bluuebunny/crossref_metadata_2025 huggingface dataset:
Inverse relationship between dendritic cell CCR9 expression and maturation state
Authors: Drakes Maureen L. , Stiff Patrick J. , Blanchard Thomas G.
Published: January 2009

CCR9 has been identified on T cells as a chemokine receptor that directs these cells to migrate to the intestine. CCR9 has also been reported on different cell types in the intestine, thymus, liver and peripheral blood. Little is reported concerning the presence of or functional implications of this chemokine receptor on myeloid dendritic cells (DC). In the host, DC encounter a multiplicity of antigenic stimuli to which they mount immune responses. In addition to intracellular and functional changes on sensing antigen, maturation of DC is typically reflected in the up‐regulation of costimulatory molecules on DC. However, alterations in other surface markers may also be an indicator of DC activation. Using bone marrow‐propagated DC these studies investigated cellular maturation in the presence of microbial stimuli and analyzed the relationship of CCR9 expression with DC maturation. Fractionation of DC into CCR9high and CCR9lowsubsets revealed a distinct ability of each subset to induce division in naïve CD4+ T cells. Our results suggest that DC expressing high levels of CCR9 are less activated/mature than DC expressing low levels of CCR9.
Co‐immunization with an optimized plasmid‐encoded immune stimulatory interleukin, high‐mobility group box 1 protein, results in enhanced interferon‐γ secretion by antigen‐specific CD8 T cells
Authors: Muthumani Gowtham , Laddy Dominick J. , Sundaram Senthil G. , Fagone Paolo , Shedlock Devon J. , Kannan Senthil , Wu Ling , Chung Christopher W. , Lankaraman Karthikbabu Mallil , Burns John , Muthumani Karuppiah , Weiner David B.
Published: January 2009

DNA vaccination is a novel immunization strategy that has great potential for the development of vaccines and immune therapeutics. This strategy has been highly effective in mice, but is less immunogenic in non‐human primates and in humans. Enhancing DNA vaccine potency remains a challenge. It is likely that antigen‐presenting cells (APCs), and especially dendritic cells (DCs), play a significant role in the presentation of the vaccine antigen to the immune system. A new study reports the synergistic recruitment, expansion and activation of DCs in vivo by high‐mobility group box 1 (HMGB1) protein. Such combinational strategies for delivering vaccine in a single, simple platform will hypothetically bolster the cellular immunity in vivo. Here, we combined plasmid encoding human immunodeficiency virus‐1 (HIV‐1) Gag and Env with an HMGB1 plasmid as a DNA adjuvant in BALB/c mice (by intramuscular immunization via electroporation), and humoral and cellular responses were measured. Co‐administration of this potent immunostimulatory adjuvant strongly enhanced the cellular interferon‐γ (IFN‐γ) and humoral immune response compared with that obtained in mice immunized with vaccine only. Our results show that co‐immunization with HMGB1 can have a strong adjuvant activity, driving strong cellular and humoral immunity that may be an effective immunological adjuvant in DNA vaccination against HIV‐1.
CX3CR1‐deficiency is associated with increased severity of disease in experimental autoimmune uveitis
Authors: Dagkalis Athanasios , Wallace Carol , Hing Benjamin , Liversidge Janet , Crane Isabel J.
Published: January 2009

The role of CX3CR1 in regulating the function of monocytes and microglia was examined in mice in which CX3CR1 had been replaced by green fluorescent protein (GFP). Induction of experimental autoimmune uveitis (EAU) in these mice resulted in increased disease severity at day 23 postimmunization with uveitogenic peptide when compared with CX3CR1‐positive mice and increased apoptosis of neuronal cells in the inner nuclear layer. Resident microglia within the retina were activated equally as EAU developed in mice with or without CX3CR1, as determined by changes in morphology, suggesting that the microglial cell response did not account for the differences. Although the inflammatory infiltrate had increased in mice without CX3CR1 at day 23 postimmunization, the percentage of natural killer cells in the infiltrate was not changed in these mice. Similarly, increased disease severity at this stage was not associated with an overall increased percentage of macrophages in the retinal inflammatory infiltrate or in increased activation of these cells. The increased recruitment of monocytes to the retina in response to EAU induction in CX3CR1GFP/GFP mice compared with CX3CR1GFP/+ mice was not reflected in increased migration away from vessels, leading to marked clustering of GFP+ cells around veins and venules in these mice. It is possible that this monocyte/macrophage clustering leads to the increased severity of disease seen in the mice by focusing and so intensifying the inflammatory response.
Effect of sialic acid loss on dendritic cell maturation
Authors: Crespo Hélio J. , Guadalupe Cabral M. , Teixeira Alexandra V. , Lau Joseph T. Y. , Trindade Hélder , Videira Paula A.
Published: January 2009

