Alpha Locus Research Articles

Effect of CpG dinucleotides within IgH switch region repeats on immunoglobulin class switch recombination

Immunoglobulin (Ig) heavy chains undergo class switch recombination (CSR) to change the heavy chain isotype from IgM to IgG, A or E. The switch regions are several kilobases long, repetitive, and G-rich on the nontemplate strand. They are also relatively depleted of CpG (also called CG) sites for unknown reasons. Here we use synthetic switch regions at the IgH switch alpha (Sα) locus to test the effect of CpG sites and to try to understand why the IgH switch sequences evolved to be relatively depleted of CpG. We find that even just two CpG sites within an 80bp synthetic switch repeat iterated 15 times (total switch region length of 1200bp containing 30 CpG sites) are sufficient to dramatically reduce both Ig CSR and transcription through the switch region from the upstream Iα sterile transcript promoter, which is the promoter that directs transcripts through the Sα region. De novo DNA methylation occurs at the four CpG sites in and around the Iα promoter when each 80bp Iα switch repeat contains the two CpG sites. Thus, a relatively low density of CpG sites within the switch repeats can induce upstream CpG methylation at the IgH alpha locus, and cause a substantial decrease in transcription from the sterile transcript promoter. This effect is likely the reason that switch regions evolved to contain very few CpG sites. We discuss these findings as they relate to DNA methylation and to Ig CSR.

Opsin clines in butterflies suggest novel roles for insect photopigments.

Opsins are ancient molecules that enable animal vision by coupling to a vitamin-derived chromophore to form light-sensitive photopigments. The primary drivers of evolutionary diversification in opsins are thought to be visual tasks related to spectral sensitivity and color vision. Typically, only a few opsin amino acid sites affect photopigment spectral sensitivity. We show that opsin genes of the North American butterfly Limenitis arthemis have diversified along a latitudinal cline, consistent with natural selection due to environmental factors. We sequenced single nucleotide (SNP) polymorphisms in the coding regions of the ultraviolet (UVRh), blue (BRh), and long-wavelength (LWRh) opsin genes from ten butterfly populations along the eastern United States and found that a majority of opsin SNPs showed significant clinal variation. Outlier detection and analysis of molecular variance indicated that many SNPs are under balancing selection and show significant population structure. This contrasts with what we found by analysing SNPs in the wingless and EF-1 alpha loci, and from neutral amplified fragment length polymorphisms, which show no evidence of significant locus-specific or genome-wide structure among populations. Using a combination of functional genetic and physiological approaches, including expression in cell culture, transgenic Drosophila, UV-visible spectroscopy, and optophysiology, we show that key BRh opsin SNPs that vary clinally have almost no effect on spectral sensitivity. Our results suggest that opsin diversification in this butterfly is more consistent with natural selection unrelated to spectral tuning. Some of the clinally varying SNPs may instead play a role in regulating opsin gene expression levels or the thermostability of the opsin protein. Lastly, we discuss the possibility that insect opsins might have important, yet-to-be elucidated, adaptive functions in mediating animal responses to abiotic factors, such as temperature or photoperiod.

Mutation analysis of inhibitory guanine nucleotide binding protein alpha (GNAI) loci in young and familial pituitary adenomas.

Pituitary adenomas are neoplasms of the anterior pituitary lobe and account for 15–20% of all intracranial tumors. Although most pituitary tumors are benign they can cause severe symptoms related to tumor size as well as hypopituitarism and/or hypersecretion of one or more pituitary hormones. Most pituitary adenomas are sporadic, but it has been estimated that 5% of patients have a familial background. Germline mutations of the tumor suppressor gene aryl hydrocarbon receptor-interacting protein (AIP) predispose to hereditary pituitary neoplasia. Recently, it has been demonstrated that AIP mutations predispose to pituitary tumorigenesis through defective inhibitory GTP binding protein (Gαi) signaling. This finding prompted us to examine whether germline loss-of-function mutations in inhibitory guanine nucleotide (GTP) binding protein alpha (GNAI) loci are involved in genetic predisposition of pituitary tumors. To our knowledge, this is the first time GNAI genes are sequenced in order to examine the occurrence of inactivating germline mutations. Thus far, only somatic gain-of-function hot-spot mutations have been studied in these loci. Here, we have analyzed the coding regions of GNAI1 , GNAI2, and GNAI3 in a set of young sporadic somatotropinoma patients (n = 32; mean age of diagnosis 32 years) and familial index cases (n = 14), thus in patients with a disease phenotype similar to that observed in AIP mutation carriers. In addition, expression of Gαi proteins was studied in human growth hormone (GH), prolactin (PRL), adrenocorticotropic hormone (ACTH)-secreting and non-functional pituitary tumors. No pathogenic germline mutations affecting the Gαi proteins were detected. The result suggests that loss-of-function mutations of GNAI loci are rare or nonexistent in familial pituitary adenomas.

