OP0017 VALIDATION OF GWAS-IDENTIFIED VARIANTS FOR ANTI-TNF DRUG RESPONSE IN RHEUMATOID ARTHRITIS: A META-ANALYSIS OF THREE LARGE COHORTS

Background:

The interplay between genetics and drug response in rheumatoid arthritis (RA) has shown that response to biologics varies between individuals and that a large proportion of patients show no clinical improvement (Plenge and Bridges, 2011). Despite the disappointing scenario, to date, only a few genetic markers have been consistently identified and we are far from being able to optimize drug dosing or prioritize drug combinations based on genetic findings.

Objectives:

With this background, we sought to validate the association of GWAS-identified variants for response to TNF inhibitors (TNFi) in a two-stage case control association study and to shed some light into the functional role of the most interesting markers.

Methods:

The discovery population consisted of 1361 RA patients ascertained through the REPAIR consortium and the DANBIO registry. RA patients fulfilled the 1987 revised American College of Rheumatology (ACR) and the ACR/EULAR 2010 classification criteria. The validation cohort included 706 Dutch RA patients from the DREAM registry. The study followed the Declaration of Helsinki and study participants gave their written informed consent to participate in the study, which was approved by the ethical review committee of participant institutions. Twenty-seven single-nucleotide polymorphisms (SNPs) were selected through a literature search of relevant GWAS. Linear regression analysis adjusted for age, sex and country of origin was used to determine the association between GWAS-identified SNPs and changes in DAS28 (ΔDAS28) after 3 or 6 months of treatment. The meta-analysis of both populations was performed using a fixed effect model. Correction for multiple testing was performed using the Bonferroni method but also considering the number of inheritance models tested (P=0.0009). To assess the role of the most interesting markers in modulating immune responses, stimulation experiments in whole blood, peripheral mononuclear cells (PBMCs) and monocyte-derived macrophages using a large number of pathogens and microbiome bacteria were performed in 408 subjects from the Human Functional Genomic Project cohort. We also evaluated the correlation of these SNPs with plasmatic levels of 108 inflammatory proteins, 7 serum steroid hormones and counts of 91 blood-derived immune cell populations.

Results:

The meta-analysis of the discovery cohort and DREAM registry including 2067 RA patients treated with TNFi revealed an overall association of the LINC02549rs7767069 SNP with a decreased drop in DAS28 that remained significant after correction for multiple testing (per-allele ORMeta=0.83, PMeta=0.000077; PHet=0.61). In addition, the meta-analysis of these large cohorts showed that each copy of the LARRC55rs717117G allele significantly decreased the drop in DAS28 in RF-positive patients (per-allele ORMeta=0.67, P=0.00058; PHet=0.06) whereas an opposite but not significant effect was found in RF-negative subjects (per-allele ORMeta=1.38, P=0.10; PInteraction=0.00028; PHet=0.45). Interestingly, the meta-analysis also showed potentially interesting but not statistically significant overall and RF-specific associations for the MAFBrs6071980 and CNTN5rs1813443 SNPs with ΔDAS28 (per-allele ORMeta_rs6071980=0.84, P=0.0059; PHet=0.63 and ORMeta_rs1813443_RF+=0.81, P=0.0059; PHet=0.69 and ORMeta_rs1813443_RF-=1.00, P=0.99; PHet=0.12; PInteraction=0.032). Although analysis of functional data is ongoing, so far, we found that carriers of the LARRC55rs717117G allele showed decreased levels of IL6 after stimulation of PBMCs with Borrelia burgdorferi and Escherichia Coli bacteria (P=0.00046 and 0.00044), which suggested a reduced IL6-mediated anti-inflammatory effect of this marker to worsen the response to TNFi.

Conclusion:

This study confirmed the influence of the LINC02549 and LARRC55 loci to determine the response to TNFi in RA patients and a weak effect of the MAFB and CNTN5 loci that needs to be further investigated.

References:

[1]Plenge RM et al 2011. Arthritis Rheum 63, 590-3.

ACKNOWLEDGEMENTS:

We thank all participants who have agreed to participate in this study. Authors also thank María Dolores Casares, Ángeles Molina, Carmen Oloriz for the collection of Spanish samples and Hans Jurgen Hoffmann, Marianne Thomsen, Vibeke Østergaard Thomsen, Malene Rohr Andersen, Lise Lotte B. Laursen, Helle Jørgensen, Ram Benny Christian Dessau, Niels Steen Krogh, Ulla Vogel, Paal Skytt Andersen, Ivan Brandslund, Steffen Bank, Frederik Trier Møller, Nikolai Toft and Niels Møller Andersen for the participation in collection and purification of Danish samples. We also thank the Danish Departments of Rheumatology for their implication in the collection of clinical data from RA patients included in the DANBIO cohort and the Danish Rheumatologic Biobank. Likewise, we would like to thank Teun van Herwaarden for steroid hormone measurements in serum samples from subjects ascertained through the HFGP initiative.