Sialic acids are key structural determinants and contribute to the functionality of a number of immune cell receptors. Previously, we demonstrated that differentiation of human dendritic cells (DCs) is accompanied by an increased expression of sialylated cell surface structures, putatively through the activity of the ST3Gal.I and ST6Gal.I sialyltransferases. Furthermore, DC endocytosis was reduced upon removal of the cell surface sialic acid residues by neuraminidase. In the present work, we evaluate the contribution of the sialic acid modifications in DC maturation. We demonstrate that neuraminidase‐treated human DCs have increased expression of major histocompatibility complex (MHC) and costimulatory molecules, increased gene expression of specific cytokines and induce a higher proliferative response of T lymphocytes. Together, the data suggest that clearance of cell surface sialic acids contributes to the development of a T helper type 1 proinflammatory response. This postulate is supported by mouse models, where elevated MHC class II and increased maturation of specific DC subsets were observed in DCs harvested from ST3Gal.I−/− and ST6Gal.I−/− mice. Moreover, important qualitative differences, particularly in the extent of reduced endocytosis and in the peripheral distribution of DC subsets, existed between the ST3Gal.I−/− and ST6Gal.I−/− strains. Together, the data strongly suggest not only a role of cell surface sialic acid modifications in maturation and functionality of DCs, but also that the sialic acid linkages created by different sialyltransferases are functionally distinct. Consequently, with particular relevance to DC‐based therapies, cell surface sialylation, mediated by individual sialyltransferases, can influence the immunogenicity of DCs upon antigen loading.
Granulocyte colony‐stimulating factor‐induced immature myeloid cells inhibit acute graft‐versus‐host disease lethality through an indoleamine dioxygenase‐independent mechanism
Authors: Joo Young‐Don , Lee Sun‐Mi , Lee Soo‐Woong , Lee Won‐Sik , Lee Sang‐Min , Park Ji‐Kyoung , Choi Il‐Whan , Park Sae‐Gwang , Choi Inhak , Seo Su‐Kil
Published: January 2009

Granulocyte colony‐stimulating factor (G‐CSF)‐mobilized donor graft tissue used for peripheral blood stem cell transplantation contains a large number of immature myeloid cells that suppress alloreactive donor T cells, resulting in an inhibition of acute graft‐versus‐host disease (GVHD). However, the molecular mechanism underlying the suppressive function of immature myeloid cells is not fully understood. Here, we investigated whether indoleamine 2,3‐dioxygenase (IDO) is related to the suppressive mechanism of G‐CSF‐induced immature myeloid cells (gMCs). We found that Gr‐1+ CD11b+ cells were highly induced in G‐CSF‐injected donor graft tissue, which is a phenotype of immature myeloid cells, resulting in an inhibition of acute GVHD lethality by suppressing alloreactive donor T‐cell expansion. IDO was not detected in primary isolated gMCs; however, this enzyme was markedly induced after treatment with interferon‐γ (IFN‐γ). This level was significantly higher in IFN‐γ‐treated gMCs than in bone marrow myeloid cells, which promote alloreactive T‐cell responses. We next investigated the functional role of IDO in gMC‐mediated inhibition of acute GVHD lethality. We found no changes in gMC‐mediated survival or alloreactive donor T‐cell suppression when IDO activity was blocked using 1‐methyl tryptophan. In addition, there was no difference in gMC‐mediated survival rates between recipients transferred with either wild‐type gMCs or IDO−/− gMCs. Taken together, our data suggest that gMC‐mediated inhibition of lethal acute GVHD is through an IDO‐independent mechanism.
A continuous T‐bet expression is required to silence the interleukin‐4‐producing potential in T helper type 1 cells
Authors: Zhuang Yonghua , Huang Zan , Nishida Jun , Brown Melissa , Zhang Lin , Huang Hua
Published: January 2009

To develop into committed T helper type 1 (Th1) cells, naive CD4+ T cells not only need to acquire the capacity to produce interferon‐γ (IFN‐γ), but they also need to gain the ability to silence their interleukin‐4 (IL‐4) ‐producing potential. How Th1 cells silence their Th2 cytokine‐producing potential is an important yet unresolved issue in Th1 immunity. We found that a lack of IL‐4 stimulation was not sufficient to silence the IL‐4‐producing potential in activated CD4+ T cells and that Th1‐promoting factor was required. Although it has been shown that T‐bet is a crucial factor in suppressing Il4 gene expression, it is unclear whether a continuous presence of T‐bet is required to silence the Il4 gene in Th1 cells. To address this problem, we used an inducible form of T‐bet – a T‐bet‐oestrogen receptor fusion molecule (T‐bet‐ER). We found that the activation of T‐bet during primary or secondary culture was sufficient to silence IL‐4‐producing potential. On the other hand, the inactivation of T‐bet after naïve CD4+ T cells had differentiated into Th1 cells resulted in derepression of Il4 gene transcription. Additionally, we found that T‐bet is required to maintain Ifng expression. Our data demonstrate that the continuous expression of T‐bet is required for Th1 cells to silence their IL‐4‐producing potential.
The immunogenicity of L1210 lymphoma clones correlates with their ability to function as antigen‐presenting cells
Authors: Cycon Kelly A. , Clements James L. , Holtz Renae , Fuji Hiroshi , Murphy Shawn P.
Published: January 2009

Major histocompatibility complex class II (MHCII) antigen expression is directly correlated with immunogenicity, and inversely correlated with tumorigenicity, in clones of the L1210 murine B lymphoma. Moreover, loss of MHCII expression on human diffuse large B‐cell lymphoma is associated with dramatic decreases in patient survival. Thus, the role that MHCII antigens play in the progression of B‐cell lymphomas is clinically important. In this study, we investigated the basis for the immunogenicity of MHCII+ L1210 clones. Immunogenic, but not tumorigenic L1210 clones stimulated the proliferation of naïve T cells and their interleukin (IL)‐2 production, which indicates that the immunogenic clones can function as antigen‐presenting cells (APCs). However, subclonal variants of the immunogenic L1210 clones, which form tumours slowly in mice, could not activate T cells. The costimulatory molecules B7‐1, B7‐2 and CD40 were expressed on the immunogenic L1210 clones, but not the tumorigenic clones. Importantly, the tumour‐forming subclonal variants expressed MHCII and B7‐1, but lacked B7‐2 and CD40. These results suggest that MHCII and B7‐1 expression on L1210 cells is insufficient to activate naïve T cells, and, furthermore, loss of B7‐2 and/or CD40 expression contributes to the decreased immunogenicity of L1210 subclones. Blocking B7‐1 or B7‐2 function on immunogenic L1210 cells reduced their capacity to activate naïve T cells. Furthermore, incubation of immunogenic L1210 cells with CD40 antibodies significantly enhanced APC function. Therefore, the immunogenicity of L1210 cells directly correlates (i) with their ability to stimulate naïve T cells, and (ii) with the concomitant expression of MHCII, B7‐1, B7‐2, and CD40.
The aryl hydrocarbon receptor: a perspective on potential roles in the immune system
Authors: Stevens Emily A. , Mezrich Joshua D. , Bradfield Christopher A.
Published: January 2009