Reduced FOXP3+ regulatory T cells in patients with primary sclerosing cholangitis are associated with IL2RA gene polymorphisms

Recently, genome wide association studies in primary sclerosing cholangitis (PSC) revealed associations with gene polymorphisms that potentially could affect the function of regulatory T cells (Treg). The aim of this study was to investigate Treg in patients with PSC and to associate their numbers with relevant gene polymorphisms. Treg frequency in blood was assessed by staining for CD4(+)CD25(high)FOXP3(+)CD127(low) lymphocytes and determination of Treg-specific FOXP3 gene locus demethylation. Single nucleotide polymorphisms (SNP) in the interleukin-2 receptor alpha (IL2RA), the interleukin-2 (IL2) and interleukin-21 (IL21) gene locus were analysed. Liver biopsies taken at the time of diagnosis were stained for FOXP3 and CD3. Treg function was assessed in a CFSE-based suppression assay. The frequency of Treg in peripheral blood of PSC patients was significantly decreased. We confirmed this finding by demonstrating a reduction of non-methylated DNA in the Treg-specific demethylated FOXP3 gene region of peripheral blood cells in PSC patients. Reduced peripheral Treg numbers were significantly associated with homozygosity for the major allele of the SNP "rs10905718" in the IL2RA gene. Intrahepatic FOXP3(+) cell numbers at the time of initial diagnosis were decreased in PSC as compared to PBC. In addition to reduced numbers, the suppressive capacity of Treg isolated from PSC patients seemed to be impaired as compared to healthy controls. Our findings indicate that Treg impairment may play a role in the immune dysregulation observed in PSC. Reduced Treg numbers in patients with PSC are associated with polymorphisms in the IL2RA gene.

Autoantibodies against distinct neuronal populations in narcoleptic patients – A possible link to vaccine induced autoimmunity?

Introduction Narcolepsy is a neurological sleep disorder that is characterized by excessive daytime sleepiness and cataplexy. The aetiology is unknown but genetic analyses have revealed a strong link to the HLA DQB1 ∗ 06:02 and T-cell receptor alpha loci. Thus, narcolepsy is proposed to be an autoimmune disease. During 2009–2010, a link between vaccination with the adjuvanted H1N1 influenza vaccine Pandemrix and onset of narcolepsy was observed in Finland and Sweden. We hypothesized that vaccination triggered generation of autoantibodies against orexinergic neurons in the lateral hypothalamus (LH) of affected patients. We searched for autoantibodies using immunohistochemistry using a rat brain ‘neuroanatomical array’. Materials and methods Sera from 45 narcoleptic patients, 20 patients with other sleep related disorders (OSRD) and 20 healthy controls were included in the study, all of Finnish origin. All patients were HLA DQB1 ∗ 06:02 positive. Clinical information was collected. Sections of formalin- fixed rat brains were processed for immunohistochemistry using patient sera as primary antibody, followed by FITC-conjugated antibodies. Double-labelling with antisera to various relevant markers was carried out: Orexin, melanocyte-concentrating hormone (MCH), s-endorphin (marker for pro-opiomelanocortin (POMC) neurons), glutamic acid decarboxylase and more. Results Three distinct groups of immunoreactivity were recorded: group A (4/45) encompassed the MCH, but not the orexin neurons in the LH and the POMC neurons in the hypothalamic arcuate nucleus; group B (5/45) GABAergic interneurons in the cortex, many of them being calretinin or calbindin immunoreactive; and group C (4/45) neurons in the globus pallidus. In total 13/45 (29%) of narcoleptic sera stained some of the groups A, B or C. In the OSRD-group one positive serum was found (group B), whereas none of the sera in the healthy controls showed any staining. There was no clear link between the staining patterns and a previous history of Pandemrix-vaccination. Conclusion Almost one third of narcoleptic sera of Finnish patients contains autoantibodies against neuronal subpopulations, at least one of which has been associated with sleep-regulation. Acknowledgements The study was funded by the Swedish Medical Product Agency, the Swedish Research Council (VR) and Academy of Finland (26063) is a part of the NARPA- NORD consortium between Finland and Sweden.