Disclosure of Interests:

None declared

Activation of nuclear receptor NR5A2 increases Glut4 expression and glucose metabolism in muscle cells

NR5A2 is a nuclear receptor which regulates the expression of genes involved in cholesterol metabolism, pluripotency maintenance and cell differentiation. It has been recently shown that DLPC, a NR5A2 ligand, prevents liver steatosis and improves insulin sensitivity in mouse models of insulin resistance, an effect that has been associated with changes in glucose and fatty acids metabolism in liver. Because skeletal muscle is a major tissue in clearing glucose from blood, we studied the effect of the activation of NR5A2 on muscle metabolism by using cultures of C2C12, a mouse-derived cell line widely used as a model of skeletal muscle. Treatment of C2C12 with DLPC resulted in increased levels of expression of GLUT4 and also of several genes related to glycolysis and glycogen metabolism. These changes were accompanied by an increased glucose uptake. In addition, the activation of NR5A2 produced a reduction in the oxidation of fatty acids, an effect which disappeared in low-glucose conditions. Our results suggest that NR5A2, mostly by enhancing glucose uptake, switches muscle cells into a state of glucose preference. The increased use of glucose by muscle might constitute another mechanism by which NR5A2 improves blood glucose levels and restores insulin sensitivity.

Contrast-enhanced nanofocus computed tomography images the cartilage subtissue architecture in three dimensions

We describe a non-destructive imaging method, named contrast-enhanced nanofocus X-ray computed tomography (CE-nanoCT), that permits simultaneously imaging and quantifying in 3D the (sub)tissue architecture and (biochemical) composition of cartilage and bone in small animal models at a novel contrast and spatial resolution. To demonstrate the potential of this novel methodology, a newborn mouse was scanned using CE-nanoCT. This allowed simultaneously visualising the bone and cartilage structure much like the traditional alcian blue-alizarin red skeletal stain. Additionally, it enabled a 3D visualisation at such a high spatial image resolution that internal, micro-scale structures could be digitally dissected and evaluated for size, structure and composition. Ex vivo treatment with papain, that is known to specifically remove the non-calcified cartilage layer but keep the calcified cartilage intact, proved CE-nanoCT to be applicable to visualise the subdivisions within the hyaline cartilage of the articular joint of mice. The quantitative power of CE-nanoCT in vivo was evaluated using a mouse model for osteoarthritis (OA), where OA-like cartilage lesions are induced by meniscus destabilisation surgery. The thickness of both the non-calcified and calcified cartilage layer in the knee joint of such mice was visualised and quantified in 3D and compared to unaffected mice. Finally, to show that different forms of cartilage and tissue combinations can be distinguished using CE-nanoCT, different cartilaginous body parts of the mouse were imaged. In conclusion, CE-nanoCT can provide novel insights in preclinical research by quantifying in a non-destructive 3D manner pathological differences, in particular in developing mice, newborns or adults.

Association of ACACB polymorphisms with obesity and diabetes

Acetyl-CoA carboxylase beta, encoded by the ACAB gene, plays an important role in the oxidation of fatty acids. The aim of this study was to check the hypothesis that allelic variants of ACACB influence the risk of obesity and type 2 diabetes mellitus. Twenty five tagging single nucleotide polymorphisms (SNPs) capturing common variants of the ACACB gene were selected and analyzed in two cohorts including 1695 postmenopausal women of the general population and in 161 women with severe obesity (BMI>35). In vitro binding of transcription factors was explored by electrophoretic mobility shift assays (EMSA). T alleles at the rs2268388 locus were overrepresented in women with severe obesity (18% vs. 10% in controls; OR 1.74 [95% confidence interval 1.30-2.47]), which was statistically significant after multiple-test adjustment (p=0.0004). Likewise, T alleles at the rs2268388 locus and C alleles at the rs2239607 locus were associated with diabetes, in the discovery as well as in the replication cohorts, even after women with severe obesity were excluded (OR 3.6 and 2.8, for TT and CC homozygotes, respectively). Allelic differences in the binding affinity for nuclear proteins were revealed in vitro by EMSA and competition experiments were consistent with the binding of glucorticoid receptor and serum response factor. In conclusion, common polymorphisms of ACACB gene are associated with obesity and, independently, with type 2 diabetes in postmenopausal women, suggesting that the activity of acetyl-CoA carboxylase beta plays an important role in these disorders related to energy metabolism.