The aryl hydrocarbon receptor (AHR) is a protein best known for its role in mediating toxicity. Over 30 years of research has uncovered additional roles for the AHR in xenobiotic metabolism and normal vascular development. Activation of the AHR has long been known to cause immunotoxicity, including thymic involution. Recent data suggesting a role for the AHR in regulatory T‐cell (Treg) and T‐helper 17 (Th17) cell development have only added to the excitement about this biology. In this review, we will attempt to illustrate what is currently known about AHR biology in the hope that data from fields as diverse as evolutionary biology and pharmacology will help elucidate the mechanism by which AHR modifies immune responses. We also will discuss the complexities of AHR pharmacology and genetics that may influence future studies of AHR in the immune system.
Meta‐analysis of immune epitope data for all Plasmodia: overview and applications for malarial immunobiology and vaccine‐related issues
Authors: VAUGHAN K. , BLYTHE M. , GREENBAUM J. , ZHANG Q. , PETERS B. , DOOLAN D. L. , SETTE A.
Published: January 2009

We present a comprehensive meta‐analysis of more than 500 references, describing nearly 5000 unique B cell and T cell epitopes derived from the Plasmodium genus, and detailing thousands of immunological assays. This is the first inventory of epitope data related to malaria‐specific immunology, plasmodial pathogenesis, and vaccine performance. The survey included host and pathogen species distribution of epitopes, the number of antibody vs. CD4+ and CD8+ T cell epitopes, the genomic distribution of recognized epitopes, variance among epitopes from different parasite strains, and the characterization of protective epitopes and of epitopes associated with parasite evasion of the host immune response. The results identify knowledge gaps and areas for further investigation. This information has relevance to issues, such as the identification of epitopes and antigens associated with protective immunity, the design and development of candidate malaria vaccines, and characterization of immune response to strain polymorphisms.
Hepatosplenomegaly associated with chronic malaria exposure: evidence for a pro‐inflammatory mechanism exacerbated by schistosomiasis
Authors: WILSON S. , JONES F. M. , MWATHA J. K. , KIMANI G. , BOOTH M. , KARIUKI H. C. , VENNERVALD B. J. , OUMA J. H. , MUCHIRI E. , DUNNE D. W.
Published: January 2009

In sub‐Saharan Africa, chronic hepatosplenomegaly, with palpable firm/hard organ consistency, is common, particularly among school‐aged children. This morbidity can be caused by long‐term exposure to malaria, or by Schistosoma mansoni, and it is exacerbated when these two occur together. Although immunological mechanisms probably underlie the pathogenic process, these mechanisms have not been identified, nor is it known whether the two parasites augment the same mechanisms or induce unrelated processes that nonetheless have additive or synergistic effects. Kenyan primary schoolchildren, living in a malaria/schistosomiasis co‐transmission area, participated in cross‐sectional parasitological and clinical studies in which circulating immune modulator levels were also measured. Plasma IL‐12p70, sTNF‐RII, IL‐10 and IL‐13 levels correlated with relative exposure to malaria, and with hepatosplenomegaly. Soluble‐TNF‐RII and IL‐10 were higher in children infected with S. mansoni. Hepatosplenomegaly caused by chronic exposure to malaria was clearly associated with increased circulating levels of pro‐inflammatory mediators, with higher levels of regulatory modulators, and with tissue repair cytokines, perhaps being required to control the inflammatory response. The higher levels of regulatory modulators amongst S. mansoni infected children, compared to those without detectable S. mansoni and malarial infections, but exposed to malaria, suggest that S. mansoni infection may augment the underlying inflammatory reaction.
Platinum‐group element signature of the primitive mantle rejuvenated by melt‐rock reactions: evidence from Sumail peridotites (Oman Ophiolite)
Authors: Lorand J.‐P. , Alard O. , Godard M.
Published: January 2009

Platinum‐group element (PGE) abundances in mantle rocks are generally considered to result from a late meteorite addition to the early Earth, post‐dating the core separation event. As such, PGEs are key tracers for the Earth accretion history. For decades, the PGEs systematics of undepleted mantle peridotites has been used to constrain the composition of meteorite impactors involved in the late veneer material. Despite multiple evidence of considerable modifications by partial melting, harzburgites from the Sumail ophiolite (Oman) display a mean PGE composition very akin to recently refined estimates for the Primitive Upper Mantle (PUM) of the Earth. These rocks document a resetting of the PUM signature by percolating basaltic melts, which precipitated Pd‐enriched Cu–Ni sulphides within a strongly Pd‐depleted residual harzburgitic protolith. Such a resetting casts doubt on both the reliability of any PUM estimates and relevance of the PUM concept itself, at least for PGEs.
Extinction, survival and recovery of corals from the Triassic to Middle Jurassic time
Authors: Lathuilière Bernard , Marchal Denis
Published: January 2009

