Abstract 4614: Genome-wide association analysis of pro-inflammatory cytokines and gene-lifestyle interaction for invasive breast cancer risk: The WHI Database for Genotypes and Phenotypes Study

Purpose: Pro-inflammatory biomarkers and their genetic variants may interact with obesity and obesity-related lifestyle factors, influencing breast cancer risk in postmenopausal women, but the interrelated metabolic pathways are incompletely understood.

Methods: We used data from the Women's Health Initiative Database for Genotypes and Phenotypes Study including 16,088 postmenopausal women, a population highly susceptible to obesity and increased risk for breast cancer. We conducted a genome-wide association (GWA) analysis in two steps: 1) with six GWA substudies, GWA meta-analysis of pro-inflammatory cytokines (Interleukin-6 [IL-6] and C-reactive protein [CRP]) for their gene-lifestyle interactions and 2) test for the association between identified single-nucleotide polymorphisms (SNPs) at the genome-wide level and breast cancer risk.

Results: In women overall and stratified by obesity status (body mass index, waist circumference, and waist-to-hip circumference) and obesity-related lifestyle factors (physical activity and high fat-diet), 88 loci were associated with pro-inflammatory phenotypes at genome-wide significance: 3 associated with IL-6 (1 index SNP in MAPK1 and 1 independent SNP in DEC1); 85 with CRP (3 index SNPs in CRP/CRPP1/HNF1A and 2 SNPs in APOE/APOC1, independently). Of those, 27 loci had significantly increased risk for breast cancer.

Conclusions: We found a number of novel genetic markers in relation to pro-inflammatory phenotypes, which interacted with obesity and related lifestyle factors. A substantial proportion of those SNPs' susceptibility influences breast cancer risk in the identical subgroup populations. Our findings may contribute to improved prediction accuracy for cancer and suggest intervention strategies for women who carry the risk genotypes, eventually reducing breast cancer risk.

Citation Format: Su Yon Jung, Peter Scott, Sihao Han, Matteo Pellegrini, Jeanette Papp, Eric Sobel, Herbert Yu, Zuo-Feng Zhang. Genome-wide association analysis of pro-inflammatory cytokines and gene-lifestyle interaction for invasive breast cancer risk: The WHI Database for Genotypes and Phenotypes Study [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4614.

Abstract 2361: Mendelian randomization study: The association between metabolic pathways and colorectal cancer risk

Purpose: The roles of obesity-related biomarkers and their molecular pathways in the development of postmenopausal colorectal cancer (CRC) have been inconclusive. We examined insulin resistance (IR) as a major hormonal pathway mediating the association between obesity and CRC risk in a Mendelian randomization (MR) framework.

Methods: We performed MR analysis using individual-level data of 11,078 non-Hispanic white postmenopausal women from our earlier genome-wide association study. We identified four independent single-nucleotide polymorphisms associated with fasting glucose (FG), three with fasting insulin (FI), and six with homeostatic model assessment-IR (HOMA-IR), which were not associated with obesity. We estimated hazard ratios (HRs) for CRC by adjusting for potential confounding factors plus genetic principal components.

Results: Overall, we observed no direct association between the combined 13 IR genetic instruments and CRC risk (HR = 0.96, 95% confidence interval [CI]: 0.78 - 1.17). In phenotypic analysis, genetically raised HOMA-IR exhibited its effects on the increased risk while FG and FI on the reduced risk for CRC, but with a lack of statistical power. Subgroup analyses by physical activity level and dietary fat intake with combined phenotypes showed that genetically determined IR was associated with reduced CRC risk in both physical activity-stratified (single contributor: MTRR rs722025; HR = 0.12, 95% CI: 0.02 - 0.62) and high-fat diet subgroups (main contributor: G6PC2 rs560887; HR = 0.59, 95% CI: 0.37 - 0.94).

Conclusions: Complex evidence was observed for a potential causal association between IR and CRC risk, which may contribute to an additional value of intervention trials to lower IR and reduce CRC risk.

Citation Format: Su Yon Jung, Jeanette Papp, Eric Sobel, Zuo-Feng Zhang. Mendelian randomization study: The association between metabolic pathways and colorectal cancer risk [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2361.

Abstract 1201: A mendelian randomization study for the potential causal effect of genetically driven insulin resistance on invasive breast cancer

Objectives

Insulin resistance (IR), traditionally measured by fasting blood levels of glucose (FG) and fasting insulin (FI), has been considered a potential risk factor for breast cancer development. However, findings from previous epidemiologic studies of the relationships between IR and breast cancer were inconsistent, partially due to selection bias, confounding, short time exposure to biomarkers, measurement errors, and reverse causation. We tried to address those challenges by using a Mendelian Randomization (MR) method where FG and FI were analyzed via genetic instrumental variables. Our study aimed to examine the potential causal effect of genetically driven IR on breast cancer development and hoped to understand the underlying mechanisms between IR and breast cancer.

Methods

We conducted a two-sample MR analysis using the most updated publicly available data from a genome-wide association study (GWAS) of Meta-Analysis of Glucose and Insulin related traits Consortium (MAGIC), Breast Cancer Association Consortium (BCAC), and Atlas of GWAS Summary Statistics (ATLAS), focusing on European women. We utilized different datasets for breast cancer outcomes to complement MR analyses with the inverse-variance weighted method. To determine the extent of pleiotropic signal, we applied Cochran's Q test and the MR-Egger regression analysis. Given obesity and diabetes's established role for breast cancer, we excluded those related single-nucleotide polymorphisms (SNPs) from the MR analysis.

Results

Of 44 SNPs associated with IR, 38 FG SNPs showed slightly positive effects on breast cancer risk across datasets (OncoArray/iCOGS, odds ratio (OR) = 1.002, 95% confidence interval (CI): 0.831- 1.209; ATLAS-General: OR = 1.146, 95% CI: 0.507 - 2.592; ATLAS-GEEA: OR = 1.034, 95% CI: 0.748 - 1.429; ATLAS-GEEAB: OR = 1.029, 95% CI: 0.747 - 1.416). After excluding SNPs associated with diabetes and obesity, the directions of the association between FG and breast cancer in the OncoArray/iCOGS datasets changed but not in the ATLAS-General dataset. Similarly, 6 FI SNPs had a positive association with breast cancer across the datasets. No significant directional pleiotropy was observed.

Conclusions

Our findings indicate a marginal association between genetically driven IR and breast cancer risk suggesting complex evidence for causal association. Our study may support the potential value of interventions to lower IR, thus reducing breast cancer risk.

Citation Format: Sihao Han, Nicholas Mancuso, Zuofeng Zhang, Jeanette Papp, Eric Sobel, Jiemin Yao, Su Yon Jung. A mendelian randomization study for the potential causal effect of genetically driven insulin resistance on invasive breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1201.

The utility of trough mycophenolic acid levels for the management of lupus nephritis

Background

Monitoring of mycophenolic acid (MPA) levels may be useful for effective mycophenolate mofetil (MMF) dosing. However, whether commonly obtained trough levels are an acceptable method of surveillance remains debatable. We hypothesized that trough levels of MPA would be a poor predictor of area under the curve (AUC) for MPA.

Methods

A total of 51 patients with lupus nephritis who were on MMF 1500 mg twice a day and had a 4-h AUC done were included in this study. MPA levels were measured prior to (C0) and at 1 (C1), 2 (C2) and 4 (C4) h, followed by 1500 mg of MMF. The MPA AUC values were calculated using the linear trapezoidal rule. Regression analysis was used to examine the relationship between the MPA trough and AUC. Differences in the MPA trough and AUC between different clinical and demographic categories were compared using t-tests.

Results

When grouped by tertiles there was significant overlap in MPA, AUC 0-4 and MPA trough in all tertiles. Although there was a statistically significant correlation between MPA trough levels and AUC, this association was weak and accounted for only 30% of the variability in MPA trough levels. This relationship might be even more unreliable in men than women. The use of angiotensin-converting enzyme inhibitors or angiotensin receptor blockers was associated with increased MPA trough levels and AUC at 0-4 h (AUC0-4).

Conclusion

Trough levels of MPA do not show a strong correlation with AUC. In clinical situations where MPA levels are essential to guide therapy, an AUC0-4 would be a better indicator of the adequacy of treatment.

Abstract 1596: Genome-wide gene-environmental interaction and random survival forest analyses: Insulin resistance and breast cancer risk

Purpose: Obesity–insulin connections have been considered potential risk factors for postmenopausal breast cancer, and the association between insulin resistance (IR) genotypes and phenotypes can be modified by obesity-lifestyle factors, affecting breast cancer risk. We explored the role of IR in those pathways at the genome-wide level. With identified IR genetic factors and selected lifestyles, we further generated risk profiles for breast cancer risk.