Association of genetic polymorphisms in ESR2, HSD17B1, ABCB1, and SHBG genes with colorectal cancer risk

The incidence rates and relative risks for colorectal cancer (CRC) are higher in men than in women. Sex steroids may play a role in this gender-associated difference in CRC risk. This study was conducted to explore the relationship of single nucleotide polymorphisms (SNPs) in steroid hormone signaling (ESR1, ESR2, PGR, NR1I2, and SHBG), phase I- and II-metabolizing enzyme (COMT, HSD17B1, CYP1A1, CYP17A1, CYP1A2, CYP1B1, CYP2C9, CYP3A4, CYP2C19, and GSTP1), and hormone transporter (ABCB1) genes with the risk of CRC in German women and men, separately. From the population-based DACHS study (South Germany), 47 putatively functional SNPs were genotyped in 1798 CRC cases (746 women and 1052 men) and 1810 controls (732 women and 1078 men). Significant allele dose-response associations were observed with ESR2_rs1255998, ESR2_rs928554, HSD17B1_rs605059, and ABCB1_rs2229109 in women (P trend=0.004, 0.05, 0.03, and 0.05 respectively) and with ABCB1_rs1045642, ABCB1_rs9282564, and SHBG_rs6259 in men (P trend=0.01, 0.03, and 0.02 respectively). The ESR2_rs1255998_G allele showed the most significant association with risk for CRC in women, with a per-allele odds ratio (OR) of 0.68 (95% confidence interval (CI) 0.52-0.88). This finding was replicated in an independent study from North Germany including 1076 female CRC cases and 1151 controls (OR=0.84, 95% CI 0.71-1.04), yielding a per-allele OR of 0.80 (95% CI 0.69-0.93, P trend=0.003) in the pooled sample. These findings implicate a role of ESR2 in the risk for developing CRC in women and suggest that HSD17B1, ABCB1, and SHBG genes may contribute to sex steroid-mediated effects on CRC development.

[Association between genetic polymorphism in the promotor region of CD209 and propensity to develop invasive pulmonary aspergillosis]

Fungi of the genus Aspergillus are found everywhere in the natural environment; they cause invasive pulmonary aspergillosis (IPA), an infectious complication common in immunocompromised individuals, which has a mortality rate of up to 90% in patients with hematological malignancy. The first line of defense of innate immunity is the recognition of Aspergillus conidia by dendritic cells or alveolar macrophages. DC-SIGN is an integrin directly involved in this recognition; its degree of expression in immune cells and its functionality may be partly determined by genetic variations. The objective of this study was to determine whether the presence of polymorphisms of a single nucleotide in the DC-SIGN gene increases the risk of invasive pulmonary aspergillosis. For this purpose, the variants DC-SIGN-139A/G (rs2287886) and DC-SIGN+11C/G (rs7252229) were analyzed In 314 subjects (152 patients with hematologic malignancy and 162 healthy controls). Of the 152 hematologic cancer patients, 81 were diagnosed with demonstrated invasive pulmonary aspergillosis per EORTC/IFICG criteria, and the remaining 71 patients had no symptoms of the infection. An association was found between the variant DC-SIGN-139(A/G) and resistance to IPA. Carriers of the allele A (A/A + A/G) were significantly more resistant to the infection than patients with the G/G genotype (p = 0.0574). Analysis of the serum concentration of the galactomannan antigen supported the hypothesis that this polymorphism may be implicated in the susceptibility to suffer invasive pulmonary aspergillosis. Although the difference was not statistically significant, carriers of the allele G had a higher frequency of positive galactomannans than subjects with the genotype A/A (p = 0.1921). These results suggest that the variant DC-SIGN-139(A/G) in the DC-SIGN gene promoter influences the risk of invasive pulmonary aspergillosis and may therefore be used as a genetic biomarker to stratify patients according to risk.

TNFR1 mRNA expression level and TNFR1 gene polymorphisms are predictive markers for susceptibility to develop invasive pulmonary aspergillosis

Tumour necrosis factor (TNF) is primarily secreted by monocytes/macrophages and activated T lymphocytes in response to fungal infections. TNF acts through TNF receptor 1 (TNFR1) triggering a pro-inflammatory response, and therefore plays a pivotal role in immune regulation and host immune responses. We hypothesized that single nucleotide polymorphisms (SNPs) in TNFR1 gene may influence the innate immune response against Aspergillus. Three SNPs were genotyped in 275 individuals (144 immunocompromised haematological patients with high-risk of developing IPA and 131 healthy controls): TNFR1(-383(A/C)) (rs2234649) and TNFR1(-609(G/T)) (rs4149570) in the 5 prime UTR region, and TNFR1(+36(A/G)) SNP (rs767455) in the first exon of the gene. Of the 144 haematological patients, 77 patients developed Invasive Pulmonary Aspergillosis (IPA) infection and the remaining 67 patients were not infected. TNFR1(+36(A/G)) and TNFR1(-609(G/T)) were associated with IPA susceptibility (p=0.033 and p=0.018, respectively). A role of TNFR1 genetic variants in the susceptibility of patients to develop IPA was also supported by the significantly lower TNFR1 mRNA expression level in IPA than in IPA-resistant patients and the strong correlation between the TNFR1(-609) genetic variant and the expression levels of TNFR1. There was also a tendency for a higher frequency of galactomannan (GM) positivity in patients with TNFR1(-609G/G) genotype than in patients with TNFR1(-609G/T) (p=0.0909) or TNFR1(-609T/T) (p=0.0913) genotype. Predictive sequence analysis of the effects of TNFR1(-609) promoter polymorphism revealed that this SNP might play a critical role in modifying the affinity of ICSBP/IRF-8, a transcription factor that is involved in the TNFR1-mediated activation of NFkappaB signalling pathway. Taken together, these data suggest that TNFR1 polymorphisms influence the risk of IPA disease and might be useful for risk stratification strategies. These findings need to be confirmed in validation studies with larger samples of haematological patients.

