Monozygotic (MZ) twins do not show complete concordance for many complex diseases; for example, discordance rates for autoimmune diseases are 20%-80%. MZ discordance indicates a role for epigenetic ...or environmental factors in disease. We used MZ twins discordant for psoriasis to search for genome-wide differences in DNA methylation and gene expression in CD4(+) and CD8(+) cells using Illumina's HumanMethylation27 and HT-12 expression assays, respectively. Analysis of these data revealed no differentially methylated or expressed genes between co-twins when analyzed separately, although we observed a substantial amount of small differences. However, combined analysis of DNA methylation and gene expression identified genes where differences in DNA methylation between unaffected and affected twins were correlated with differences in gene expression. Several of the top-ranked genes according to significance of the correlation in CD4(+) cells are known to be associated with psoriasis. Further, gene ontology (GO) analysis revealed enrichment of biological processes associated with the immune response and clustering of genes in a biological pathway comprising cytokines and chemokines. These data suggest that DNA methylation is involved in an epigenetic dysregulation of biological pathways involved in the pathogenesis of psoriasis. This is the first study based on data from MZ twins discordant for psoriasis to detect epigenetic alterations that potentially contribute to development of the disease.
Celotno besedilo
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Cosegregation analysis is a powerful tool for identifying pathogenic genetic variants, but its implementation remains challenging. Existing software is either limited in scope or too demanding for ...many end users. Moreover, current solutions lack methods for assessing the robustness of cosegregation evidence, which is important due to its reliance on uncertain estimates.
We present shinyseg, a comprehensive web application for clinical cosegregation analysis. Our app streamlines penetrance specification based on either liability classes or epidemiological data such as risks, hazard ratios, and age of onset distribution. In addition, it incorporates sensitivity analyses to assess the robustness of cosegregation evidence, and offers support in clinical interpretation.
The shinyseg app is freely available at https://chrcarrizosa.shinyapps.io/shinyseg, with documentation and complete R source code on https://chrcarrizosa.github.io/shinyseg and https://github.com/chrcarrizosa/shinyseg.
Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq) offers high resolution, genome-wide analysis of DNA-protein interactions. However, current standard methods ...require abundant starting material in the range of 1-20 million cells per immunoprecipitation, and remain a bottleneck to the acquisition of biologically relevant epigenetic data. Using a ChIP-seq protocol optimised for low cell numbers (down to 100,000 cells/IP), we examined the performance of the ChIP-seq technique on a series of decreasing cell numbers.
We present an enhanced native ChIP-seq method tailored to low cell numbers that represents a 200-fold reduction in input requirements over existing protocols. The protocol was tested over a range of starting cell numbers covering three orders of magnitude, enabling determination of the lower limit of the technique. At low input cell numbers, increased levels of unmapped and duplicate reads reduce the number of unique reads generated, and can drive up sequencing costs and affect sensitivity if ChIP is attempted from too few cells.
The optimised method presented here considerably reduces the input requirements for performing native ChIP-seq. It extends the applicability of the technique to isolated primary cells and rare cell populations (e.g. biobank samples, stem cells), and in many cases will alleviate the need for cell culture and any associated alteration of epigenetic marks. However, this study highlights a challenge inherent to ChIP-seq from low cell numbers: as cell input numbers fall, levels of unmapped sequence reads and PCR-generated duplicate reads rise. We discuss a number of solutions to overcome the effects of reducing cell number that may aid further improvements to ChIP performance.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Objective: Primary adrenal insufficiency Addison’s disease (AD) is rare, and systematic studies are few, mostly conducted on small patient samples. We aimed to determine the clinical, immunological, ...and genetic features of a national registry-based cohort.
Design: Patients with AD identified through a nationwide search of diagnosis registries were invited to participate in a survey of clinical features, health-related quality of life (HRQoL), autoantibody assays, and human leukocyte antigen (HLA) class II typing.
Results: Of 664 registered patients, 64% participated in the study. The prevalence of autoimmune or idiopathic AD in Norway was 144 per million, and the incidence was 0.44 per 100,000 per year (1993–2007). Familial disease was reported by 10% and autoimmune comorbidity by 66%. Thyroid disease was most common (47%), followed by type 1 diabetes (12%), vitiligo (11%), vitamin B12 deficiency (10%), and premature ovarian insufficiency (6.6% of women). The mean daily treatment for AD was 40.5 mg cortisone acetate and 0.1 mg fludrocortisone. The mean Short Form 36 vitality scores were significantly diminished from the norm (51 vs. 60), especially among those with diabetes. Concomitant thyroid autoimmunity did not lower scores. Anti-21-hydroxylase antibodies were found in 86%. Particularly strong susceptibility for AD was found for the DR3-DQ2/ DRB1*0404-DQ8 genotype (odds ratio, 32; P = 4 × 10−17), which predicted early onset.
