragweed pollen allergen Ra5. I. Response resulting primarily from natural antigenic exposure.

Ultra-pure short ragweed pollen allergen Ra5 (5,000 mol wt) was used to investigate the relationship between human leukocyte antigen (HLA) type and IgE and IgG antibody (Ab) responses to Ra5 in two groups of Caucasian subjects, totaling 447 people. Using highly sensitive radioimmunoassay procedures to measure serum IgE and IgG Ab, qualitative responses to Ra5 in both groups were found to be strongly associated with HLA-Dw2 (P less than 0.0001). For example, 95% of 38 people with IgE Ab vs. 22% of 139 ragweed-allergic persons having no detectable IgE Ab to Ra5 were Dw2+. Quantitative log [IgE Ab] and log[IgG Ab] responses to Ra5 were highly correlated with Dw2 (P = 10(-5) to 10(-14)) in four separate multiple regression analyses, examining the relationship between HLA type (and other variables) and Ab levels in the two study groups. Further studies showed that the primary association of Ra5 response was with Dw2 rather than DR2 and that various combinations of A3, B7, and Dw2 were less strongly associated than Dw2 alone.

Huntington's disease: two families with differing clinical features show linkage to the G8 probe.

To test the hypothesis that interfamily variability in Huntington's Disease (HD) is due to mutation at different loci, linkage analysis was undertaken in two large HD kindreds that differed in ethnicity, age-at-onset, and neurologic and psychiatric features. Both families showed linkage of the HD locus to the G8 probe. Several recombinants were documented in each family, and the best estimate of the recombination fraction for the two families was 6 percent with a 95 percent confidence interval of 0 to 12 percent. Although the data support the existence of a single HD locus, use of the G8 probe for presymptomatic testing in these kindreds would have resulted in a 12 percent error rate in genotype assignment at the HD locus.

Major susceptibility locus for prostate cancer on chromosome 1 suggested by a genome-wide search.

Despite its high prevalence, very little is known regarding genetic predisposition to prostate cancer. A genome-wide scan performed in 66 high-risk prostate cancer families has provided evidence of linkage to the long arm of chromosome 1 (1q24-25). Analysis of an additional set of 25 North American and Swedish families with markers in this region resulted in significant evidence of linkage in the combined set of 91 families. The data provide strong evidence of a major prostate cancer susceptibility locus on chromosome 1.

Early age at diagnosis in families providing evidence of linkage to the hereditary prostate cancer locus (HPC1) on chromosome 1.

In a recent study of 91 families having at least three first degree relatives with prostate cancer, we reported the localization of a major susceptibility locus for prostate cancer (HPC1) to chromosome 1 [band q24; J. R. Smith et al., Science (Washington DC), 274: 1371-1373, 1996]. There was significant evidence for locus heterogeneity, with an estimate of 34% of the families being linked to this locus. In this report, we investigate the importance of age at diagnosis of prostate cancer and number of affected individuals within a family as variables in the linkage analysis of an expanded set of markers on 1q24. Under two different models for the prostate cancer locus, we find that the evidence for linkage to HPC1 is provided primarily by large (five or more members affected) families with an early average age at diagnosis. Specifically, for 40 North American families with an average age at diagnosis <65 years, the multipoint lod score is 3.96, whereas for 39 families with an older average age at diagnosis, this value is -0.84. Assuming heterogeneity, the proportion of families linked is 66% for the 14 families with the earliest average ages at diagnoses, but it decreases to 7% for the families with the latest ages at diagnoses. A similar age effect is observed in 12 Swedish pedigrees analyzed. To test the hypotheses generated by these analyses, we examined an additional group of 13 newly identified prostate cancer families. Overall, these families provided additional evidence for linkage to this region (nonparametric linkage Z = 1.91; P = 0.04 at marker D1S1660), contributed primarily by the families in this group with early age at diagnosis [nonparametric linkage Z = 2.50 (P = 0.01) at D1S422]. These results are consistent with the existence of a locus in this region that predisposes men to develop early-onset prostate cancer.

Assessment of lineality in bipolar I linkage studies.