IL1 gene cluster polymorphisms and its haplotypes may predict the risk to develop invasive pulmonary aspergillosis and modulate C-reactive protein level

OBJECTIVE

The aim of this study was to determine whether interleukin-1 alpha (IL1alpha), interleukin-1 beta (IL1beta), and IL1 receptor antagonist (IL1Ra) polymorphisms are implicated in invasive pulmonary aspergillosis (IPA) pathogenesis.

MATERIALS AND METHODS

Subjects comprised 110 hematological patients and 148 healthy controls. Genotypic and allelic frequencies were similar between hematological patients and controls. IPA was diagnosed in 59 of the 110 patients according to consensus criteria published by the European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group (EORTC/IFICG).

RESULTS AND DISCUSSIONS

Individual locus analysis showed that IL1alpha and IL1Ra polymorphisms were not associated with the presence of IPA (p = 0.560 and p = 0.680, respectively). However, a trend towards a higher presence of IL1beta( - ) (511TT) genotype (or IL1beta(-511T) allele) in the IPA group than in the non-IPA patient group (p = 0.092 and p = 0.095, respectively) was found. Haplotype analysis revealed that VNTR2/-889C/-511T haplotype was strongly associated with susceptibility to develop IPA infection (p = 0.020). Haplotype analysis also showed an association between VNTR2/-889C/-511C haplotype and resistance to IPA infection (p = 0.028). Furthermore, patients with IL1Ra VNTR2/2 and IL1beta(-511)T/T genotypes had a higher positive serum galactomannan percentage versus patients with other genotypes. Finally, C-reactive protein (CRP) production was significantly associated with IL1 gene cluster polymorphisms, although CRP values were similar between IPA and non-IPA groups.

CONCLUSION

These findings indicate a critical role of IL1 gene cluster polymorphisms in the susceptibility to IPA infection and CRP production.

Loss of alleles in vestibular schwannomas: use of microsatellite markers on chromosome 22

OBJECTIVE

Using highly informative microsatellite markers flanking the neurofibromatosis type 2 gene, we determined the frequency of chromosome 22 allele loss in vestibular schwannomas.

DESIGN

Peripheral lymphocyte/vestibular schwannoma DNA pairs were analyzed with five different microsatellite markers on chromosome 22.

PATIENTS

Samples were taken from 32 patients (17 females and 15 males). Twenty-seven tumors occurred sporadically, and five were from patients with neurofibromatosis type 2.

RESULTS

Using the microsatellite markers D22S351, CRYB2, D22S268, D22S304, and interleukin type 2RP3, we found loss of heterozygosity for at least two markers in 12 tumors. Ten tumors showed loss of heterozygosity for markers flanking the neurofibromatosis type 2 gene. Although microsatellite markers require little DNA for analysis and are highly informative, allele patterns may be difficult to interpret in some cases.

CONCLUSIONS

Loss of heterozygosity of chromosome 22 alleles was a frequent event in vestibular schwannomas. In 10 tumors, heterozygosity was lost for centromeric and telomeric markers indicating likely monosomy 22. However, 63% of tumors did not reveal a detectable chromosomal loss. Unless a second vestibular schwannoma locus exists, these tumors likely harbor point mutations in the neurofibromatosis type 2 gene or deletions below the level of resolution of the markers used in this study.

Effects of deoxycorticosterone on renal vascular reactivity and flow-pressure curve in spontaneously hypertensive rats

The role of mineralocorticoids as sodium retaining hormones has been recently enlarged to include their function as modulators of cardiovascular function and injury. This study evaluated the contribution of possible functional changes in resistance vessels to the additional BP increase produced by the chronic administration of DOCA to SHR. The flow-pressure curve and renal responses to vasoconstrictors (phenylephrine [Phe] and angiotensin II [AII]) and vasodilators (acetylcholine [ACh] and nitroprusside [NP]) were characterized in isolated kidneys from Wistar Kyoto (WKY) and SHR treated or untreated with DOCA for nine weeks. DOCA increased BP in SHR but did not modify BP in WKY rats. Kidneys from SHR showed enhanced reactivity to Phe and AII that was not increased by DOCA. DOCA reduced sensitivity to AII in SHR. Responsiveness to ACh was increased in SHR and was not attenuated by DOCA in WKY or SHR. Vasodilator response to NP was not significantly affected by DOCA in WKY or SHR. The flow-pressure curve was markedly up-shifted in SHR when compared with kidneys from WKY rats. DOCA administration did not modify the flow-pressure curve in WKY but produced attenuation at low flow levels in SHR. Our results demonstrate that DOCA increases BP in SHR but does not increase the flow-pressure curve or renal vascular reactivity to vasoconstrictors, and does not reduce responsiveness to endothelium-dependent and independent vasodilators in SHR or WKY rats. Therefore, our data suggest that the BP increase produced by DOCA in SHR is not related to abnormalities in vascular function in resistance vessels.