Conclusions: AD is almost exclusively autoimmune, with high autoimmune comorbidity. Both anti-21-hydroxylase antibodies and HLA class II can be clinically relevant predictors of AD. HRQoL is reduced, especially among diabetes patients, whereas thyroid disease did not have an impact on HRQoL. Treatment modalities that improve HRQoL are needed.
Autoimmune Addison’s disease has high polyendocrine comorbidity, reduced HRQoL, 10% familial disease, and a strong HLA II association to the DR3- DQ2/DR4(DRB1*0404)-DQ8 genotype.
Background: Underlying causes of adrenal insufficiency include congenital adrenal hyperplasia (CAH) and autoimmune adrenocortical destruction leading to autoimmune Addison's disease (AAD). Here, we ...report a patient with a homozygous stop-gain mutation in 3β-hydroxysteroid dehydrogenase type 2 (3βHSD2), in addition to impaired steroidogenesis due to AAD.
Case Report: Whole exome sequencing revealed an extremely rare homozygous nonsense mutation in exon 2 of the HSD3B2 gene, leading to a premature stop codon (NM_000198.3: c.15C>A, p.Cys5Ter) in a patient with AAD and premature ovarian insufficiency. Scrutiny of old medical records revealed that the patient was initially diagnosed with CAH with hyperandrogenism and severe salt-wasting shortly after birth. However, the current steroid profile show complete adrenal insufficiency including low production of pregnenolone, dehydroepiandrosterone (DHEA) and DHEA sulfate (DHEA-S), without signs of overtreatment with steroids.
Conclusion: To the best of our knowledge, this is the first description of autoimmune adrenalitis in a patient with 3βHSD2 deficiency and suggests a possible association between AAD and inborn errors of the steroidogenesis.
Mutations in the Insulin Gene Can Cause MODY and Autoantibody-Negative Type 1 Diabetes
Anders Molven 1 2 ,
Monika Ringdal 3 4 ,
Anita M. Nordbø 3 4 ,
Helge Ræder 5 ,
Julie Støy 6 ,
Gregory M. Lipkind ...7 ,
Donald F. Steiner 6 7 ,
Louis H. Philipson 6 ,
Ines Bergmann 8 ,
Dagfinn Aarskog 9 ,
Dag E. Undlien 10 11 ,
Geir Joner 12 13 ,
Oddmund Søvik 3 ,
the Norwegian Childhood Diabetes Study Group * ,
Graeme I. Bell 6 14 and
Pål R. Njølstad 3 5
1 Gade Institute, University of Bergen, Norway
2 Department of Pathology, Haukeland University Hospital, Bergen, Norway
3 Department of Clinical Medicine, University of Bergen, Bergen, Norway
4 Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
5 Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
6 Department of Medicine, The University of Chicago, Chicago, Illinois
7 Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
8 Kristiansund Hospital, Kristiansund, Norway
9 Buskerud Hospital, Drammen, Norway
10 Institute of Medical Genetics, Faculty Division, Ullevål University Hospital, University of Oslo, Oslo, Norway
11 Department of Medical Genetics, Ullevål University Hospital, Oslo, Norway
12 Department of Pediatrics, Ullevål University Hospital, Oslo, Norway
13 Faculty of Medicine, University of Oslo, Oslo, Norway
14 Department of Human Genetics, The University of Chicago, Chicago, Illinois
Address correspondence and reprint requests to Dr. Pål R. Njølstad, Department of Pediatrics, Haukeland University Hospital,
N-5021 Bergen, Norway. E-mail: pal.njolstad{at}uib.no
Abstract
OBJECTIVE— Mutations in the insulin ( INS ) gene can cause neonatal diabetes. We hypothesized that mutations in INS could also cause maturity-onset diabetes of the young (MODY) and autoantibody-negative type 1 diabetes.
RESEARCH DESIGN AND METHODS— We screened INS in 62 probands with MODY, 30 probands with suspected MODY, and 223 subjects from the Norwegian Childhood Diabetes Registry
selected on the basis of autoantibody negativity or family history of diabetes.
RESULTS— Among the MODY patients, we identified the INS mutation c.137G>A (R46Q) in a proband, his diabetic father, and a paternal aunt. They were diagnosed with diabetes at 20,
18, and 17 years of age, respectively, and are treated with small doses of insulin or diet only. In type 1 diabetic patients,
we found the INS mutation c.163C>T (R55C) in a girl who at 10 years of age presented with ketoacidosis and insulin-dependent, GAD, and insulinoma-associated
antigen-2 (IA-2) antibody-negative diabetes. Her mother had a de novo R55C mutation and was diagnosed with ketoacidosis and
insulin-dependent diabetes at 13 years of age. Both had residual β-cell function. The R46Q substitution changes an invariant
arginine residue in position B22, which forms a hydrogen bond with the glutamate at A17, stabilizing the insulin molecule.