OBJECTIVE: To assess lineality in families of bipolar I probands, the authors used direct interviews of family members to reclassify families initially categorized as unilineal by family history. METHOD: The families of 1,800 treated bipolar I probands were screened by the family history method with multiple informants. If the proband had one or more affected sibs and one apparently unaffected parent, the parents (and then other available first- and second-degree relatives) were directly interviewed by psychiatrists. RESULTS: Of the 1,800 families screened, 56 were apparently suitable unilineal families with multiple affected members; 46 families were interviewed directly. After interviews with the parents, 12 families (26.1%) were found to be bilineal. Direct interviews of all available relatives in the 34 remaining families revealed that only 22 (47.8% of the 46 interviewed families) were unilineal or probably unilineal and 12 were probably bilineal. The probably bilineal families had a significantly higher proportion of siblings with unipolar disorder. In addition, the affected sibs from the probably bilineal families tended to have earlier onsets but had significantly fewer symptoms in the most severe depressive episode. CONCLUSIONS: Fewer than 50% of bipolar I families appearing unilineal according to family history were found to be unilineal by direct interviews. The phenotypic differences between the affected sibs from the probably bilineal families and those from the unilineal and probably unilineal families suggest differences in genetic mechanisms. These findings highlight the need to systematically assess lineality in all families considered for bipolar I linkage studies and support the preferential inclusion of unilineal families in linkage studies.

Bipolar II: the most common bipolar phenotype?

OBJECTIVE: The purpose of this study was to compare the pattern of affective psychopathology in families ascertained for genetic linkage studies through bipolar I probands to that in families ascertained through bipolar II probands. METHOD: All available first-degree relatives (N = 266) of 48 bipolar I and eight bipolar II probands were interviewed with the Schedule for Affective Disorders and Schizophrenia--Lifetime Version by one of two psychiatrists who had attained high interrater reliability for bipolar II disorder and other diagnoses. RESULTS: Bipolar II disorder was the most common affective disorder in both family sets. Forty percent of the 47 first-degree relatives of the bipolar II probands and 22% of the 219 first-degree relatives of the bipolar I probands were diagnosed with bipolar II disorder. On the other hand, only one bipolar I relative was found in the bipolar II families. CONCLUSIONS: Bipolar II disorder was the most prevalent affected phenotype in both bipolar I and bipolar II families and was the only expressed phenotype in half of the bipolar II families. This suggests that bipolar II disorder is genetically related to but less complex than bipolar I disorder. Accurate diagnosis of bipolar II disorder may be crucial in finding the genetic loci underlying bipolar disorders generally.

Influence of clinical subtype, sex, and lineality on age at onset of major affective disorder in a family sample.

OBJECTIVE: The authors analyzed data from a family sample ascertained for a genetic linkage study of bipolar disorder to address the following questions: Do the major clinical subtypes of familial affective disorder have distinct distributions of age at onset? What factors other than clinical subtype affect these distributions? After controlling for these factors, do the differences in age at onset persist among the subtypes? METHODS: Eighty-two families were ascertained through a treated proband with bipolar disorder who had a family history of two or more affected siblings or one affected sibling and one affected parent. After participating in an interview conducted by a psychiatrist using the Schedule for Affective Disorders and Schizophrenia--Lifetime Version, 274 probands and their first-degree relatives were diagnosed as having bipolar I, bipolar II, or recurrent unipolar disorder according to Research Diagnostic Criteria. Age at first major affective episode and other clinical data were collected. RESULTS: Onset age distributions were similar for bipolar I and bipolar II disorder but significantly different for recurrent unipolar disorder. This finding persisted after adjustment for a significantly earlier onset among females. Subjects with affective disorder in both parental lines (bilineal) also experienced a significantly earlier onset. Substance abuse, physical illness, and sex of the affected parent had no significant impact on onset age. CONCLUSIONS: Although differences in age at onset may reflect several factors, these results provide indirect support for the view that bipolar I and bipolar II disorders are genetically related phenotypes and suggest that bilineal families may be more complex than previously assumed.

Evaluation of sleep-disordered breathing. Is polysomnography necessary?