Phylogenetic Analysis Reveals a High Prevalence of Sporothrix brasiliensis in Feline Sporotrichosis Outbreaks

Sporothrix schenckii, previously assumed to be the sole agent of human and animal sporotrichosis, is in fact a species complex. Recently recognized taxa include S. brasiliensis, S. globosa, S. mexicana, and S. luriei, in addition to S. schenckii sensu stricto. Over the last decades, large epidemics of sporotrichosis occurred in Brazil due to zoonotic transmission, and cats were pointed out as key susceptible hosts. In order to understand the eco-epidemiology of feline sporotrichosis and its role in human sporotrichosis a survey was conducted among symptomatic cats. Prevalence and phylogenetic relationships among feline Sporothrix species were investigated by reconstructing their phylogenetic origin using the calmodulin (CAL) and the translation elongation factor-1 alpha (EF1α) loci in strains originated from Rio de Janeiro (RJ, n = 15), Rio Grande do Sul (RS, n = 10), Paraná (PR, n = 4), São Paulo (SP, n = 3) and Minas Gerais (MG, n = 1). Our results showed that S. brasiliensis is highly prevalent among cats (96.9%) with sporotrichosis, while S. schenckii was identified only once. The genotype of Sporothrix from cats was found identical to S. brasiliensis from human sources confirming that the disease is transmitted by cats. Sporothrix brasiliensis presented low genetic diversity compared to its sister taxon S. schenckii. No evidence of recombination in S. brasiliensis was found by split decomposition or PHI-test analysis, suggesting that S. brasiliensis is a clonal species. Strains recovered in states SP, MG and PR share the genotype of the RJ outbreak, different from the RS clone. The occurrence of separate genotypes among strains indicated that the Brazilian S. brasiliensis epidemic has at least two distinct sources. We suggest that cats represent a major host and the main source of cat and human S. brasiliensis infections in Brazil.

A genome‐wide association study of recipient genotype and medium‐term kidney allograft function

We examined, through genome-wide association studies (GWAS), the correlation between recipient genetic variation and renal function at fiveyr. Our cohort contained 326 Irish, first time, kidney-only, deceased donor, transplant recipients on calcineurin inhibitors (263 had a functioning graft at fiveyr) between 1993 and 2002. Outcomes were creatinine at fiveyr and long-term graft function. Two variants were identified showing borderline genome-wide significance - one on chromosome 18 (p=4.048e-08, rs6565887) and another on chromosome 14 (p=7.631e-08, rs3811321). Individually, the two SNPs explained up to 8.8% and 11.29% of five-yr creatinine variance, respectively, while together they explained up to 17.4% of trait variance. Both variants were predictors of long-term allograft function (p=0.004, 70% vs 30% survival at 10yr). The chromosome 14 variant is located in the intergenic region of the T-Cell Receptor Alpha locus. Using a genome-wide approach, we have identified two associations with five-yr creatinine levels in renal transplant recipients treated with calcineurin inhibitors. Independent replication is now warranted to clarify the clinical significance of these results.

In-vitro characterization of novel and functional regulatory SNPs in the promoter region of IL2 and IL2R alpha in a Gabonese population

BackgroundThe selection pressure imposed by the parasite has a functional consequence on the immune genes, leading to altered immune function in which regulatory T cells (Tregs) induced by parasites during infectious challenges modulate or thwart T effector cell mechanism.MethodsWe identified and investigated regulatory polymorphisms in the immune gene IL2 and its receptor IL2R alpha (also known as CD25) in Gabonese individuals exposed to plentiful parasitic infections.ResultsWe identified two reported variants each for IL2 and its receptor IL2R alpha gene loci. Also identified were two novel variants, -83 /-84 CT deletions (ss410961576) for IL2 and -409C/T (ss410961577) for IL2R alpha. We further validated all identified promoter variants for their allelic gene expression using transient transfection assays. Three promoter variants of the IL2 locus revealed no significant expression of the reporter gene. The identified novel variant (ss410961577C/T) of the IL2R alpha revealed a significant higher expression of the reporter gene in comparison to the major allele (P<0.05). In addition, the rs12722616C/T variant of the IL2R alpha locus altered the transcription factor binding site TBP (TATA box binding protein) and C/EBP beta (CCAAT/enhancer binding protein beta) that are believed to regulate the Treg function.ConclusionsThe identification and validation of such regulatory polymorphisms in the immune genes may provide a basis for future studies on parasite susceptibility in a population where T cell functions are compromised.