Contribution of endothelium-derived relaxing factors to P2Y-purinoceptor-induced vasodilation in the isolated rat kidney

We examined the role of endothelium-derived relaxing factors nitric oxide (NO), endothelium-derived hyperpolarising factor (EDHF), and prostaglandins (PGs) to P(2Y1)- and P(2Y2)-purinoceptor-induced vasodilation in isolated rat kidney. To do it, we analysed the renal response to ATP, 2-methylthio ATP, and UTP in rat renal vasculature under normal conditions and after the administration of: N(w)-nitro-L-arginine (L-NAME), increased K(+) concentration, indomethacin, and L-NAME and increased K(+) together. Our results indicate that the vasodilator response to P(2Y1)- and P(2Y2)-purinoceptor activation in the isolated perfused kidney of rats is subserved by EDHF and NO.

[Scedosporium apiospermum external otitis.]

We report a case of Scedosporium apiospermum external otitis. The patient was topically treated with miconazole cream and achieved a clinical and mycological cure. The etiology, diagnosis and treatment of external fungal otitis are discussed.

Association of collagen type 1 alpha1 gene polymorphism with bone density in early childhood

Osteoporosis is a disease characterized by the development of nontraumatic fractures, most commonly in the vertebrae of elderly women. Approximately 500,000 elderly women in the United States are newly diagnosed with vertebral fractures every year, as the compressive strength of the vertebra, mainly determined by the density of cancellous bone and its cross-sectional area, declines with age. A recent study in women suggested that a polymorphism in the Sp1 binding site of the collagen type I gene (COLIA1) was related to decreased vertebral bone mass and vertebral fractures. Determining the phenotypic trait(s) responsible for this relationship and whether this association is manifested in childhood would further define the structural basis for decreased bone mass and help identify children "at risk" for fractures later in life. We therefore studied the COLIA1 gene polymorphism and measurements of the size and the density of vertebral bone in 109 healthy, prepubertal girls. On average, 22 girls with the Ss genotype and one girl with the ss genotype had 6.7% and 49.4% lower cancellous bone density in the vertebrae than girls with the SS genotype. In contrast, there was no association between the size of the vertebrae and the COLIA1 genotypes.

Genetic locus heterogeneity in Lafora's progressive myoclonus epilepsy

In 1995, we mapped a gene for Lafora's progressive myoclonus epilepsy in chromosome 6q23-25. In 1997 and 1998, we reduced the size of the locus to 300 kb, and an international collaboration identified mutations in the protein tyrosine phosphatase gene. Here, we examine for heterogeneity through the admixture test in 22 families and estimate the proportion of linked families to be 75 to 85%. Extremely low posterior probabilities of linkage (Wi), exclusionary LOD scores, and haplotypes identify 4 families unlikely to be linked to chromosome 6q24.

Mapping and positional cloning of common idiopathic generalized epilepsies: juvenile myoclonus epilepsy and childhood absence epilepsy

Among the 40 to 100 million persons with epilepsy worldwide and the 2 to 2.5 million persons with epilepsies in the United States, approximately 50% have generalized epilepsies. Among all epilepsies, the most common are juvenile myoclonus epilepsy (JME) with 10% to 30% of cases, childhood absence epilepsy (CAE) with 5% to 15% of cases, and pure grand mal on awakening with 22% to 37% of cases. In the last decade, six different chromosomal loci for common generalized epilepsies have been identified. These include two separate loci for JME in chromosomes 6p and 15q. The epilepsy locus in chromosome 6p expresses the phenotypes of classic JME, pure grand mal on awakening, and possibly JME mixed with absences. Two separate loci also are present for pyknoleptic CAE, namely, CAE that evolves to JME in chromosome 1p and CAE with grand mal in chromosome 8q24. Pandolfo et al. from the Italian League Against Epilepsy have reported two other putative susceptibility loci for idiopathic generalized epilepsies, namely, grand mal and generalized spike waves 35l in chromosome 3p and generalized epilepsies with febrile convulsions, grand mal, JME, absences, and electroencephalographic spike waves in 8q24. This chapter reports on the debate concerning whether there may be two separate epilepsy loci in chromosome 6p, one in the HLA region and one below HLA. The chapter then discusses the progress made in our laboratories as a result of the Genetic Epilepsy Studies (GENES) International Consortium. We discuss (a) the 2 to 6 cM critical region for classic JME located some 20 cM below HLA in chromosome 6p, (b) the 7-cM area for pyknoleptic CAE that evolves to JME in chromosome 1p, and (c) the 3.2 cM area for pyknoleptic CAE with grand mal and irregular 3 to 4 Hz spike waves in chromosome 8q24. We discusses efforts underway to refine the genetic map of JME in chromosome 6p11 and the advances in physical mapping and positioning of candidate genes, such as the gamma-aminobutyric acid receptor gene, the potassium channel gene of the long-QT family (KvLQT), named KCNQ3, and the human homologue of the mouse jerky gene for CAE in chromosome 8q24 and JME in chromosome 6p11.