To determine whether polysomnography is necessary to assess the presence and severity of sleep-disordered breathing, bedside observations by physicians were compared with the results of polysomnography in 37 patients with clinically suspected obstructive sleep apnea. Physician observations correlated with objective findings from polysomnography in detecting the presence of obstructive apnea (p less than 0.01), and had a high specificity and positive predictive value. The 20 patients correctly identified by clinical observation had a longer duration of apneic episodes (p = 0.02), increased severity of snoring (p = 0.02), resuscitative snoring (p less than 0.02), and paradoxic thoracoabdominal movement (p less than 0.05). However, 11 other patients with sleep-disordered breathing were not identified clinically; therefore, the sensitivity (64.5 percent) and diagnostic accuracy (70.3 percent) of brief clinical observation were low. Furthermore, the physicians' determinations of the severity of the condition on the basis of bedside estimates of disordered breathing rate, duration of episodes, and the degree of associated hemoglobin oxygen desaturation did not correlate with objective measurements. These findings suggest that a single, brief clinical observation alone is an ineffective screening procedure for detecting obstructive sleep apnea.

Theophylline reduces the response to nasal challenge with antigen.

A nasal challenge model of allergic rhinitis was used to determine if pretreatment with oral theophylline reduces histamine release in vivo. Ten subjects were entered into a double-blind, cross-over trial. The results showed that both the physiologic response (sneezing) (p = 0.02) and the amount of mediators (histamine, kinins, toluene sulfonyl arginine methyl ester esterase activity) (p less than 0.01 for all) released into nasal secretions were significantly reduced after one week of pretreatment with theophylline. At the time of challenge, the serum concentrations of theophylline were between 8 and 22 micrograms/ml. It is speculated that the ability of theophylline to block the clinical response to antigen challenge and to decrease the release of mast cell mediators contributes to its clinical efficacy in the treatment of asthma.

Genetic factors predisposing to autoimmune diseases. Autoimmune hemolytic anemia, chronic thrombocytopenic purpura, and systemic lupus erythematosus.

Genetic factors predisposing to autoimmune diseases were investigated in 10 families having more than one affected member. Seventy relatives and 23 spouses from two large kindreds (one in whom the proband had autoimmune hemolytic anemia and the other immune thrombocytopenic purpura) were examined for immunologically mediated disorders, autoantibodies, immunoglobulin abnormalities, and HLA genotypes. Significant differences between relatives and spouses were found for immune diseases (21 percent versus 0 percent; p = 0.02), antinuclear antibody titer of 1:80 or more (18 percent versus 0 percent; p = 0.04), single-strand DNA antibodies (18 percent versus 0 percent; p = 0.04), high-titer antinuclear antibody or antibodies to single-strand DNA or both (33 percent versus 0 percent; p = 0.001), and the combined frequencies of immune diseases and serologic abnormalities (44 percent versus 4 percent; p = 0.0004). Similar frequencies were found in 41 relatives from eight families in whom the proband had SLE. Segregation analyses using these abnormalities as genetic traits were most compatible with a Mendelian dominant model. Impressive odds (100:1) against linkage to HLA were calculated.

Human immune responsiveness to Lolium perenne pollen allergen Lol p III (rye III) is associated with HLA-DR3 and DR5.

A well-characterized allergen of Lolium perenne (perennial rye grass) pollen, Lol p III, has been used as a model antigen to study the genetic control of the human immune response. Associations between HLA type and IgE or IgG antibody (Ab) responsiveness to Lol p III were studied in two groups of skin-test-positive Caucasoid adults (N = 135 and 67). We found by nonparametric and parametric analyses that immune responsiveness to Lol p III was significantly associated with HLA-DR3 and DR5. No association was found between any DQ type and immune responsiveness to Lol p III. Geometric mean IgE or IgG Ab levels to Lol p III were not different between B8+, DR3+ subjects and B8-, DR3+ subjects, showing that HLA-B8 had no influence on the association. Lol p III IgG Ab data obtained on subjects after grass antigen immunotherapy showed that 100% of DR3 subjects and 100% of DR5 subjects were Ab+. A comparison of all the available protein sequences of DRB gene products showed that the first hypervariable region of DR3 and DR5 (and DRw6), and no other region, contains the sequence Glu9-Tyr-Ser-Thr-Ser13. Our observations are consistent with the possibility that immune responsiveness to the allergen Lol p III is associated with this amino acid sequence in the first hypervariable region of the DR beta 1 polypeptide chain.

Effect of laboratory or clerical error on presymptomatic risk calculations for Huntington disease: a simulation study.