Recognizing extinction events and determining their cause at the Triassic/Jurassic (T/J) transition and near the Pliensbachian–Toarcian (Lower Jurassic) boundary is a field of growing interest. We provide arguments for these events through a literature based new evaluation of coral diversity from Triassic to Dogger and a new palaeobiogeographical map. The T/J extinction of corals is clearly related to the breakdown of reef environments. Origination curves show that Hettangian (the lowest Jurassic stage) was not only a survival phase but already rather a recovery phase. Post‐extinction evolution of reefs and their survival only in the northernmost margin of the Tethys support the hothouse hypothesis for the T/J extinction event. During Pliensbachian, many new taxa appear, but mostly solitary corals, not really framebuilders. Many of these taxa do not occur anymore during the following stages. The new increase in diversity is related to the development of Bajocian (Middle Jurassic) reefs.
Skin testing and drug provocation in the diagnosis of nonimmediate reactions to aminopenicillins in children
Authors: Blanca‐López N. , Zapatero L. , Alonso E. , Torres M. J. , Fuentes V. , Martínez‐Molero M. I. , Blanca M.
Published: January 2009

Background:  Nonimmediate allergic reactions (NIR) to aminopenicillin include several entities, the most common of which are urticaria‐like and maculopapular exanthemas.

Aims of the study:  To evaluate a group of children who developed one or more episodes of skin reactions suggestive of NIR after aminopenicillin administration.

Methods:  The inclusion criteria required negative immediate skin tests and absence of specific IgE antibodies to different penicillins. Intradermal and patch tests were carried out with delayed readings and, if negative, a drug‐provocation test including a full therapeutic course of the drug was given. Two different groups were compared: A) children with positive skin testing or a positive drug‐provocation test and B) children with negative skin testing and good tolerance after a drug‐provocation test.

Results:  Group A was composed of 20 patients. Positive intradermal/patch tests were found in one patient and in the remaining 19, a positive response to a drug‐provocation test confirmed the diagnosis. Group B (the control group) consisted of 19 patients with similar symptoms after aminopenicillin intake but good tolerance. No differences in age, dose or number of previous treatments were observed between the groups. The clinical entities were also similar in both groups.

Conclusions:  Reproducible nonimmediate skin reactions to aminopenicillins may occur in children in spite of negative skin testing. The value of this diagnostic procedure seems to be limited in this type of reaction, with drug‐provocation tests (DPT) being a reasonable and safe alternative if the diagnosis has to be confirmed.
Fruit fly liquid larval diet technology transfer and update
Authors: Chang C. L.
Published: January 2009

Since October 2006, the US Department of Agriculture–Agricultural Research Service (USDA–ARS) has been implementing a fruit fly liquid larval diet technology transfer, which has proceeded according to the following steps: (1) recruitment of interested groups through request; (2) establishment of the Material Transfer Agreement with agricultural research service; (3) fruit fly liquid larval diet starter kit sent to the requestor for preliminary evaluation; (4) problem‐solving through email or onsite demonstration; (5) assessment on feedback from the participants to decide whether to continue the project. Up to date, the project has involved 35 participants from 29 countries and 26 species of fruit flies. Fourteen participants have concluded their evaluation of the process, and 11 of these 14, have deemed it to be successful. One participant has decided to implement the project on a larger scale.

The 14 participants were, Argentina (Ceratitis capitata and Anastrepha fraterculus), Bangladesh (Bactrocera cucurbitae, C. capitata, and Bactrocera dorsalis), China (Fujia province) (B. dorsalis), Italy (C. capitata), Fiji (Bactrocera passiflorae), Kenya (Bactrocera invadens, Ceratitis cosyra), Mauritius (Bactrocera zonata and B. cucurbitae), Mexico (Anastrepha species), Philippines (Bactrocera philippinese), Thailand (Bactrocera correcta), Austria (C. capitata, Vienna 8 and A. fraterculus), Israel (Dacus ciliatus and C. capitata), South Africa (C. capitata, Vienna 8) and Australia (C. capitata).

The Stellenbosch medfly mass‐rearing facility in South Africa and the CDFA in Hawaii were two mass‐scale rearing facilities that allowed us to demonstrate onsite rearing in a larger scale. Demonstrations were performed in CDFA in 2007, and in Stellenbosch, South Africa in 2008; both were found to be successful. The Stellenbosch medfly mass‐rearing facility in South Africa decided to adopt the technology and is currently evaluating the quality control of the flies that were reared as larvae on a liquid diet.
Hierarchical models facilitate spatial analysis of large data sets: a case study on invasive plant species in the northeastern United States
Authors: Latimer A. M. , Banerjee S. , Sang Jr H. , Mosher E. S. , Silander Jr J. A.
Published: January 2009

Many critical ecological issues require the analysis of large spatial point data sets – for example, modelling species distributions, abundance and spread from survey data. But modelling spatial relationships, especially in large point data sets, presents major computational challenges. We use a novel Bayesian hierarchical statistical approach, ‘spatial predictive process’ modelling, to predict the distribution of a major invasive plant species,Celastrus orbiculatus, in the northeastern USA. The model runs orders of magnitude faster than traditional geostatistical models on a large data set ofc. 4000 points, and performs better than generalized linear models, generalized additive models and geographically weighted regression in cross‐validation. We also use this approach to model simultaneously the distributions of a set of four major invasive species in a spatially explicit multivariate model. This multispecies analysis demonstrates that some pairs of species exhibit negative residual spatial covariation, suggesting potential competitive interaction or divergent responses to unmeasured factors.
Community genetics: resource addition has opposing effects on genetic and species diversity in a 150‐year experiment
Authors: Silvertown Jonathan , Biss Pamela M. , Freeland Joanna
Published: January 2009