The R55C substitution involves the first of the two arginine residues localized at the site of proteolytic processing between
the B-chain and the C-peptide.
CONCLUSIONS— Our findings extend the phenotype of INS mutation carriers and suggest that INS screening is warranted not only in neonatal diabetes, but also in MODY and in selected cases of type 1 diabetes.
IA-2, insulinoma-associated antigen-2
MODY, maturity-onset diabetes of the young
Footnotes
Published ahead of print at http://diabetes.diabetesjournals.org on 11 January 2008. DOI: 10.2337/db07-1467.
*
* Other members of the Norwegian Childhood Diabetes Study Group are listed in the appendix .
The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore
be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
See accompanying original articles on pgs. 1034 and 1115 and commentary on p. 799 .
Accepted January 6, 2008.
Received October 14, 2007.
DIABETES
Linkage analysis and DNA sequencing in a family exhibiting an X-linked mental retardation (XLMR) syndrome, characterized by microcephaly, epilepsy, ataxia, and absent speech and resembling Angelman ...syndrome, identified a deletion in the SLC9A6 gene encoding the Na+/H+ exchanger NHE6. Subsequently, other mutations were found in a male with mental retardation (MR) who had been investigated for Angelman syndrome and in two XLMR families with epilepsy and ataxia, including the family designated as having Christianson syndrome. Therefore, mutations in SLC9A6 cause X-linked mental retardation. Additionally, males with findings suggestive of unexplained Angelman syndrome should be considered as potential candidates for SLC9A6 mutations.
Of 300 persons selected for early-onset obesity, hyperphagia, and consanguineous parentage, 8 had mutations in the leptin-receptor gene (
LEPR
). Biochemical and clinical analyses of the affected ...subjects suggest that the assay of serum leptin levels is not an appropriate screening tool for
LEPR
mutations and that the
LEPR
protein product may not be the only leptin receptor in humans.
Biochemical and clinical analyses suggest that the assay of serum leptin levels is not an appropriate screening tool for
LEPR
mutations and that the
LEPR
protein product may not be the only leptin receptor in humans.
The assessment of patients with severe early-onset obesity conventionally includes screening for potentially treatable neurologic and endocrine conditions and identifying known genetic conditions so that appropriate genetic counseling and, in some cases, treatment can be instituted.
1
Classically, patients with genetic obesity syndromes have been identified in childhood as a result of associated mental retardation and developmental abnormalities.
2
However, several monogenic disorders have been identified in which obesity itself is the predominant presenting feature. These disorders result from disruption of the hypothalamic leptin–melanocortin signaling pathway.
3
–
8
Twelve subjects with congenital leptin deficiency due to loss-of-function mutations in the gene encoding leptin . . .
A genome-wide map of single nucleotide polymorphisms (SNP) and a pattern of linkage disequilibrium (LD) between their alleles are being established in three main ethnic groups. An important question ...is the applicability of such maps to different populations within a main ethnic group. Therefore, we have developed high-resolution SNP, haplotype and LD maps of vitamin D receptor gene region in large samples from five populations. Comparative analysis reveals that the LD patterns are identical in all four European populations tested with two small regions of 1.3 and 5.7 kb at which LD is disrupted completely resulting in three block-like regions over which there is significant and extensive LD. In an African population the pattern is similar, but two additional LD-breaking spots are also apparent. This LD pattern suggests combined action of recombination hotspots and founder effects, but cannot be explained by random recombination and genetic drift alone. Direct comparison indicates that the tag SNPs selected in one European population effectively predict the non-tag SNPs in the other Europeans, but not in the Gambians, for this region.
Genes and mechanisms involved in common complex diseases, such as the autoimmune disorders that affect approximately 5% of the population, remain obscure. Here we identify polymorphisms of the ...cytotoxic T lymphocyte antigen 4 gene (CTLA4)--which encodes a vital negative regulatory molecule of the immune system--as candidates for primary determinants of risk of the common autoimmune disorders Graves' disease, autoimmune hypothyroidism and type 1 diabetes. In humans, disease susceptibility was mapped to a non-coding 6.1 kb 3' region of CTLA4, the common allelic variation of which was correlated with lower messenger RNA levels of the soluble alternative splice form of CTLA4. In the mouse model of type 1 diabetes, susceptibility was also associated with variation in CTLA-4 gene splicing with reduced production of a splice form encoding a molecule lacking the CD80/CD86 ligand-binding domain. Genetic mapping of variants conferring a small disease risk can identify pathways in complex disorders, as exemplified by our discovery of inherited, quantitative alterations of CTLA4 contributing to autoimmune tissue destruction.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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