Methods: Using large-scale cohort data from postmenopausal women in the Women’s Health Initiative Database for Genotypes and Phenotypes Study, our previous genome-wide association gene–behavior interaction study identified 58 loci for associations with IR phenotypes (homeostatic model assessment–IR, hyperglycemia, and hyperinsulinemia). We evaluated those single-nucleotide polymorphisms (SNPs) and additional 31 lifestyles in relation to breast cancer risk by conducting a two-stage multimodal random survival forest analysis.

Results: We identified the most predictive genetic and lifestyle variables in overall and subgroup analyses (stratified by body mass index [BMI], exercise, and dietary fat intake). Two SNPs (LINC00460 rs17254590 and MKLN1 rs117911989), endogenous and exogenous factors related to lifetime cumulative exposure to estrogen, BMI, and dietary alcohol intake were the most common influential factors across the analyses. Individual SNPs did not have significant associations with breast cancer, but the combined SNPs and lifestyles synergistically increased the risk of breast cancer in a dose-dependent manner. In subgroup analysis, we further stratified women by the two strongest variables (durations of oral contraceptive [OC] and opposed estrogen use). Shorter-duration OC and ever-opposed estrogen users with both risks of genotypes and lifestyles had greater risk (2.5 times and 6.3 times, respectively) than their counterparts without risks in both. This indicates the combined effect of SNPs and lifestyles and the joint effect with OC use and opposed estrogen on breast cancer risk.

Conclusions: Our findings may contribute to more accurate prediction of breast cancer and suggest intervention strategies for those women with genetic risk to reduce their breast cancer risk.

Citation Format: Su Yon Jung, Herbert Yu, Matteo Pellegrini, Jeanette Papp, Eric Sobel, Zuo-Feng Zhang. Genome-wide gene-environmental interaction and random survival forest analyses: Insulin resistance and breast cancer risk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1596.

Post genome-wide gene-environment interaction study: The effect of genetically driven insulin resistance on breast cancer risk using Mendelian randomization

PURPOSE

The role of insulin resistance (IR) in developing postmenopausal breast cancer has not been thoroughly resolved and may be confounded by lifestyle factors such as obesity. We examined whether genetically determined IR is causally associated with breast cancer risk.

METHODS

We conducted Mendelian randomization (MR) analyses using individual-level data from our previous meta-analysis of a genome-wide association study (GWAS) (n = 11,109 non-Hispanic white postmenopausal women). Four single-nucleotide polymorphisms were associated with fasting glucose (FG), 2 with fasting insulin (FI), and 6 with homeostatic model assessment-IR (HOMA-IR) but were not associated with obesity. We used this GWAS to employ hazard ratios (HRs) for breast cancer risk by adjusting for potential confounding factors.

RESULTS

No direct association was observed between comprising 12 IR genetic instruments and breast cancer risk (HR = 0.93, 95% CI: 0.76-1.14). In phenotype-specific analysis, genetically elevated FG was associated with reduced risk for breast cancer (main contributor of this MR-effect estimate: G6PC2 rs13431652; HR = 0.59, 95% CI: 0.35-0.99). Genetically driven FI and HOMA-IR were not significantly associated. Stratification analyses by body mass index, exercise, and dietary fat intake with combined phenotypes showed that genetically elevated IR was associated with greater breast cancer risk in overall obesity and inactive subgroups (single contributor: MTRR/LOC729506 rs13188458; HR = 2.21, 95% CI: 1.03-4.75).

CONCLUSIONS

We found complex evidence for causal association between IR and risk of breast cancer, which may support the potential value of intervention trials to lower IR and reduce breast cancer risk.

Genome-Wide Meta-analysis of Gene-Environmental Interaction for Insulin Resistance Phenotypes and Breast Cancer Risk in Postmenopausal Women

Insulin resistance (IR)-related genetic variants are possibly associated with breast cancer, and the gene-phenotype-cancer association could be modified by lifestyle factors including obesity, physical inactivity, and high-fat diet. Using data from postmenopausal women, a population highly susceptible to obesity, IR, and increased risk of breast cancer, we implemented a genome-wide association study (GWAS) in two steps: (1) GWAS meta-analysis of gene-environmental (i.e., behavioral) interaction (G*E) for IR phenotypes (hyperglycemia, hyperinsulinemia, and homeostatic model assessment-insulin resistance) and (2) after the G*E GWAS meta-analysis, the identified SNPs were tested for their associations with breast cancer risk in overall or subgroup population, where the SNPs were identified at genome-wide significance. We found 58 loci (55 novel SNPs; 5 index SNPs and 6 SNPs, independent of each other) that are associated with IR phenotypes in women overall or women stratified by obesity, physical activity, and high-fat diet; among those 58 loci, 29 (26 new loci; 2 index SNPs and 2 SNPs, independently) were associated with postmenopausal breast cancer. Our study suggests that a number of newly identified SNPs may have their effects on glucose intolerance by interplaying with obesity and other lifestyle factors, and a substantial proportion of these SNPs' susceptibility can also interact with the lifestyle factors to ultimately influence breast cancer risk. These findings may contribute to improved prediction accuracy for cancer and suggest potential intervention strategies for those women carrying genetic risk that will reduce their breast cancer risk.

A Novel Mechanism for Generating the Interferon Signature in Lupus: Opsonization of Dead Cells by Complement and IgM

OBJECTIVE

In vitro studies suggest that the type I interferon (IFN) signature seen in most lupus patients results from Fcγ receptor-mediated uptake of nucleic acid-containing immune complexes by plasmacytoid dendritic cells and engagement of endosomal Toll-like receptors. The aim of this study was to reexamine the pathogenesis of the IFN signature in vivo.

METHODS

Lupus was induced in mice by injecting pristane. Some mice were treated with normal immunoglobulin or with cobra venom factor to deplete complement. The IFN signature was evaluated by polymerase chain reaction. The IFN signature also was determined in C4-deficient patients and control subjects.

RESULTS

Wild-type C57BL/6 mice with pristane-induced lupus developed a strong IFN signature, which was absent in immunoglobulin-deficient (μMT), C3^-/- , and CD18^-/- mice. Intravenous infusion of normal IgM, but not IgG, restored the IFN signature in μMT mice, and the IFN signature in wild-type mice was inhibited by depleting complement, suggesting that opsonization by IgM and complement is involved in IFN production. Consistent with that possibility, the levels of "natural" IgM antibodies reactive with dead cells were increased in pristane-treated wild-type mice compared with untreated controls, and in vivo phagocytosis of dead cells was impaired in C3-deficient mice. To examine the clinical relevance of these findings, we identified 10 C4-deficient patients with lupus-like disease and compared them with 152 C4-intact patients and 21 healthy controls. In comparison with C4-intact patients, C4-deficient patients had a different clinical/serologic phenotype and lacked the IFN signature.

CONCLUSION

These studies define previously unrecognized roles of natural IgM, complement, and complement receptors in generating the IFN signature in lupus.

Metformin attenuates the Type I Interferon response in human peripheral blood leukocytes

Metformin (Dimethylbiguanide) is used for controlling blood sugar levels in patients with Type 2 Diabetes, primarily by suppression of hepatic gluconeogenesis. Recently, it has drawn attention in a clinical trial (ChiCTR-TRC-12002419) for its ability to reduce disease flares and lower effective prednisone dosage in Systemic Lupus Erythematosus (SLE) patients. We have previously demonstrated that a therapy combining metformin and a glucose inhibitor can reverse lupus in mouse models by normalizing CD4+ T cell metabolism. Studies in mouse and isolated ex vivo human CD4+ T cells have characterized metformin’s capacity to downregulate oxidative metabolism and skew differentiation away from Th1 and Th17 towards a Treg lineage. To investigate the mechanisms by which metformin modulates CD4+ T cells we performed a microarray study of CD4+ T cells from n=5 SLE patients and n = 5 healthy controls (HCs). CD4+ T cells were isolated from subjects and activated (anti-CD3, anti-CD28) in media or 1mM metformin for 24 hr. Multiple ANOVA analysis yielded 1,211 transcripts with a FDR <0.05 between groups. Pathway analysis determined that type I interferon stimulated genes (ISG) were significantly downregulated in the CD4+ T cells of both cohorts, but to a greater extent in the HC cohort. Downregulation of ISGs by metformin was validated in primary PBMCs stimulated with IFNα ex vivo by qRT-PCR. Luciferase reporter assays suggest that metformin reduces IL-6-induced activation of STAT3. These experiments provide evidence that the therapeutic potential of metformin in SLE may be multifaceted, including the modulation of type I IFN stimulated genes, as well as STAT3 signaling. Studies are ongoing to characterize the key mediators involved in these pathways.