We used the Park Grass Experiment, begun in 1856, to test alternative hypotheses about the relationship between genetic diversity and plant species diversity. The niche variation hypothesis predicts that populations with few interspecific competitors and hence broader niches are expected to contain greater genetic diversity. The coexistence hypothesis predicts that genetic diversity within species favours coexistence among species and therefore species and genetic diversity should be positively correlated. Amplified Fragment Length Polymorphism (AFLP) markers were used to measure the genetic diversity of populations of Anthoxanthum odoratum growing in 10 plots of differing species richness that lie along resource and soil pH gradients. Genetic diversity in A. odoratum was positively correlated with the number of resources added to a plot, but not correlated with species richness. However, separate analyses have shown a negative correlation between resource addition and species richness at Park Grass and elsewhere, so genetic and species diversity appear to respond in opposite directions.
Overview of the MHC fine mapping data
Authors: Brown W. M. , Pierce J. , Hilner J. E. , Perdue L. H. , Lohman K. , Li L. , Venkatesh R. B. , Hunt S. , Mychaleckyj J. C. , Deloukas P. ,   Diabetes Genetics Consortium
Published: January 2009

Aim:  The aim of this study was to perform quality control (QC) and initial family‐based association analyses on the major histocompatibility complex (MHC) single nucleotide polymorphism (SNP) and microsatellite marker data for the MHC Fine Mapping Workshop through the Type 1 Diabetes Genetics Consortium (T1DGC).

Methods:  A random sample of blind duplicates was sent for analysis of QC. DNA samples collected from participants were shipped to the genotyping laboratory from several T1DGC DNA Repository sites. Quality checks including examination of plate‐panel yield, marker yield, Hardy–Weinberg equilibrium, mismatch error rate, Mendelian error rate and allele distribution across plates were performed.

Results:  Genotypes from 2325 families within nine cohorts were obtained and subjected to QC procedures. The MHC project consisted of three marker panels – two 1536 SNP sets (Illumina Golden Gate platform performed at the Wellcome Trust Sanger Institute, Cambridge, UK) and one 66 microsatellite marker panel (performed at deCODE). In the raw SNP data, the overall concordance rate was 99.1% (±0.02).

Conclusions:  The T1DGC MHC Fine Mapping project resulted in a 2300 family, 9992 genotyped individuals database comprising of two 1536 SNP panels and a 66 microsatellite panel to densely cover the 4 Mb MHC core region for use in statistical genetic analyses.
Haplotype‐based search for SNPs associated with differential type 1 diabetes risk among chromosomes carrying a specific HLA DRB1–DQA1–DQB1 haplotype
Authors: McGinnis R. , McLaren W. , Ranganath V. , Whittaker P. , Hunt S. , Deloukas P. ,   Diabetes Genetics Consortium
Published: January 2009

Aim:  The aim of this study was to test chromosomes carrying the same DRB1–DQA1–DQB1 haplotype for single nucleotide polymorphisms (SNPs) in the major histocompatibility complex (MHC) that might mark subgroups of the haplotype with different risks for type 1 diabetes (T1D).

Methods:  Chromosomes from T1D children, their parents and non‐diabetic siblings in families of the Type 1 Diabetes Genetics Consortium (T1DGC) were analysed by two haplotype‐based methods: (i) logistic regression analysis restricted to phased chromosomes carrying the same DRB1–DQA1–DQB1 haplotype but differentiated by the two alleles at MHC SNPs, which were individually tested for association with T1D and (ii) homozygous parent transmission disequilibrium test (TDT) for biased transmission of a SNP allele to diabetic children from parents who are heterozygous at the SNP but homozygous for the specific DRB1–DQA1–DQB1 haplotype being evaluated.

Results:  A number of SNPs gave nominally significant (p < 0.05) evidence of marking two subsets of the 301–501–201 haplotype that might differ with respect to their diabetogenic potency. However, none of the SNPs achieved experiment‐wide significance and hence may be false‐positive associations.

Conclusions:  We discuss limitations and possible deficiencies of our study suggesting further work that might yield more robust SNP associations marking two subgroups of a DRB1–DQA1–DQB1 haplotype with different T1D risks.
The frequent and conserved DR3‐B8‐A1 extended haplotype confers less diabetes risk than other DR3 haplotypes
Authors: Baschal E. E. , Aly T. A. , Jasinski J. M. , Steck A. K. , Johnson K. N. , Noble J. A. , Erlich H. A. , Eisenbarth G. S. ,   Diabetes Genetics Consortium
Published: January 2009

Aim:  The goal of this study was to develop and implement methodology that would aid in the analysis of extended high‐density single nucleotide polymorphism (SNP) major histocompatibility complex (MHC) haplotypes combined with human leucocyte antigen (HLA) alleles in relation to type 1 diabetes risk.

Methods:  High‐density SNP genotype data (2918 SNPs) across the MHC from the Type 1 Diabetes Genetics Consortium (1240 families), in addition to HLA data, were processed into haplotypes using PedCheck and Merlin, and extended DR3 haplotypes were analysed.