[Gammography using Tc 99m MIBI in patients with suspected breast cancer. Proposed diagnostic protocol]

The aim of this work has been to determine whether the joint use of mammography and scintimammography is capable of reducing the number of biopsies required in patients with suspected breast cancer. We have performed scintimammography in 90 patients, 97 lesions, with breast cancer suspicion. In the mammography was evaluated the degree of malignancy suspicion and the size of the lesion. Only 41 of the biopsies revealed the presence of cancer. The sensitivity, specificity, PPV and NPV of scintimammography were 85%, 79%, 74% and 88%. According to the mammography findings 20 lesions (1 breast cancer) were included as low, 31 lesions (4 breast cancer) as indeterminate and 46 lesions (36 breast cancer) as high malignancy suspicion. 14 lesions (2 low, 2 indeterminate and 10 high suspicion) were smaller than 1 cm. The scintimammography was positive in all breast cancer of low and indeterminate suspicion of malignancy and in 30 of high probability. On the basis of this results we propose that a biopsy must be carried out to those lesions with a high suspicion of malignancy, and to lesions with low or indeterminate suspicion that are smaller than 1 cm or that present a positive scintimammography. Following this protocol, only 64 of the 97 biopsies would have been necessary, with a reduction of the 34% in the total number of biopsies and, more important, a 65% of reduction in the number of biopsies carried out in the groups of low and indeterminate suspicion of malignancy. At the same time we would indicate biopsy in all cases of breast cancer.

Vitamin D-receptor gene polymorphisms and bone density in prepubertal American girls of Mexican descent

BACKGROUND

Bone mass is under strong genetic control, and recent studies in adults have suggested that allelic differences in the gene for the vitamin D receptor may account for inherited variability in bone mass. We studied the relations of the vitamin D-receptor genotype to skeletal development and variation in the size, volume, and density of bone in children.

METHODS

We identified three allelic variants of the vitamin D-receptor gene using the polymerase chain reaction and three restriction enzymes (ApaI, BsmI, and TaqI) in 100 normal prepubertal American girls of Mexican descent. We then determined the relations of the different vitamin D-receptor genotypes (AA, Aa, aa, BB, Bb, bb, TT, Tt, and tt) to the cross-sectional area, cortical area, and cortical bone density of the femoral shaft and the cross-sectional area and density of the lumbar vertebrae.

RESULTS

The vitamin D-receptor genotype was associated with femoral and vertebral bone density. Girls with aa and bb genotypes had 2 to 3 percent higher femoral bone density (P=0.008 and P=0.04, respectively) and 8 to 10 percent higher vertebral bone density (P=0.01 and P=0.03, respectively) than girls with AA and BB genotypes. There was no association between the cross-sectional area of the vertebrae or the cross-sectional or cortical area of the femur and the vitamin D-receptor genotype. The chronologic age, bone age, height, weight, body-surface area, and body-mass index did not differ significantly among girls with different vitamin D-receptor genotypes.

CONCLUSIONS

Vitamin D-receptor gene alleles predict the density of femoral and vertebral bone in prepubertal American girls of Mexican descent.

Presymptomatic diagnosis of neurofibromatosis 2 using linked genetic markers, neuroimaging, and ocular examinations

Neurofibromatosis 2 (NF2) is an autosomal dominant disorder that causes nervous system tumors and ocular abnormalities such as early-onset lenticular opacities. We assessed the clinical spectrum of NF2 at the time of presymptomatic DNA diagnosis in at-risk first-degree relatives. We studied five multigeneration NF2 families with short tandem repeat markers near the NF2 gene (NF2); gadolinium-enhanced high-resolution magnetic resonance imaging (GE-MRI); and ocular, dermatologic, and neurologic examinations. Eleven of 31 asymptomatic at-risk first-degree relatives were predicted by segregation analysis to be NF2 mutation carriers. Nine of the 11 NF2 mutation carriers were clinically evaluated. Four mutation carriers, including a 7-year-old, had vestibular schwannomas, early-onset cataracts, or both. However, five mutation carriers did not have clinical abnormalities, including a 38-year-old with normal cranial and spinal GE-MRIs and a normal ocular examination. These results indicate that clinical abnormalities can be present in young, but absent in middle-aged, presymptomatic NF2 mutation carriers. By identifying presymptomatic NF2 mutation carriers, DNA diagnosis of NF2 can improve genetic counseling and clinical management, and possibly reduce psychosocial difficulties in at-risk individuals.