A case of isolated renal involvement of polyarteritis nodosa successfully treated with steroid monotherapy

Polyarteritis nodosa (PAN) is a systemic necrotising vasculitis that affects medium-sized and small-sized arteries. The spectrum of disease ranges from involving a single organ to polyvisceral failure. We report a case of a 75-year-old male presented with solely hypertension and mild renal function impairment as a consequence of diffuse renal necrotising vasculitis with occlusive but non-stenotic lesions associated with PAN. The overall prognosis of PAN has been improved in recent decades, primarily reflecting early diagnosis and more effective treatments. Therefore, early diagnosis is critical and it warrants full investigations even in those patients without obvious multiorgan manifestations. In those instances, with mild disease, steroid monotherapy has been shown to be effective with excellent response. Our patient responded well to steroid monotherapy and we were able to gauge his response by improvement in his blood pressure.

MDM2 ubiquitin ligase in Lupus CD4 T-Cell pathology

Systemic Lupus Erythmatosus (SLE) is an autoimmune condition of complex etiology involving genetic susceptibility and environmental factors. CD4+ Helper T-Cells provide co-stimulation to B-Cells to facilitate the production of a large repertoire of high affinity autoantibodies against numerous self-antigens such as dsDNA, histones, and snRNPs. Microarray analyses have been utilized previously to interrogate relevant pathways in disease pathology based on mRNA expression differences in T-Cells from healthy donors and SLE patients. Elevated levels of the E3 ubiquitin ligase MDM2 have been reported in immune cells of MRL.lpr mice and linked to resistance to activation-induced cell death (AICD), but the role of MDM2 in CD4+ T-Cells of human SLE subjects remains unclear. Here, we provide evidence for increased expression of MDM2 in CD4+ T-Cells of human SLE CD4+ T cells and a spontaneous genetic murine model of lupus, NZM2410 derived triple congenic (TC). Moreover, our data also support reduced AICD as a direct consequence of high MDM2. MDM2 has potential roles in the proteasome/ubiquitination pathways as well as inhibitory interactions with apoptotic regulators such as p73 and p53. Further work is needed to elucidate the contribution of this proto-oncogene to autoimmunity in humans and its suitability as a target for therapeutic intervention.

Serpin treatment suppresses inflammatory vascular lesions in temporal artery implants (TAI) from patients with giant cell arteritis

Giant cell arteritis (GCA) and Takayasu’s disease are inflammatory vasculitic syndromes (IVS) causing sudden blindness and widespread arterial obstruction and aneurysm formation. Glucocorticoids and aspirin are mainstays of treatment, predominantly targeting T cells. Serp-1, a Myxomavirus-derived serpin, blocks macrophage and T cells in a wide range of animal models. Serp-1 also reduced markers of myocardial injury in a Phase IIa clinical trial for unstable coronary disease. In recent work, we detected improved survival and decreased arterial inflammation in a mouse Herpesvirus model of IVS. Here we examine Serp-1 treatment of human temporal artery (TA) biopsies from patients with suspected TA GCA arteritis after implant (TAI) into the aorta of immunodeficient SCID (severe combined immunodeficiency) mice. TAI positive for arteritis (GCA^pos) had significantly increased inflammation and plaque when compared to negative TAI (GCA^neg). Serp-1 significantly reduced intimal inflammation and CD11b⁺ cell infiltrates in TAI, with reduced splenocyte Th1, Th17, and Treg. Splenocytes from mice with GCA^pos grafts had increased gene expression for interleukin-1beta (IL-1β), IL-17, and CD25 and decreased Factor II. Serp-1 decreased IL-1β expression. In conclusion, GCA^pos TAI xenografts in mice provide a viable disease model and have increased intimal inflammation as expected and Serp-1 significantly reduces vascular inflammatory lesions with reduced IL-1β.

Increased IFN-α-producing plasmacytoid dendritic cells (pDCs) in human Th1-mediated type 1 diabetes: pDCs augment Th1 responses through IFN-α production

Increasing evidence suggests that type 1 IFN (IFN-αβ) is associated with pathogenesis of Th1-mediated type 1 diabetes (T1D). A major source of IFN-αβ is plasmacytoid dendritic cells (pDCs). In this study, we analyzed peripheral blood pDC numbers and functions in at-risk, new-onset, and established T1D patients and controls. We found that subjects at risk for T1D and new-onset and established T1D subjects possessed significantly increased pDCs but similar number of myeloid DCs when compared with controls. pDC numbers were not affected by age in T1D subjects but declined with increasing age in control subjects. It was demonstrated that IFN-α production by PBMCs stimulated with influenza viruses was significantly higher in T1D subjects than in controls, and IFN-α production was correlated with pDC numbers in PBMCs. Of interest, only T1D-associated Coxsackievirus serotype B4 but not B3 induced majority of T1D PBMCs to produce IFN-α, which was confirmed to be secreted by pDCs. Finally, in vitro studies demonstrated IFN-α produced by pDCs augmented Th1 responses, with significantly greater IFN-γ-producing CD4(+) T cells from T1D subjects. These findings indicate that increased pDCs and their IFN-αβ production may be associated with this Th1-mediated autoimmune disease, especially under certain viral infections linked to T1D pathogenesis.

Metabolic inhibitors normalize CD4 T cell metabolism and functions, and reverse disease in a murine model of lupus (THER5P.839)

Autoreactive CD4 T cells are key effectors in Systemic Lupus Erythematosus (SLE). Cell metabolism is an important checkpoint for T cell activation, proliferation, and differentiation. We hypothesized that 1) SLE T cells have metabolic defects that cause abnormal T cell functions; 2) Targeting T cell metabolism may abrogate T cell inflammatory functions and reduce disease symptoms in SLE mice. Metabolism of CD4 T cells from lupus-resistant B6 mice and the congenic lupus model B6.Sle1.Sle2.Sle3 (B6.TC) were studied. Here it was observed that compared to B6, CD4 T cells from B6.TC mice have a stronger glycolysis and a higher mitochondrial oxygen consumption, as well as an enhanced mTOR activity. To normalize T cell metabolism in B6.TC mice, we used metformin, which activates the AMPK pathway and inhibits mitochondrial oxygen consumption, and 2-DG, an inhibitor of glycolysis. In vitro, metformin blocks IFNγ production by CD4 T cells and facilitates Treg development. 2-DG also blocks IFNγ production, but only after T cell activation. In vivo, a combined treatment with metformin and 2-DG of B6.TC mice normalized T cell metabolism and reversed disease phenotypes, including T cell activation and autoantibody production. Further, CD4 T cells from SLE patients have an enhanced metabolism as compared to healthy controls, and excessive IFNγ production was significantly reduced by metformin. Our research suggests that T cell metabolism is a novel target for SLE treatment.

Abstract 561: Serpin Suppression of Macrophage and T Helper Cell Response in Temporal Artery Biopsy Xenograft Implants from Patients with Giant Cell Inflammatory Arteritis

Background

Glucocorticoids are a principal treatment for giant cell arteritis (GCA), with some studies reporting predominate effect on T helper17 (Th17) cell activity in GCA, with lesser effects on other inflammatory cells. Serp-1 is a 55kDa myxomaviral serpin that modifies macrophage, Th1, and Th17 responses in aortic transplants in animal models.

Objectives

We have analyzed the effects of a virus-derived anti-inflammatory ser ine p rotease in hibitor ( serpin ) on human temporal artery (TA) biopsies isolated from patients with suspected GCA.

Methods

Using a newly developed “Aortic Window Xenopatch” model, human TA biopsy sections were divided implanted as full thickness grafts into the abdominal aorta of SCID mice in parallel and tested for response to Serp-1, with and without human PBMC infusion (N = 32).

Results

TA sections positive for arteritis (GCA pos ) displayed significantly increased inflammatory plaque when compared to negative sections (GCA neg ). Serp-1 reduced plaque in GCA pos sections (<0.01) with concommitant reduction in Th1, and Th17 splenocytes on flow cytometry (P < 0.01), with decreased IFNγ and IL-17 gene expression by RT-PCR array analysis. Serp-1 also reduced arterial CD11b + cells after PBMC infusion with reduced TNF-α expression in spleen, but not CD3 + , CCR6 + , nor CD86 + . Splenocytes from mice with GCA pos grafts had increased interleukin-1beta (Il-1β), IL-17, and CD25 expression, while IL-1β was significantly reduced by Serp-1.Serp-1 also markedly reducedt gene expression for the FII, FXa-PAR2, tPA, uPA in splenocytes (P <0.05).