Results:  With this large dense set of SNPs, the conservation of DR3‐B8‐A1 (8.1) haplotypes spanned the MHC (≥99% SNP identity). Forty‐seven individuals homozygous for the 8.1 haplotype also shared the same homozygous genotype at four ‘sentinel’ SNPs (rs2157678 ‘T’, rs3130380 ‘A’, rs3094628 ‘C’ and rs3130352 ‘T’). Conservation extended from HLA‐DQB1 to the telomeric end of the SNP panels (3.4 Mb total). In addition, we found that the 8.1 haplotype is associated with lower risk than other DR3 haplotypes by both haplotypic and genotypic analyses [haplotype: p = 0.009, odds ratio (OR) = 0.65; genotype: p = 6.3 × 10−5, OR = 0.27]. The 8.1 haplotype (from genotypic analyses) is associated with lower risk than the high‐risk DR3‐B18‐A30 haplotype (p = 0.01, OR = 0.23), but the DR3‐B18‐A30 haplotype did not differ from other non‐8.1 DR3 haplotypes relative to diabetes association.

Conclusion:  The 8.1 haplotype demonstrates extreme conservation (>3.4 Mb) and is associated with significantly lower risk for type 1 diabetes than other DR3 haplotypes.
Confirmation of HLA class II independent type 1 diabetes associations in the major histocompatibility complex including HLA‐B and HLA‐A
Authors: Howson J. M. M. , Walker N. M. , Clayton D. , Todd J. A. ,   Diabetes Genetics Consortium
Published: January 2009

Aim:  Until recently, human leucocyte antigen (HLA) class II‐independent associations with type 1 diabetes (T1D) in the Major Histocompatibility Complex (MHC) region were not adequately characterized owing to insufficient map coverage, inadequate statistical approaches and strong linkage disequilibrium spanning the entire MHC. Here we test for HLA class II‐independent associations in the MHC using fine mapping data generated by the Type 1 Diabetes Genetics Consortium (T1DGC).

Methods:  We have applied recursive partitioning to the modelling of the class II loci and used stepwise conditional logistic regression to test ∼1534 loci between 29 and 34 Mb on chromosome 6p21, typed in 2240 affected sibpair (ASP) families.

Results:  Preliminary analyses confirm that HLA‐B (at 31.4 Mb), HLA‐A (at 30.0 Mb) are associated with T1D independently of the class II genes HLA‐DRB1 and HLA‐DQB1 (P = 6.0 × 10−17 and 8.8 × 10−13, respectively). In addition, a second class II region of association containing the single‐nucleotide polymorphism (SNP), rs439121, and the class II locus HLA‐DPB1, was identified as a T1D susceptibility effect which is independent of HLA‐DRB1, HLA‐DQB1 and HLA‐B (P = 9.2 × 10−8). A younger age‐at‐diagnosis of T1D was found for HLA‐B*39 (P = 7.6 × 10−6), and HLA‐B*38 was protective for T1D.

Conclusions:  These analyses in the T1DGC families replicate our results obtained previously in ∼2000 cases and controls and 850 families. Taking both studies together, there is evidence for four T1D‐associated regions at 30.0 Mb (HLA‐A), 31.4 Mb (HLA‐B), 32.5 Mb (rs9268831/HLA‐DRA) and 33.2 Mb (rs439121/HLA‐DPB1) that are independent of HLA‐DRB1/HLA‐DQB1. Neither study found evidence of independent associations at HLA‐C, HLA‐DQA1 loci nor in the UBD/MAS1L or ITPR3 gene regions. These studies show that to find true class II‐independent effects, large, well‐powered sample collections are required and be genotyped with a dense map of markers. In addition, a robust statistical methodology that fully models the class II effects is necessary. Recursive partitioning is a useful tool for modelling these multiallelic systems.
Identification of T1D susceptibility genes within the MHC region by combining protein interaction networks and SNP genotyping data
Authors: Brorsson C. , Hansen N. T. , Lage K. , Bergholdt R. , Brunak S. , Pociot F. ,   Diabetes Genetics Consortium
Published: January 2009

Aim:  To develop novel methods for identifying new genes that contribute to the risk of developing type 1 diabetes within the Major Histocompatibility Complex (MHC) region on chromosome 6, independently of the known linkage disequilibrium (LD) between human leucocyte antigen (HLA)‐DRB1, ‐DQA1, ‐DQB1 genes.

Methods:  We have developed a novel method that combines single nucleotide polymorphism (SNP) genotyping data with protein–protein interaction (ppi) networks to identify disease‐associated network modules enriched for proteins encoded from the MHC region. Approximately 2500 SNPs located in the 4 Mb MHC region were analysed in 1000 affected offspring trios generated by the Type 1 Diabetes Genetics Consortium (T1DGC). The most associated SNP in each gene was chosen and genes were mapped to ppi networks for identification of interaction partners. The association testing and resulting interacting protein modules were statistically evaluated using permutation.

Results:  A total of 151 genes could be mapped to nodes within the protein interaction network and their interaction partners were identified. Five protein interaction modules reached statistical significance using this approach. The identified proteins are well known in the pathogenesis of T1D, but the modules also contain additional candidates that have been implicated in β‐cell development and diabetic complications.

Conclusions:  The extensive LD within the MHC region makes it important to develop new methods for analysing genotyping data for identification of additional risk genes for T1D. Combining genetic data with knowledge about functional pathways provides new insight into mechanisms underlying T1D.
Effect of linkage status of affected sib‐pairs on the search for novel type 1 diabetes susceptibility genes in the HLA complex
Authors: Morahan G. , Mehta M. , McKinnon E. , James I. ,   Diabetes Genetics Consortium
Published: January 2009

Aim:  Type 1 diabetes susceptibility is influenced by a number of genes, of which those with the strongest effects map to the human leucocyte antigen (HLA) complex. Evidence for linkage of non‐HLA genes in several affected sib‐pair analyses was increased if the HLA or gender status of the sibs was considered independently. We investigated whether linkage status at the HLA complex differentially affected transmission of alleles to sibs depending on their HLA or gender linkage status.