Identification of three neurofibromatosis type 2 (NF2) gene mutations in vestibular schwannomas

Vestibular schwannomas (VSs) are common benign tumors of Schwann cell origin and are frequently found in patients with neurofibromatosis type 2 (NF2). We analyzed 15 sporadic VSs for mutations in the tumors, two of which contained loss of heterozygosity (LOH). One of the tumors contained a novel mutation, a 19-bp deletion in exon 4. The two other tumors contained an identical mutation, a complete exon 4 deletion. The exon 4 deletion represents the second most frequently reported mutation of the NF2 gene in VSs.

Ocular abnormalities in neurofibromatosis 2

PURPOSE

To evaluate the ocular abnormalities in patients with clinically diagnosed neurofibromatosis 2 and asymptomatic gene carriers.

METHODS

Probands were ascertained through a surgical otolaryngology practice. In a cross-sectional study, we examined 49 patients with neurofibromatosis 2, 30 offspring of patients, and, as a comparison group, 18 parents and siblings of patients with sporadic neurofibromatosis 2. The examination included a complete neuro-ophthalmic assessment, physical examination, and, for patients and first-degree relatives at risk, cranial and spinal magnetic resonance imaging with gadolinium enhancement, if not previously performed.

RESULTS

The most common ocular abnormalities were posterior subcapsular or capsular, cortical, or mixed lens opacities in 33 (67%) of 49 patients with neurofibromatosis 2 and retinal hamartomas in 11 (22%). We used segregation analysis to determine the mutation carrier status of six at-risk offspring who were 30 years old or younger in two multigeneration families. Three asymptomatic mutation carriers had cataracts, whereas those who were predicted not to carry the mutation did not have cataracts. Asymptomatic mutation carriers may have developmental abnormalities of the eye that are detectable in childhood or adolescence, a finding that may assist in early diagnosis of the disease.

CONCLUSIONS

A variety of ocular abnormalities are present in neurofibromatosis 2, including cataracts, retinal hamartomas, and ocular motor deficits. Many of these are developmental or acquired early in life and may assist in presymptomatic diagnosis. For screening at-risk relatives of patients with neurofibromatosis 2, the types of cataract that are most suggestive of neurofibromatosis 2 are plaque-like posterior subcapsular or capsular cataract and cortical cataract with onset under the age of 30 years.

Construction and utility of a human chromosome 22-specific Fosmid library

We have previously demonstrated the capability of the Fosmid vector based on Escherichia coli F-factor replicon to stably propagate cosmid-sized human genomic DNA fragments. Using the Fosmid vector, we have constructed and arrayed a 10 x human chromosome 22-specific library, partly by picking human positive clones from a total Fosmid library constructed using DNA from human-hamster hybrid cell line containing human chromosome 22, and partly by using flow-sorted chromosomal DNA. The clones and physical contig maps of the clones in the library will serve as a valuable resource for detailed analysis of the chromosome by providing reliable materials for high resolution mapping and sequencing. In order to efficiently build physical maps for the chromosomal regions of interest spanning several hundred kilobases to a megabase, it is necessary to rapidly identify subsets of the Fosmid clones from the library that cover such regions. In this report, we describe a method of using random amplification products derived from YAC clones to rapidly identify a subset of Fosmid clones that cover a specific genomic subregion.

Mutations of the neurofibromatosis type 2 gene and lack of the gene product in vestibular schwannomas

Schwannomas are common tumors of the nervous system and are frequently found in patients with neurofibromatosis (NF) 2. Although loss of heterozygosity in NF2 tumors suggests that the NF2 gene functions as a tumor suppressor gene, the NF2 gene shows amino acid sequence homology to structural proteins in one of which dominantly acting mutations have been described. We performed a mutational analysis in 30 vestibular schwannomas and examined the effect of mutations on the NF2 protein. We detected 18 mutations in 30 vestibular schwannomas of which seven contained loss or mutation of both NF2 alleles. Most mutations were predicted to result in a truncated protein. Mutational hot spots were not identified. Immunocytochemical studies using antibodies to the NF2 protein showed complete absence of staining in tumor Schwann cells, whereas staining was observed in normal vestibular nerve. These data indicate that loss of NF2 protein function is a necessary step in schwannoma pathogenesis and that the NF2 gene functions as a recessive tumor suppressor gene.

Organization of repetitive DNA sequences in the genome of the echinoderm Holothuria tubulosa

The abundance of repetitive DNA in the haploid sea cucumber genome has been determined by screening a Holothuria genomic DNA library for clones containing repeated sequences using reverse genome hybridization. Analysis by in situ plaque hybridization of a set of 1132 clones has revealed the presence of repetitive DNA sequences in about 38.1% of the clones screened. The distribution of the reiterated DNA has been further analyzed by restriction endonuclease digestion of seven randomly selected repetitive clones. The repeated sequences have a fairly uniform distribution of lengths with an average length value of 7.3 kb. Analysis of the measurements suggests that the repetitive sequences are interspersed among longer single copy sequences with an average spacing interval of about 47.3 kb indicating that the repetitive and single copy DNA in the Holothuria genome are arranged in a long-period interspersion pattern.