Conclusions

Treatment with a virus-derived serpin, significantly reduces inflammation and plaque thickness in human GCA pos TA xenograft implants with associated reductions in macrophage and Th1 and Th17 responses in mice.

CD40 exon 8 deficiency causes a novel form of immunodeficiency with hyper-IgM (P3327)

Introduction: The germinal center (GC) reaction generates switched memory B cells and plasma cells. Mutation of CD40L or other genes involved in the GC reaction causes hyper-IgM syndrome (HIM). Hypothesis: We evaluated a 56-year-old woman who had an immunological phenotype resembling HIM but only mild immunodeficiency. The age, gender, and clinical presentation were not readily explained by known HIM mutations and we hypothesized that the patient might have a novel mutation. Method: The patient’s immune function was evaluated and CD40 DNA/RNA sequences were determined. The patient’s CD40 cDNA lacking exon 8 (Δexon8) was cloned and transfected into 293 cells. Signaling downstream of CD40 was assessed. Results: By flow cytometry, the patient’s peripheral blood lacked switched memory B cells. The patient mounted a robust IgG response to tetanus toxoid immunization, but antibody levels dropped precipitously suggesting that there was a problem generating long-lived plasma cells. Although CD40 expression was mildly decreased, cDNA sequences showed a deletion of the entire exon 8 of CD40 in 67% of her cDNA clones. This was rare in controls. Expression of CD40-Δexon8 in 293 cells resulted in surface expression of CD40, but signaling downstream of CD40 upon sCD40L stimulation was impaired. Conclusion: This patient has a novel immunodeficiency syndrome due to deletion of exon 8 of CD40, which encodes a cytoplasmic domain critical for signal transduction.

Maintenance of anti-Sm/RNP autoantibody production by plasma cells residing in ectopic lymphoid tissue and bone marrow memory B cells

Although ectopic lymphoid tissue formation is associated with many autoimmune diseases, it is unclear whether it serves a functional role in autoimmune responses. 2,6,10,14-Tetramethylpentadecane causes chronic peritoneal inflammation and lupus-like disease with autoantibody production and ectopic lymphoid tissue (lipogranuloma) formation. A novel transplantation model was used to show that transplanted lipogranulomas retain their lymphoid structure over a prolonged period in the absence of chronic peritoneal inflammation. Recipients of transplanted lipogranulomas produced anti-U1A autoantibodies derived exclusively from the donor, despite nearly complete repopulation of the transplanted lipogranulomas by host lymphocytes. The presence of ectopic lymphoid tissue alone was insufficient, as an anti-U1A response was not generated by the host in the absence of ongoing peritoneal inflammation. Donor-derived anti-U1A autoantibodies were produced for up to 2 mo by plasma cells/plasmablasts recruited to the ectopic lymphoid tissue by CXCR4. Although CD4(+) T cells were not required for autoantibody production from the transplanted lipogranulomas, de novo generation of anti-U1A plasma cells/plasmablasts was reduced following T cell depletion. Significantly, a population of memory B cells was identified in the bone marrow and spleen that did not produce anti-U1A autoantibodies unless stimulated by LPS to undergo terminal differentiation. We conclude that 2,6,10,14-tetramethylpentadecane promotes the T cell-dependent development of class-switched, autoreactive memory B cells and plasma cells/plasmablasts. The latter home to ectopic lymphoid tissue and continue to produce autoantibodies after transplantation and in the absence of peritoneal inflammation. However, peritoneal inflammation appears necessary to generate autoreactive B cells de novo.

Viral serpin therapeutics from concept to clinic

Over the past 19 years, we have developed a novel myxoma virus-derived anti-inflammatory serine protease inhibitor, termed a serpin, as a new class of immunomodulatory therapeutic. This review will describe the initial identification of viral serpins with anti-inflammatory potential, beginning with preclinical analysis of viral pathogenesis and proceeding to cell and molecular target analyses, and successful clinical trial. The central aim of this review is to describe the development of two serpins, Serp-1 and Serp-2, as a new class of immune modulating drug, from inception to implementation. We begin with an overview of the approaches used for successful mining of the virus for potential serpin immunomodulators in viruses. We then provide a methodological overview of one inflammatory animal model used to test for serpin anti-inflammatory activity followed by methods used to identify cells in the inflammatory response system targeted by these serpins and molecular responses to serpin treatment. Finally, we provide an overview of our findings from a recent, successful clinical trial of the secreted myxomaviral serpin, Serp-1, in patients with unstable inflammatory coronary arterial disease.

Quantitative three-dimensional photoacoustic tomography of the finger joints: an in vivo study

We present for the first time in vivo full three-dimensional (3-D) photoacoustic tomography (PAT) of the distal interphalangeal joint in a human subject. Both absorbed energy density and absorption coefficient images of the joint are quantitatively obtained using our finite-element-based photoacoustic image reconstruction algorithm coupled with the photon diffusion equation. The results show that major anatomical features in the joint along with the side arteries can be imaged with a 1-MHz transducer in a spherical scanning geometry. In addition, the cartilages associated with the joint can be quantitatively differentiated from the phalanx. This in vivo study suggests that the 3-D PAT method described has the potential to be used for early diagnosis of joint diseases such as osteoarthritis and rheumatoid arthritis.

Comparison of diffusion approximation and higher order diffusion equations for optical tomography of osteoarthritis

In this study, a simplified spherical harmonics approximated higher order diffusion model is employed for 3-D diffuse optical tomography of osteoarthritis in the finger joints. We find that the use of a higher-order diffusion model in a stand-alone framework provides significant improvement in reconstruction accuracy over the diffusion approximation model. However, we also find that this is not the case in the image-guided setting when spatial prior knowledge from x-rays is incorporated. The results show that the reconstruction error between these two models is about 15 and 4%, respectively, for stand-alone and image-guided frameworks.

Type-I interferon modulates monocyte recruitment and maturation in chronic inflammation (94.4)

Chronic inflammation is characterized by continuous recruitment and activation of immune cells such as monocytes in response to a persistent stimulus. Production of pro-inflammatory mediators by monocytes leads to tissue damage and perpetuates the inflammatory response. However, the mechanism(s) responsible for the sustained influx of monocytes in chronic inflammation are not well defined. In chronic peritonitis induced by 2,6,10,14-tetramethylpentadecane (TMPD; pristane), the persistent recruitment of Ly6Chi inflammatory monocytes into the peritoneum was abolished in type-I interferon (IFN-I) receptor deficient mice but was unaffected by the absence of IFN-γ, TNF-α, IL-6 or IL-1. IFN-I signaling stimulated the production of chemokines (CCL2, CCL7, and CCL12) that recruited Ly6Chi monocytes via interactions with the chemokine receptor CCR2. Interestingly, after TMPD treatment, the rapid turnover of inflammatory monocytes in the inflamed peritoneum was associated with a lack of differentiation into Ly6Clo monocytes/macrophages, a more mature subset with enhanced phagocytic capacity. In contrast, Ly6Chi monocytes/macrophages differentiated normally into Ly6Clo cells in IFN-I receptor deficient mice. The effects of IFN-I were specific for monocytes as granulocyte migration was unaffected in the absence of IFN-I signaling. Taken together, our findings reveal a novel role of IFN-I in promoting the recruitment of inflammatory monocytes via the chemokine receptor CCR2. Continuous monocyte recruitment and the lack of terminal differentiation induced by IFN-I may help sustain the chronic peritoneal inflammatory response.

Genome-wide association analysis by lasso penalized logistic regression

MOTIVATION

In ordinary regression, imposition of a lasso penalty makes continuous model selection straightforward. Lasso penalized regression is particularly advantageous when the number of predictors far exceeds the number of observations.

METHOD

The present article evaluates the performance of lasso penalized logistic regression in case-control disease gene mapping with a large number of SNPs (single nucleotide polymorphisms) predictors. The strength of the lasso penalty can be tuned to select a predetermined number of the most relevant SNPs and other predictors. For a given value of the tuning constant, the penalized likelihood is quickly maximized by cyclic coordinate ascent. Once the most potent marginal predictors are identified, their two-way and higher order interactions can also be examined by lasso penalized logistic regression.