Methods:  Genotypes of 2437 markers typed on 11 279 individuals from 2363 families, stratified according to HLA and gender, were examined using the transmission disequilibrium test.

Results:  Several significant single nucleotide polymorphisms (SNPs) loci were found near the class II genes; no significant SNPs were found by these analyses near the class I or class II genes. Other significant effects were found when the gender of the sibs or the parents was considered. There was not a significant difference in HLA‐DRB genotypes between the stratified sets.

Conclusions:  These results suggest the presence of novel recessive susceptibility gene(s) within the HLA complex.
Mating in parents of type 1 diabetes families as a function of the HLA DR‐DQ haplotype
Authors: Kahles H. , Kordonouri O. , Ramos Lopez E. , Walter M. , Rosinger S. , Boehm B. O. , Badenhoop K. , Seidl C. , Ziegler A. ,   Diabetes Genetics Consortium
Published: January 2009

Aim:  The Major Histocompatibility Complex (MHC) region on chromosome 6p21 (IDDM1) contributes about half of the familial clustering of type 1 diabetes (T1D). Several studies have revealed that highly polymorphic genes within the MHC may associate with the mating choice. Our study should determine whether a specific mating effect is detectable in T1D families as a function of human leucocyte antigen (HLA) DR‐DQ, which could contribute to disease susceptibility.

Methods:  We analysed the parental HLA‐DR genotypes in 829 diabetic families. The families derive from the Type 1 Diabetes Genetics Consortium (T1DGC) in addition to those of our own centre and the original UK, US and SCAND diabetic families.

Results:  A total of 307 of 829 parental couples (37.0%) were matched for at least one known T1D risk haplotype (DR3 or DR4), which is significantly less than the expected 374.9 (45.2%), derived from population genotype frequencies (p < 0.0009). Parents share less susceptibility haplotypes and rather complement each other as both carry one different risk haplotype (DR3 or DR4). The number of such parental couples was significantly higher than expected (293 vs. 223.4; p < 0.0003). All non‐transmitted DR haplotype pairs were also analysed. More often than expected, both parents did not transmit DR1 (94 vs. 59.1; p < 0.003) and DRy (y: not DR1, not DR3, not DR4; 63 vs. 30.3; p < 0.0005). In contrast, the parental non‐transmitted pair of haplotypes DR1‐DRy was observed to a far lesser extent than expected (26 vs. 84.7; p < 10‐8). These observations were only made in multiplex families, whereas in simplex families, no deviation from the expected frequencies was observed.

Conclusions:  Our data are consistent with the conclusion that genes in the HLA region may influence the mating choice in parents of T1D patients, thus contributing to familial clustering of T1D in multiplex families. This may indicate a different parental background of multiplex compared with simplex T1D families.
Missingness in the T1DGC MHC fine‐mapping SNP data: association with HLA genotype and potential influence on genetic association studies
Authors: James I. , McKinnon E. , Gaudieri S. , Morahan G. ,   Diabetes Genetics Consortium
Published: January 2009

Aim:  The absence or ‘missingness’ of single nucleotide polymorphism (SNP) assay values because of genotype or related factors of interest may bias association and other studies. Missingness was determined for the Type 1 Diabetes Genetics Consortium (T1DGC) Major Histocompatibility Complex (MHC) data and was found to vary across the region, ranging up to 11.1% of the non‐null proband SNPs, with a median of 0.3%. We consider factors related to missingness in the T1DGC data and briefly assess its possible influence on association studies.

Methods:  We assessed associations of missingness in the SNP assay data with human leucocyte antigen (HLA) genotype of the individual and with SNP genotypes of the parents. Within‐cohort analyses were combined (over all cohorts) using (i) Mantel–Haenszel tests for two‐by‐two tables or (ii) by combining test statistics for larger tables and regression models. Mixed effect regression models were used to assess association of the SNP genotypes with affected status of the offspring after adjustment for parental SNP genotypes, cohort membership and HLA genotypes. Log‐linear models were used to assess association of missingness in the unaffected sib assays with SNP genotypes of the probands.

Results:  Missingness of SNP values near the HLA class I (A, B and C) and class II (DR, DQ and DP) loci is strongly associated with carriage of corresponding HLA genotypes within these groups. Similar associations pertain to missing values among the microsatellite data. In at least some of these cases, regions of missingness coincided with known deletion regions corresponding to the associated HLA haplotype. We conjecture that other regions of associated missingness may point to similar haplotypic deletions. Analysis of association patterns of SNP genotypes with affected status of offspring does not indicate strong informative missingness. However, association of missingness in proband data with parental SNP genotypes may impact transmission disequilibrium test (TDT)‐type analyses. Comparisons of affected and unaffected siblings point to possible susceptibility regions additional to the classical HLA‐DR3/4 alleles near BAT4‐LY6G5B‐BAT5 and NOTCH4.

Conclusions:  Potentially informative missingness in SNP assay values in the MHC region may impact on association and related analyses based on the T1DGC data. These results suggest that it would be prudent to assess the degree to which missingness may abrogate assessed SNP disease markers in such studies. Initial analyses based on comparison of affected and unaffected status in offspring suggest that at least these may be little affected.
Genetic alterations and chemosensitivity profile in newly established human renal collecting duct carcinoma cell lines
Authors: Wu Zheng‐Sheng , Lee Ju‐Han , Kwon Jung‐Ah , Kim Seo‐Hee , Han Sun‐Hee , An Jung‐Suk , Lee Ji‐Hye , Lee Eung‐Seok , Park Heum‐Rye , Kim Young‐Sik
Published: January 2009

OBJECTIVE

To determine the genetic alterations and chemosensitivity profile of collecting duct carcinoma (CDC) of the kidney, as it is a rare, highly aggressive malignant tumour with frequent distant metastases.