Linked markers are useful in prenatal diagnosis as well as presymptomatic diagnosis in late age-of-onset diseases such as Huntington disease (HD). It is widely assumed that most laboratory or clerical errors will be detected because of incompatibility of marker haplotypes within the family. However, errors in marker phenotypes that are compatible but wrong may result in a consultand being given an incorrect risk estimate. We have addressed this issue using simulated marker data in pedigrees similar to those seen in our HD testing program. In Family Structure I (an 11-member, 3-generation family), a particular family was more likely to be detected as inconsistent than incorrectly assigned. In a small nuclear family (Family Structure IV), fewer errors would be detected, and more would appear consistent but give incorrect risk estimates (e.g., low risk misclassified as noninformative or high). Given the presence of tight linkage, risk estimates are often calculated based on a small number of relatives. However, these computer simulations demonstrated that increasing the number of relatives typed decreases the probability that the family will remain consistent with an error present, and, therefore, decreases the probability of an incorrect assignment of risk. It is important to decrease the level of such errors by duplicated readings of raw marker data and validation of computer input.

Genetic ascertainment with heterogeneous risk.

Analysis of the bias of ascertainment is reformulated to deal with more general patterns commonly encountered in practice. The goal is to provide a unifying theory that will both replace the traditional, rather piecemeal, treatment of the problem and free it from certain restrictive assumptions. A compact algebraic method is furnished for analyzing the properties of the distributions by means of the probability generating function (PGF). The scope of the generalization is illustrated by applying it to the various classical patterns of bias of ascertainment. It is extended to other patterns in which the conditions of ascertainment, though more plausible, are also logically more complicated. It also accommodates cases hitherto inadequately dealt with, such as where the segregation ratios are heterogeneous (for example because of age-dependence); and cases where the ascertainment function is of arbitrary form and denies us such valuable, but demanding, assumptions as independence. Not only is the result unifying, but it leads to usable results in specific application such as diseases that depend on age or birth order. While the commonest applications are in human genetics, there are many other issues (such as the use of batteries of tests) in which it is equally important.

Inheritance of immunoglobulin E: genetic model fitting.

Total serum immunoglobulin E (IgE) concentration was measured on 316 members of five pedigrees selected through breast cancer probands. Sex- and age-adjusted natural logarithm-transformed IgE level was not found to differ between individuals with breast cancer or with cancer of any site and other relatives. Likelihoods of the polygenic and of one-locus, two-allele major gene and mixed models were computed. The analysis provided evidence for the presence of a polygenic component in the determination of IgE; it did not show evidence of a major gene effect.

Marfan syndrome: exclusion of genetic linkage to three major collagen genes.

The Marfan syndrome is an autosomal dominant connective tissue disorder with pleiotropic manifestations affecting skeletal, ocular and cardiovascular systems. Because the fibrillar collagens are major structural components of connective tissue, the hypothesis has long been set forth that the Marfan syndrome is a disorder of fibrillar collagen. We have investigated this hypothesis by performing linkage studies in 12 multiplex families with the Marfan syndrome, using restriction fragment length polymorphisms (RFLP's) associated with 3 genes encoding chains of fibrillar collagens. The data exclude linkage to all 3 candidate genes in 2 families and at least 1 of the candidates is excluded in 6 additional families. Each candidate was excluded in at least 3 families. In no case was strong evidence in favor of linkage of the Marfan syndrome to any of the 3 genes observed. These data speak against the hypothesis that mutations in one or more of these 3 fibrillar collagens cause the classic Marfan syndrome.

Predicting recurrence risks under epistatic models.

We present the expected recurrence risks to a sib of an affected proband under 4 simple 2-locus epistatic models for various allele frequencies at both the disease locus and the epistatic locus. Four obvious epistatic models are considered: an autosomal recessive disease with both 1) dominant and 2) recessive masking by the epistatic locus, and an autosomal dominant disease again with both 3) dominant and 4) recessive masking. Expected recurrence risks to a sib of an affected proband and to a sib of an affected proband with another normal sib are presented in the absence of information on parental status. Similar risks are presented for the case where both parents are known to be phenotypically normal. These recurrence risks were calculated using a convenient matrix notation which allows sequential calculation of genotypic probabilities. In general, 2-locus epistatic models can give surprisingly low recurrence risks, and often these risks, especially for models of recessive diseases, fall into the range associated with a more general multifactorial model for liability.