RESULTS

This strategy is tested on both simulated and real data. Our findings on coeliac disease replicate the previous SNP results and shed light on possible interactions among the SNPs.

AVAILABILITY

The software discussed is available in Mendel 9.0 at the UCLA Human Genetics web site.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Colocalization of antigen-specific B and T cells within ectopic lymphoid tissue following immunization with exogenous antigen

Chronic inflammation promotes the formation of ectopic lymphoid tissue morphologically resembling secondary lymphoid tissues, though it is unclear whether this is a location where Ag-specific immune responses develop or merely a site of lymphocyte accumulation. Ectopic lymphoid tissue formation is associated with many humoral autoimmune diseases, including lupus induced by tetramethylpecadentane in mice. We examined whether an immune response to 4-hydroxy-3-nitrophenyl acetyl-keyhole limpet hemocyanin (NP-KLH) and NP-OVA develops within ectopic lymphoid tissue ("lipogranulomas") induced by tetramethylpecadentane in C57BL/6 mice. Following primary immunization, NP-specific B cells bearing V186.2 and related heavy chains as well as lambda-light chains accumulated within ectopic lymphoid tissue. The number of anti-NP-secreting B cells in the ectopic lymphoid tissue was greatly enhanced by immunization with NP-KLH. Remarkably, the H chain sequences isolated from individual lipogranulomas from these mice were diverse before immunization, whereas individual lipogranulomas from single immunized mice had unique oligo- or monoclonal populations of presumptive NP-specific B cells. H chain CDR sequences bore numerous replacement mutations, consistent with an Ag-driven and T cell-mediated response. In mice adoptively transferred with OT-II or DO11 T cells, there was a striking accumulation of OVA-specific T cells in lipogranulomas after s.c. immunization with NP-OVA. The selective colocalization of proliferating, Ag-specific T and B lymphocytes in lipogranulomas from tetramethylpecadentane-treated mice undergoing primary immunization implicates ectopic lymphoid tissue as a site where Ag-specific humoral immune responses can develop. This has implications for understanding the strong association of humoral autoimmunity with lymphoid neogenesis, which may be associated with deficient censoring of autoreactive cells.

Deficiency of the type I interferon receptor protects mice from experimental lupus

OBJECTIVE

Systemic lupus erythematosus (SLE) is diagnosed according to a spectrum of clinical manifestations and autoantibodies associated with abnormal expression of type I interferon (IFN-I)-stimulated genes (ISGs). The role of IFN-I in the pathogenesis of SLE remains uncertain, partly due to the lack of suitable animal models. The objective of this study was to examine the role of IFN-I signaling in the pathogenesis of murine lupus induced by 2,6,10,14-tetramethylpentadecane (TMPD).

METHODS

IFN-I receptor-deficient (IFNAR(-/-)) 129Sv mice and wild-type (WT) 129Sv control mice were treated intraperitoneally with TMPD. The expression of ISGs was measured by real-time polymerase chain reaction. Autoantibody production was evaluated by immunofluorescence and enzyme-linked immunosorbent assay. Proteinuria and renal glomerular cellularity were measured and renal immune complexes were examined by immunofluorescence.

RESULTS

Increased ISG expression was observed in the peripheral blood of TMPD-treated WT mice, but not in the peripheral blood of TMPD-treated IFNAR(-/-) mice. TMPD did not induce lupus-specific autoantibodies (anti-RNP, anti-Sm, anti-double-stranded DNA) in IFNAR(-/-) mice, whereas 129Sv controls developed these specificities. Although glomerular immune complexes were present in IFNAR(-/-) mice, proteinuria and glomerular hypercellularity did not develop, whereas these features of glomerulonephritis were found in the TMPD-treated WT controls. The clinical and serologic manifestations observed in TMPD-treated mice were strongly dependent on IFNAR signaling, which is consistent with the association of increased expression of ISGs with lupus-specific autoantibodies and nephritis in humans.

CONCLUSION

Similar to its proposed role in human SLE, signaling via the IFNAR is central to the pathogenesis of autoantibodies and glomerulonephritis in TMPD-induced lupus. This lupus model is the first animal model shown to recapitulate the "interferon signature" in peripheral blood.

A hierarchical model for estimating significance levels of non-parametric linkage statistics for large pedigrees

The significance level of a non-parametric linkage (NPL) statistic is often found by simulation since the distribution of the test statistic is complex and unknown. Ideally, simulation occurs by randomly assigning founder genotypes and then simulating meiotic events for the descendants in the pedigree, commonly referred to as 'gene dropping'. The missing data pattern in the original pedigree, including lack of phase information (due to unordered genotypes), is then imposed on the simulated pedigree. However, this approach is usually computationally infeasible for larger pedigrees which require Markov chain Monte Carlo (MCMC) techniques to calculate the statistic, as an additional MCMC run is required to estimate the statistic for each gene drop. In this work, we propose a novel method to estimate the significance level of the NPL statistic in large pedigrees. This is accomplished by constructing a hierarchical model, which allows estimation of the NPL statistic variability via separate estimation of the Markov chain and gene dropping variability. The significance level is estimated by fitting a parametric model to the statistic and using the method of moments to obtain parameter estimates. In a simulation study we found our hierarchical model estimates to be very close to the gold standard empirical estimates, and offer substantial improvements over the existing conservative method used by the software SimWalk2. The estimation procedure significantly reduces the computational time relative to the ideal empirical estimate, allowing for an accurate estimate of the significance level in a more manageable amount of time.

Replication and refinement of linkage of posterior polymorphous corneal dystrophy to the posterior polymorphous corneal dystrophy 1 locus on chromosome 20

PURPOSE

The study purpose was to identify the genetic basis of posterior polymorphous corneal dystrophy, an autosomal dominant disorder of the corneal endothelium that is associated with the development of corneal edema, necessitating corneal transplantation for visual rehabilitation. Glaucoma also develops in up to 40% of patients with posterior polymorphous corneal dystrophy.

METHODS

Linkage analysis, using microsatellite markers previously used to demonstrate linkage of posterior polymorphous corneal dystrophy to the chromosome 20 candidate region known as posterior polymorphous corneal dystrophy 1, was performed in 29 members of a family with posterior polymorphous corneal dystrophy. Thirty-four microsatellite markers were used to refine the posterior polymorphous corneal dystrophy 1 interval. TCF8, located on chromosome 10, was screened in an affected family member to exclude posterior polymorphous corneal dystrophy 3.

RESULTS

Significant evidence of linkage to the posterior polymorphous corneal dystrophy 1 interval was obtained with both single-point and multipoint analyses. The largest single-point log odds ratio score obtained was 4.38 (theta=0) at marker D20S471; within 4.7 Mbp (7.2 cM) of D20S471 eight markers provided single-point log odds ratio scores of greater than 3.00 and three markers provided single-point log odds ratio scores greater than 4.00. The largest multipoint log odds ratio score obtained was 4.83, found across the adjacent markers D20S844, D20S191, D20S484, and D20S111. The support interval for posterior polymorphous corneal dystrophy 1 in the family we report is approximately 13.5 Mbp (10 cM) long and lies between the markers D20S182 and D20S195. Eleven markers have multipoint log odds ratio scores greater than 4.0 within this region. No coding region mutations were identified in TCF8 in an affected member of the family, effectively excluding posterior polymorphous corneal dystrophy 3.

CONCLUSIONS

The originally described 19.8 cM posterior polymorphous corneal dystrophy 1 candidate disease interval has been refined to a 10 cM interval between markers D20S182 and D20S195. A portion of this refined interval overlaps a more recently reported posterior polymorphous corneal dystrophy 1 interval, with only 20 known and predicted genes mapped to the 2.4 cM common interval.

A genetic linkage map of the vervet monkey (Chlorocebus aethiops sabaeus)

The spectacular progress in genomics increasingly highlights the importance of comparative biology in biomedical research. In particular, nonhuman primates, as model systems, provide a crucial intermediate between humans and mice. The close similarities between humans and other primates are stimulating primate studies in virtually every area of biomedical research, including development, anatomy, physiology, immunology, and behavior. The vervet monkey (Chlorocebus aethiops sabaeus) is an important model for studying human diseases and complex traits, especially behavior. We have developed a vervet genetic linkage map to enable mapping complex traits in this model organism and facilitate comparative genomic analysis between vervet and other primates. Here we report construction of an initial genetic map built with about 360 human orthologous short tandem repeats (STRs) that were genotyped in 434 members of an extended vervet pedigree. The map includes 226 markers mapped in a unique order with a resolution of 9.8 Kosambi centimorgans (cM) in the vervet monkey genome, and with a total length (including all 360 markers) of 2726 cM. At least one complex and 11 simple rearrangements in marker order distinguish vervet chromosomes from human homologs. While inversions and insertions can explain a similar number of changes in marker order between vervet and rhesus homologs, mostly inversions are observed when vervet chromosome organization is compared to that in human and chimpanzee. Our results support the notion that large inversions played a less prominent role in the evolution within the group of the Old World monkeys compared to the human and chimpanzee lineages.