MATERIALS AND METHODS

We first established and characterized two human CDC cell lines designated AP3 and AP8, respectively. The CDC cell lines were assessed using microarray‐based comparative genomic hybridization and chemosensitivity testing.

RESULTS

The CDC cells grew in vitro as an adherent monolayer with epithelial morphology, but had different growth rates. The cell lines had the characteristic immunophenotype of CDC (high molecular weight cytokeratin‐+ve/cytokeratin 7‐+ve/vimentin‐+ve). Both cell lines shared copy number gains in chromosomes 20 and X. The loci showing a copy number gain were SOX22 at 20p tel, topoisomerse I (TOP1) at 20q12‐q13.1, TPD52L2 at 20q tel, 20QTEL14 at 20q tel, KAL at Xp22.3, STS 5′ at Xp22.3, OCRL1 at Xq25, AR3′at Xq11‐q12, and XIST at Xq13.2, respectively. Immunoblot analysis confirmed that the AP3 and AP8 cell lines showed moderate and high levels of TOP1 expression, respectively. By chemosensitivity testing, the AP8 cells were most sensitive to topoisomerase I and II inhibitors such as topotecan, epirubicin and doxorubicin, but the AP3 cells did not. The chemosensitivity to these drugs was paralleled by cell death via apoptosis.

CONCLUSION

The results suggest that TOP1 might be one of the molecular targets in AP8 CDC cells. Thus, these novel CDC cell lines will be useful for discovering therapeutic targets and developing effective anticancer drugs against CDC.
Retroperitoneal decortication of simple renal cysts vs decortication with wadding using perirenal fat tissue: results of a prospective randomized trial
Authors: Porpiglia Francesco , Fiori Cristian , Billia Michele , Renard Julien , Di Stasio Andrea , Vaccino Davide , Bertolo Riccardo , Scarpa Roberto Mario
Published: January 2009

OBJECTIVES

To evaluate, in a pilot prospective randomized trial, the safety, effectiveness and radiological recurrence of retroperitoneal renal cyst decortication compared with retroperitoneal decortication with wadding using perirenal pedicled fat tissue.

PATIENTS AND METHODS

From March 2004 to December 2007, 40 patients with simple renal cysts were enrolled and randomized; 22 (group A) had a simple retroperitoneal decortication (SRD) and 18 (group B) a decortication with wadding of the cyst using perirenal fat tissue (RDCW). The following variables were recorded: age, gender, side, size on ultrasonography/computed tomography (CT), location, operative duration, blood loss, complications, pathology, presence or absence of flank pain, hypertension, urinary tract compression or urinary infection. The primary endpoint of this trial was to evaluate and compare the efficacy of both treatments. Secondary endpoints were safety and pain, hypertension and the resolution of urinary tract obstruction.

RESULTS

In all, 40 cysts were treated; there were no bilateral cysts. The mean (sd) size on CT was 11.9 (1.84) cm in group A and 12.8 (1.25) cm in group B (P = 0.1). All the procedures were completed laparoscopically and no conversion was necessary. There were no intraoperative complications. The mean (range) hospital stay was 3.4 (3–6) days. There was no statistically significant difference between the groups for all variables assessed. There was a radiological recurrence in three patients (14%) in group A, but none in group B (all successful).

CONCLUSION

To be completely successful, with maximum safety and to prevent recurrences in the treatment of renal cysts, RCDW is recommended when a retroperitoneal approach is chosen, especially if the cyst is located anteriorly. When symptom relief is considered, RCDW duplicates the results obtained with SRD.
Screening by lower urinary tract symptoms vs asymptomatic prostate‐specific antigen levels leading to radical prostatectomy in Danish men: tumour characteristics and treatment outcome
Authors: Borre Michael
Published: January 2009

OBJECTIVE

To compare the tumour characteristics and treatment outcome in men undergoing radical prostatectomy (RP) for prostate cancer diagnosed with or with no lower urinary tract symptoms (LUTS).

PATIENTS AND METHODS

In Denmark, prostate‐specific antigen (PSA) testing is recommended only in men with a family history of prostate cancer, or those with LUTS that could be caused by prostate cancer. However, increasingly many men undergoing RP are asymptomatic and are diagnosed as a result of unsystematic PSA screening. Data were collected prospectively from The Aarhus PC‐project, comprising 585 consecutive Danish men treated with RP between 1997 and 2008 at Aarhus University Hospital; of these, 47 had a family history of prostate cancer and were therefore excluded.

RESULTS

In all, 188 (35%) patients stated being asymptomatic at the diagnosis of cancer, while LUTS led to the diagnosis in 350 (65%). Except for tumour grade after RP there were no significant differences between these subpopulations in tumour characteristics and treatment outcome. Unexpectedly, the Gleason score of the RP specimen was a statistically significant prognostic indicator (P = 0.002) in favour of symptomatic patients.

CONCLUSION

This study showed no association between LUTS and tumour characteristics or treatment outcome between symptomatic and asymptomatic patients undergoing RP. The Gleason score at RP and thereby the long‐term prognosis in asymptomatic patients seems to be worse than in patients with LUTS.