Cloning and characterization of a highly conserved satellite DNA from the mollusc Mytilus edulis

Sperm DNA of the common mussel, Mytilus edulis, has been found to contain a highly repeated sequence identifiable upon restriction with the endonuclease ApaI. The repetitive nucleotide (nt) sequence amounts to 0.63% of the mollusc genome with an estimated copy number of 5.4 x 10(4) copies per haploid complement. The monomer unit with a 173-bp repeat length has been cloned. Progressive DNA digestions with ApaI yield ladder-like banding patterns on agarose gels, indicating that the repeated elements are tandemly arranged in the genome and therefore represent a sequence of satellite DNA. The degree of internal redundancy of the reiterated sequence is deemed negligible, since nt sequence analysis of a random set of cloned monomers has detected the presence of only a few direct repeats while inverted repeated motifs or any other internal substructures appear absent. The homologies found among cloned monomers are strikingly high, averaging 95%. The results suggest that the exceptional sequence homogeneity of this satellite DNA may be attributed either to some homogenizing mechanism or to evolutionary conserved trends.

Distribution of interspersed repeats (Alu and Kpn) on NotI restriction fragments of human chromosome 21

Interspersed repeated sequences (Alu and Kpn) were used as probes to detect a set of Not I restriction fragments of human chromosome 21 from the hybrid cell line WAV17. Forty different Not I fragments, ranging in size from less than 0.05 megabase (Mb) to 7.0 Mb, were identified. The total length of these fragments was 47.3 Mb. This length provides an estimate of the minimum size of the chromosome and a minimum number of fragments to be ordered to create a complete restriction map. The average length Not I fragment is 1.2 Mb. Alu and Kpn fragments are not always coincident: a 2.9-Mb fragment is detected with Kpn but not with Alu, and 13 fragments, ranging from less than 0.05 Mb to 5.6 Mb, are detected with Alu but not with Kpn; the 26 remaining fragments, covering 75% (35.3 Mb) of the total length, are detected with both repetitive probes. The presence of so many noncoincident fragments and the high variation of the hybridization signal intensities of the fragments suggest a very nonuniform distribution of Kpn and Alu repeats.

Satellite DNAs contain sequences that induced curvature

The repeating units of mouse, rat, and alpha-monkey satellites have been cloned. All three show properties that are characteristic of curved DNA: (i) their migration in polyacrylamide gels is slower than predicted from their sequences, and (ii) they appear as curved molecules when visualized by electron microscopy. All three satellite repeats contain runs of d(A.T)n greater than or equal to 3 residues that are likely to be responsible for their curvature. From analysis of 20 different satellite DNA sequences, we conclude that, in satellite DNA, adenine residues show a high tendency to cluster in groups of three or more.

Preservation of a complex satellite DNA in two species of echinoderms

The cloning and sequencing of a tandemly arrayed repetitive DNA sequence from the sea cucumber Holothuria tubulosa has been recently described (Sainz, J., Azorín, F. and Cornudella, L. 1989. Gene 80, 57-64). We have now searched the genomes of several echinoderm species for the presence of homologous repetitive elements. A close but not identical repeated sequence has been identified in a related holothuroid, H. polii. The monomeric repeat unit is 391 bp long and has a base composition of 66.8% A and T residues, lined up in tracts of 4 nt or larger. The monomeric sequence lacks any internal subrepeat organization although it displays a substantial degree of internal redundancy in the form of inverted and direct repeats. The repeated element accounts for 0.34% of the genome which corresponds to a repetition frequency of about 0.5 x 10(5) copies per haploid complement. The intra- and interspecific homologies among monomers of the satellite DNA as derived from sequence analyses are very high, averaging 97%. The results suggest that the homogeneity of the highly reiterated DNA sequence may be attributed to evolutionary conservative trends.

Detection and molecular cloning of highly repeated DNA in the sea cucumber sperm

A highly reiterated sequence in the sperm DNA of the echinoderm Holothuria tubulosa has been isolated by digestion with EcoRI, and cloned in the phagemid Bluescript. The monomeric unit has a repeat length of 391 bp and is arranged in tandem. The uncloned genomic monomer as well as two independent cloned fragments have been sequenced. The repeated element constitutes about 1.8% of total Holothuria DNA which corresponds to a repetition frequency of about 1.4 x 10(5) copies per haploid complement. The repetitive sequence has a high A + T content (66.8%) characterized by scattered tracts of A and T residues with no apparent internal sub-repeats, although several inverted and direct repeats are present. Heterogeneity between monomers derived from individual clones is low, whereas sequence similarity to known repetitive elements appears to be negligible.