Three-dimensional diffuse optical tomography of osteoarthritis: initial results in the finger joints

This work presents a pilot study to show the potential of an emerging imaging modality, near-infrared diffuse optical tomography (DOT), for the diagnosis of osteoarthritis (OA). We report quantitative absorption and scattering images of joint tissue that allow for differentiation between diseased and healthy joints. An automatic, multichannel optical imaging system is used to image finger joints from two OA patients and three healthy volunteers. 3-D optical images of the joint tissue are recovered using a finite-element-based reconstruction algorithm. The reconstructed images demonstrate differences in optical properties at the joint region (cartilage/synovial fluid) between the OA and healthy joints. Quantitative analysis from the patients and healthy volunteers also indicate that the recovered joint sizes are consistent with those from x-ray findings. The results of this pilot study show potential for quantitative imaging and diagnosis of early OA by DOT.

Accumulation of antigen-specific B and T cells in ectopic lymphoid tissue after immunization (99.11)

Objective: Ectopic lymphoid tissue is associated with autoantibody production. Although reminiscent of authentic secondary lymphoid tissue, it is unclear if it can serve as a site of cognate T-B cell interactions leading to autoimmunity. This question was examined in mice with ectopic lymphoid tissue induced by tetramethylpecadentane (TMPD).

Methods: B6 and BALB/c mice were treated i.p. with TMPD followed 3 mo later by s.c. immunization with NP-KLH or NP-OVA. NP specific B cells were identified by analysis of VH gene usage, flow cytometry, and ELISPOT. OVA transgenic T cells from DO.11 mice were transferred i.v. into BALB/c mice 3 d before immunizing with NP-OVA. OVA-specific T cells were identified by flow cytometry and proliferating B and T cells by BrDU staining.

Results: 12 d after immunizing with NP-KLH, 90% of H chain genes from ectopic lymphoid tissue of B6 mice bore V186.2 or analogous NP-specific VH sequences. B cells stained by NP-PE were identified in ectopic lymphoid tissue by flow cytometry and secretion of anti-NP antibodies shown by ELISPOT. The ectopic lymphoid tissue and draining lymph nodes also had numerous OVA-specific T cells 7 d after immunization with NP-OVA and there was a progressive increase of BrDU+ T and B cells.

Conclusion: The data suggest that following immunization, antigen-specific B and T cells undergo a local germinal center-like reaction within ectopic lymphoid tissue.

Confirmation of psoriasis susceptibility loci on chromosome 6p21 and 20p13 in French families

Plaque psoriasis is a chronic inflammatory disorder of the skin. It is inherited as a multifactorial trait, with a strong genetic component. Linkage studies have identified a large number of disease loci, but very few could be replicated in independent family sets. In this study, we present the results of a genome-wide scan carried out in 14 French extended families. Candidate regions were then tested in a second set of 32 families. Analysis of the pooled samples confirmed linkage to chromosomes 6p21 (Z(MLB) score=3.5, P=0.0002) and 20p13 (Z(MLB) score=2.9, P=0.002), although there was little contribution of the second family set to the 20p13 linkage signal. Moreover, we identified four additional loci potentially linked to psoriasis. The major histocompatibility complex region on 6p21 is a major susceptibility locus, referred to as PSORS1, which has been found in most of the studies published to date. The 20p13 locus segregates independently of PSORS1 in psoriasis families. It has previously been thought to be involved in the predisposition to psoriasis and other inflammatory disorders such as atopic dermatitis (AD) and asthma. Although psoriasis and AD rarely occur together, this reinforces the hypothesis that psoriasis is influenced by genes with general effects on inflammation and immunity.

Measurement of vaginal length: Reliability of the vaginal sound--a Gynecologic Oncology Group study

A decrease in vaginal length associated with treatments for gynecological malignancies, particularly pelvic radiotherapy, negatively impacts sexuality. Research into this important problem has been hampered by a lack of instrumentation to measure vaginal length. The Gynecologic Oncology Group recently evaluated the reliability of an instrument, the "vaginal sound," designed to measure vaginal length. Eighty-eight physicians and nurses attended a training session in the use of the vaginal sound that included a clinical practicum with live models. Reliability was assessed at the time of the practicum. The instrument performed well, with vaginal lengths in models without cancer in the upper range of normal as documented by Masters and Johnson. The vaginal sound also appeared to be sensitive to hypothesized changes in vaginal length. Interrater reliability was high with intraclass correlation coefficients of 0.88 among instructors and 0.76 among trainees. In conclusion, the vaginal sound is a simple, yet reproducible measure and adds methodologic rigor to studies of vaginal length.

Merging microsatellite data

Genotype calling procedures vary from laboratory to laboratory for many microsatellite markers. Even within the same laboratory, application of different experimental protocols often leads to ambiguities. The impact of these ambiguities ranges from irksome to devastating. Resolving the ambiguities can increase effective sample size and preserve evidence in favor of disease-marker associations. Because different data sets may contain different numbers of alleles, merging is unfortunately not a simple process of matching alleles one to one. Merging data sets manually is difficult, time-consuming, and error-prone due to differences in genotyping hardware, binning methods, molecular weight standards, and curve fitting algorithms. Merging is particularly difficult if few or no samples occur in common, or if samples are drawn from ethnic groups with widely varying allele frequencies. It is dangerous to align alleles simply by adding a constant number of base pairs to the alleles of one of the data sets. To address these issues, we have developed a Bayesian model and a Markov chain Monte Carlo (MCMC) algorithm for sampling the posterior distribution under the model. Our computer program, MicroMerge, implements the algorithm and almost always accurately and efficiently finds the most likely correct alignment. Common allele frequencies across laboratories in the same ethnic group are the single most important cue in the model. MicroMerge computes the allelic alignments with the greatest posterior probabilities under several merging options. It also reports when data sets cannot be confidently merged. These features are emphasized in our analysis of simulated and real data.

Trait components provide tools to dissect the genetic susceptibility of migraine

The commonly used "end diagnosis" phenotype that is adopted in linkage and association studies of complex traits is likely to represent an oversimplified model of the genetic background of a disease. This is also likely to be the case for common types of migraine, for which no convincingly associated genetic variants have been reported. In headache disorders, most genetic studies have used end diagnoses of the International Headache Society (IHS) classification as phenotypes. Here, we introduce an alternative strategy; we use trait components--individual clinical symptoms of migraine--to determine affection status in genomewide linkage analyses of migraine-affected families. We identified linkage between several traits and markers on chromosome 4q24 (highest LOD score under locus heterogeneity [HLOD] 4.52), a locus we previously reported to be linked to the end diagnosis migraine with aura. The pulsation trait identified a novel locus on 17p13 (HLOD 4.65). Additionally, a trait combination phenotype (IHS full criteria) revealed a locus on 18q12 (HLOD 3.29), and the age at onset trait revealed a locus on 4q28 (HLOD 2.99). Furthermore, suggestive or nearly suggestive evidence of linkage to four additional loci was observed with the traits phonophobia (10q22) and aggravation by physical exercise (12q21, 15q14, and Xp21), and, interestingly, these loci have been linked to migraine in previous studies. Our findings suggest that the use of symptom components of migraine instead of the end diagnosis provides a useful tool in stratifying the sample for genetic studies.

Type I interferon production by tertiary lymphoid tissue developing in response to 2,6,10,14-tetramethyl-pentadecane (pristane)

Lymphoid neogenesis is associated with antibody-mediated autoimmune diseases such as Sjogren's syndrome and rheumatoid arthritis. Although systemic lupus erythematosus is the prototypical B-cell-mediated autoimmune disease, the role of lymphoid neogenesis in its pathogenesis is unknown. Intraperitoneal injection of 2,6,10,14-tetramethyl-pentadecane (TMPD, pristane) or mineral oil causes lipogranuloma formation in mice, but only TMPD-treated mice develop lupus. We report that lipogranulomas are a form of lymphoid neogenesis. Immunoperoxidase staining of lipogranulomas revealed B cells, CD4(+) T cells, and dendritic cells and in some cases organization into T- and B-cell zones. Lipogranulomas also expressed the lymphoid chemokines CCL21, CCL19, CXCL13, CXCL12, and CCL22. Expression of the type I interferon (IFN-I)-inducible genes Mx1, IRF7, IP-10, and ISG-15 was greatly increased in TMPD- versus mineral oil-induced lipogranulomas. Dendritic cells from TMPD lipogranulomas underwent activation/maturation with high CD86 and interleukin-12 expression. Magnetic bead depletion of dendritic cells markedly diminished IFN-inducible gene (Mx1) expression. We conclude that TMPD-induced lupus is associated with the formation of ectopic lymphoid tissue containing activated dendritic cells producing IFN-I and interleukin-12. In view of the increased IFN-I production in systemic lupus erythematosus, these studies suggest that IFN-I from ectopic lymphoid tissue could play a role in the pathogenesis of experimental lupus in mice.

Lupus-like disease and high interferon levels corresponding to trisomy of the type I interferon cluster on chromosome 9p

OBJECTIVE

Systemic lupus erythematosus (SLE) is associated with type I interferons (IFNs) and can be induced by IFNalpha treatment. This study looked for evidence of autoimmunity in a pedigree consisting of 4 family members with a balanced translocation 9;21 and 2 members with an unbalanced translocation resulting in trisomy of the short (p) arm and part of the long (q) arm of chromosome 9. These latter 2 subjects had 3 copies of the IFN gene cluster.

METHODS

Subjects were evaluated clinically and serologically for autoimmune disease. Expression levels of IFNalpha4, IFNbeta, the type I IFN-inducible gene Mx1, the type I IFN receptor, interleukin-6, and tumor necrosis factor alpha were determined by real-time polymerase chain reaction. Circulating plasmacytoid dendritic cells, the main IFN-producing cells, were quantified by flow cytometry.

RESULTS

Both subjects with trisomy of chromosome 9p had a lupus-like syndrome with joint manifestations and antinuclear antibodies: one had anti-RNP and antiphospholipid autoantibodies, and the other had anti-Ro 60. The 3 family members with a balanced translocation 9;21 had no clinical or serologic evidence of autoimmunity, similar to that in relatives who were unaffected by the chromosomal translocation. In the 2 subjects with trisomy of 9p, high levels of IFNalpha/beta (comparable with those found in patients with SLE), increased signaling through the IFN receptor (as indicated by high Mx1 expression), and low levels of circulating plasmacytoid dendritic cells (as observed in patients with SLE) were evident. These abnormalities were not seen in individuals with a balanced translocation.

CONCLUSION

Trisomy of the type I IFN cluster of chromosome 9p was associated with lupus-like autoimmunity and increased IFNalpha/beta and IFN receptor signaling. The data support the idea that abnormal regulation of type I IFN production is involved in the pathogenesis of SLE.

Variance component models for X-linked QTLs

This paper discusses the theory and implementation of a model for mapping X-linked quantitative trait loci (QTL). As a result of X inactivation, a female's body is subdivided into a number of patches. In each patch one of her two X chromosomes is randomly switched off. This smooths the allelic contributions in a heterozygote and implies that females should show less trait variation than males for an X-linked trait. The latest version of the genetic analysis program Mendel incorporates a simple variance component version of this model. An application to head circumference in autistic children illustrates Mendel in action.

Association testing with Mendel

This report presents an overview of association testing strategies from a user's perspective, with particular attention to the capabilities of the computer program Mendel. Association testing is driven by the nature of the study sample, the nature of the disease trait, and the kind of markers employed. The practicing statistician must also choose whether to conduct parametric or nonparametric tests. Because of the complexities involved, Mendel offers users several analysis options. The different options are tied together by shared input and output conventions and a shared language for defining models. Mendel also features new statistics and theory found in no other genetics software. The most important innovations include: association testing by penetrance estimation, expansion of matched-pair designs to permutation unit designs, and a rigorous implementation of the measured genotype approach for quantitative trait loci. This report explains how Mendel imputes allele counts and conducts both asymptotic and permutation tests in the measured genotype framework.

Fine mapping of the multiple sclerosis susceptibility locus on 5p14-p12

Linkage analyses have identified four major MS susceptibility loci in Finns. Here we have fine mapped the region on chromosome 5p in 28 Finnish MS families. Marker D5S416 provided the highest pairwise LOD score, and multipoint and haplotype analyses restrict the critical region to about 5.3 Mb on 5p15 between markers D5S1987 and D5S416. Ascertaining for HLA type and geographical origin indicated that families with and without the HLA DR15 risk haplotype, as well as families within and outside an internal high-risk region, contributed to the linkage to 5p, implying the general significance for this locus in Finnish MS families.

Association of anti-nucleoprotein autoantibodies with upregulation of Type I interferon-inducible gene transcripts and dendritic cell maturation in systemic lupus erythematosus

Lupus patients selectively produce autoantibodies against nucleoproteins. Since the RNA/DNA components of these autoantigens are endogenous TLR ligands capable of stimulating Type I interferon (IFN-I) production, we asked whether autoantibodies against the ribonucleoproteins Sm/RNP and Ro60 and double-stranded DNA are associated with high levels of IFN-I. IFN-I levels were increased in SLE (n = 88) vs. other autoimmune diseases (n = 82) and controls (n = 57) (P < 0.0001) and were associated positively with autoantibodies against Sm/RNP, Ro60/La, and dsDNA but negatively with anti-phospholipid. Low numbers of circulating plasmacytoid and myeloid dendritic cells also were associated with these autoantibodies. The IFN-I and dendritic cell abnormalities correlated with disease severity and were not therapy-related. These findings suggest that immunostimulatory nucleic acid components of autoantigens may act as endogenous adjuvants by promoting IFN-I production and dendritic cell maturation, helping to explain the high prevalence of autoantibodies against nucleoprotein antigens in SLE.

Diagnostic accuracy for lupus and other systemic autoimmune diseases in the community setting

BACKGROUND

Most individuals with autoimmune and other immune disorders undergo initial evaluation in the community setting. Since misdiagnosis of systemic autoimmune diseases can have serious consequences, we evaluated community physicians' accuracy in diagnosing autoimmune diseases and the consequences of misdiagnosis.

METHODS

We studied the patients referred to our Autoimmune Disease Center for 13 months (n = 476). We estimated the degree of agreement with the final diagnosis (kappa statistic) and the accuracy indexes (sensitivity, specificity, and predictive values) of the referring physicians' diagnoses.

RESULTS

We found a 49% agreement between the referring and final diagnoses (kappa = 0.36). Of 263 patients referred with a presumptive diagnosis of systemic lupus erythematosus (SLE), 125 received a diagnosis of other conditions (kappa = 0.34). Of those referred with SLE, 76 (29%) were seropositive for antinuclear antibodies but did not have autoimmune disease. The degree of agreement for referring rheumatologists (kappa = 0.55) was better than that for nonrheumatologists (kappa = 0.32). Stepwise logistic regression indicated that rheumatologists were 4 times more likely to make an accurate diagnosis of SLE than were nonrheumatologists (P<.003). Thirty-nine patients who were seropositive for antinuclear antibodies but had no autoimmune disease had been treated with corticosteroids at dosages as high as 60 mg/d.

CONCLUSIONS

Many patients with a positive antinuclear antibody test are incorrectly given a diagnosis of SLE and sometimes treated with toxic medications. The data support the importance of continuing medical education for community physicians in screening for autoimmune diseases and identifying patients who may benefit from early referral to a specialist.

Efficient simulation of P values for linkage analysis

In many genetic linkage analyses, the P value is obtained through simulation since the underlying distribution of the test statistic is complex and unknown. However, this can be very computationally intensive. A "bootstrap/replicate pool" approach has been suggested that generates P values more efficiently in terms of computation by resampling sums from a small set of simulated replicates for each pedigree. The replicate pool idea has been successfully applied, but, to our knowledge, has never been theoretically studied. An entirely different method for increasing the computational efficiency of P value simulation is Besag and Clifford's sequential sampling method. We propose an algorithm which combines Besag and Clifford's method with the replicate pool method to efficiently estimate P values for linkage studies. We derive variance expressions for the P value estimates from the replicate pool method and from our proposed hybrid method, and use these to show that the hybrid estimator has a substantial advantage over the other methods in most situations.

Locus for quantitative HDL-cholesterol on chromosome 10q in Finnish families with dyslipidemia

Decreased HDL-cholesterol (HDL-C) and familial combined hyperlipidemia (FCHL) are the two most common familial dyslipidemias predisposing to premature coronary heart disease (CHD). These dyslipidemias share many phenotypic features, suggesting a partially overlapping molecular pathogenesis. This was supported by our previous pooled data analysis of the genome scans for low HDL-C and FCHL, which identified three shared chromosomal regions for a qualitative HDL-C trait on 8q23.1, 16q23.3, and 20q13.32. This study further investigates these regions as well as two other loci we identified earlier for premature CHD on 2q31 and Xq24 and a locus for high serum triglycerides (TGs) on 10q11. We analyzed 67 microsatellite markers in an extended study sample of 1,109 individuals from 92 low HDL-C or FCHL families using both qualitative and quantitative lipid phenotypes. These analyses provided evidence for linkage (a logarithm of odds score of 3.2) on 10q11 using a quantitative HDL-C trait. Importantly, this region, previously linked to TGs, body mass index, and obesity, provided evidence for association for quantitative TGs (P = 0.0006) and for a combined trait of HDL-C and TGs (P = 0.008) with marker D10S546. Suggestive evidence for linkage also emerged for HDL-C on 2q31 and for TGs on 20q13.32. Finnish families ascertained for dyslipidemias thus suggest that 10q11, 2q31, and 20q13.32 harbor loci for HDL-C and TGs.

The prevalence of coeliac disease antibodies in patients with the antiphospholipid syndrome

High prevalence of coeliac disease (CD) has been reported in various autoimmune disorders, buthas not been studied in the antiphospholipid syndrome (APS). We aimed to establish the prevalence of CD antibodies in a cohort of APS patients, and to examine whether CD may be responsible for some of the manifestations of APS. Fifty-seven patients (47 females, 10 males) with APS were studied for clinical manifestations and serological markers of the disease, as well as the presence of anti-endomysial antibodies using an ELISA assay (EMA-ELISA). Control subjects were 171 healthy individuals, age- and sex-matched (141 females). Eight patients with APS (14%, six females) were found to have EMA-ELISA antibodies, compared with 2/141 (1.1%) of controls (P = 0.0003). Antibodies against beta2-glycoprotein-I (beta2GPI) epitopes (GRTCPKPDDLP) were more prevalent in EMA-positive patients than in EMA-negative patients (P = 0.006). Vasculitic skin lesions were significantly more common in EMA-ELISA-positive compared with EMA-ELISA-negative patients(62.5 versus 16.3%, P = 0.01). Among the skin manifestations, superficial cutaneous necrosis (37.5 versus 2%, P = 0.007) was more prevalent in EMA-ELISA-positive than in EMA-ELISA-negative patients. EMA-ELISA antibodies are common in APS, and their presence is associated with high prevalence of antibodies recognizing certain beta2-glycoprotein epitopes, and with cutaneous manifestations of APS.

Fine mapping of a multiple sclerosis locus to 2.5 Mb on chromosome 17q22-q24

Genome-wide linkage analyses performed in a Finnish study sample have identified four potential predisposing loci for multiple sclerosis (MS). Here we made an effort to restrict the wide linkage region on chromosome 17 with a dense set of 31 markers using multipoint linkage analyses and monitoring for shared marker alleles in MS chromosomes. We carried out the linkage analyses in 22 Finnish multiplex MS families originating from a regional subisolate that shows an exceptionally high prevalence of MS in order to minimize the genetic and environmental heterogeneity of the study sample. Thirty markers on the 23 cM initial interval gave positive pairwise LOD scores. We monitored for shared haplotypes among affected family members within a family, and identified an approximately 4 cM region flanked by the markers D17S1792 and ATA43A10 in 17 out of the 22 families (77.3%). The multipoint linkage analyses using Genehunter and SIMWALK 2.40 provided further evidence for the same 4 cM region, for example a maximal multipoint NPL score of 5.98 (P<0.0002). We observed nominal evidence for association to MS, with one marker flanking the shared region, and this association was replicated in the additional set of families. Using the combined power of linkage, association and shared haplotype analyses, we were thus able to restrict the MS locus on chromosome 17q from 23 cM to a 4 cM region covering a physical interval of approximately 2.5 Mb. Thus, this study describes the restriction of an MS locus outside the HLA region into a segment approachable by molecular tools.

A susceptibility locus for migraine with aura, on chromosome 4q24

Migraine is a complex neurovascular disorder with substantial evidence supporting a genetic contribution. Prior attempts to localize susceptibility loci for common forms of migraine have not produced conclusive evidence of linkage or association. To date, no genomewide screen for migraine has been published. We report results from a genomewide screen of 50 multigenerational, clinically well-defined Finnish families showing intergenerational transmission of migraine with aura (MA). The families were screened using 350 polymorphic microsatellite markers, with an average intermarker distance of 11 cM. Significant evidence of linkage was found between the MA phenotype and marker D4S1647 on 4q24. Using parametric two-point linkage analysis and assuming a dominant mode of inheritance, we found for this marker a maximum LOD score of 4.20 under locus homogeneity (P=.000006) or locus heterogeneity (P=.000011). Multipoint parametric (HLOD = 4.45; P=.0000058) and nonparametric (NPL(all) = 3.43; P=.0007) analyses support linkage in this region. Statistically significant linkage was not observed in any other chromosomal region.

Detection and integration of genotyping errors in statistical genetics

Detection of genotyping errors and integration of such errors in statistical analysis are relatively neglected topics, given their importance in gene mapping. A few inopportunely placed errors, if ignored, can tremendously affect evidence for linkage. The present study takes a fresh look at the calculation of pedigree likelihoods in the presence of genotyping error. To accommodate genotyping error, we present extensions to the Lander-Green-Kruglyak deterministic algorithm for small pedigrees and to the Markov-chain Monte Carlo stochastic algorithm for large pedigrees. These extensions can accommodate a variety of error models and refrain from simplifying assumptions, such as allowing, at most, one error per pedigree. In principle, almost any statistical genetic analysis can be performed taking errors into account, without actually correcting or deleting suspect genotypes. Three examples illustrate the possibilities. These examples make use of the full pedigree data, multiple linked markers, and a prior error model. The first example is the estimation of genotyping error rates from pedigree data. The second-and currently most useful-example is the computation of posterior mistyping probabilities. These probabilities cover both Mendelian-consistent and Mendelian-inconsistent errors. The third example is the selection of the true pedigree structure connecting a group of people from among several competing pedigree structures. Paternity testing and twin zygosity testing are typical applications.

Multipoint estimation of identity-by-descent probabilities at arbitrary positions among marker loci on general pedigrees

OBJECTIVES

To describe, implement, and test an efficient algorithm to obtain multipoint identity-by-descent (IBD) probabilities at arbitrary positions among marker loci for general pedigrees. Unlike existing programs, our algorithm can analyze data sets with large numbers of people and markers. The algorithm has been implemented in the SimWalk2 computer package.

METHODS

Using a rigorous testing regimen containing five pedigrees of various sizes with realistic marker data, we compared several widely used IBD computation programs: Allegro, Aspex, GeneHunter, MapMaker/Sibs, Mendel, Sage, SimWalk2, and Solar.

RESULTS

The testing revealed a few discrepancies, particularly on consanguineous pedigrees, but overall excellent results in the deterministic multipoint packages. SimWalk2 was also found to be in good agreement with the deterministic multipoint programs, usually matching to two decimal places the kinship coefficient that ranges from 0 to 1. However, the packages based on single-point IBD estimation, while consistent with each other, often showed poor results, disagreeing with the multipoint kinship results by as much as 0.5.

CONCLUSIONS

Our testing has clearly shown that multipoint IBD estimation is much better than single-point estimation. In addition, our testing has validated our algorithm for estimating IBD probabilities at arbitrary positions on general pedigrees.

The effect of customized insoles on the reduction of postwork discomfort

This study examined the effect of customized insoles in relieving postwork discomfort in healthy individuals whose jobs require long periods of standing and walking. CompuSole insoles were worn by 122 New York City Police Department officers for up to 5 weeks for an average of 7 hours per day. The officers walked an average of 3 miles per day. Before the study, one-fifth of the police officers in this study experienced foot pain or discomfort at the end of their workday; 15% had calluses, corns, or athlete's foot; 18% had sought treatment for a foot problem in the past; and 20% had worn foot orthoses. There was a significant reduction in tiredness in the feet at the end of the day after wearing the insoles, but no improvement in back or leg discomfort. At the end of the workday, 68% had less foot discomfort and 60% were more comfortable at work when wearing the insoles.