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Aim Considering the incidence of solid organ transplant recipients who are sensitized with DP antibodies, improved methods of DP typing and of antigen equivalent grouping would be useful. A lack of serological information about most DP molecular genotypes impedes ready assignment into “serological equivalents” as practiced with other HLA loci. Since DP antibodies are most commonly identified by Single Antigen Bead (SAB) tests, the current state of the art requires comparing complicated DP genotyping data with SAB results from only a limited set of beads. We therefore sought a new, rapid method of molecular DP typing with practical “serological equivalent” assignments. Methods Linkage Biosciences’ real-time PCR technology combining allele specific amplification with melt curve detection (LinkSēq™) was used in blinded testing against a set of previously typed samples with a broad range of DP specificities. Since DP antibody response is most often directed toward a limited number of immunodominant hypervariable region epitopes, we focused on the six critical epitope regions of exon 2 of the beta locus as well as the four major groups of the alpha locus to assign DP Epitypes. Results LinkSēq reduced test time by 50% and hands-on time by up to 90% compared to SSP or SSO methods, and all LinkSēq types were concordant with the expected types. 149 HLA-DP alleles (IMGT v3.5.0) were readily grouped into 103 Epitypes based on the pattern of epitopes in each DP allele. SureTyper™ software then used donor and recipient DP genotyping information, combined with recipient SAB results, to enable an automated virtual crossmatching tool. Conclusions LinkSēq offers a rapid method of DP genotyping with a simple workflow and avoidance of post-amplification contamination. SureTyper software provides a practical approach to Epityping DP alleles, determining Epitype compatibility, and allowing virtual crossmatching without tedious manual identification of cognate antibody-epitope pairings. Antovich: Linkage Biosciences: Employee; Stockholder. Russnak: Linkage Biosciences: Employee; Stockholder. King: Linkage Biosciences: Employee; Stockholder. Ly: Linkage Biosciences: Employee; Stockholder. Quinto: Linkage Biosciences: Employee. Grumet: Linkage Biosciences: Consultant; Stockholder.

The Thyroid Hormone Receptor Alpha Locus and White Matter Lesions: A Role for the Clock GeneREV-ERBα

Thyroid disorders are associated with an increased risk of cognitive impairment and Alzheimer's disease. Both small vessel disease and neurodegeneration have a role in the pathogenesis of cognitive impairment and Alzheimer's disease. Thyroid hormone receptor alpha (TRα) is the predominant TR in brain. The circadian clock gene REV-ERBα overlaps with the TRα gene and interferes with TRα expression. Limited data are available on the role of the TRα/REV-ERBα locus in small vessel disease and neurodegeneration. We therefore studied genetic variation in the TRα/REV-ERBα locus in relation to brain imaging data, as early markers for small vessel disease and neurodegeneration. Fifteen polymorphisms, covering the TRα/REV-ERBα locus, were studied in relation to white matter lesion (WML), total brain, and hippocampal volumes in the Rotterdam Study I (RS-I, n=454). Associations that remained significant after multiple testing correction were subsequently studied in an independent population for replication (RS-II, n=607). No associations with total brain or hippocampal volumes were detected. A haplotype block in REV-ERBα was associated with WML volumes in RS-I. Absence of this haplotype was associated with larger WML volumes in women (0.38%±0.18% [β±SE], p=0.007), but not in men (0.04%±0.11%, p=0.24), which was replicated in RS-II (women: 0.15%±0.05%, p=0.04; men: 0.05%±0.07%, p=0.80). Meta-analysis of the two populations showed that women lacking this haplotype have a 1.9 times larger WML volume (p=0.001). Our results suggest a role for REV-ERBα in the pathogenesis of WMLs.

Interleukin-7 receptor α contributes to experimental autoimmune encephalomyelitis (171.42)

Abstract Multiple sclerosis (MS) is a neurodegenerative disease characterized by inflammation, demyelination, and axonal damage. Recently, a mutation in the interleukin-7 receptor alpha (IL7Rα) locus has been identified as a risk factor for MS. IL7Rα has well-documented roles in lymphocyte development, function, and homeostasis, but its involvement in disease settings is largely understudied. Here we show that IL7Rα defective mice (IL7RTgIL7R-/-) display a less severe form of experimental autoimmune encephalomyelitis (EAE), a model for MS. Compared to wild type (WT), IL7RTgIL7R-/- exhibit reduced levels of paralysis, myelin damage, and inflammation. Furthermore, diseased WT treated with neutralizing anti-IL7Rα show significant recovery in EAE clinical scores and reduced lymphocyte infiltration into the CNS. A series of chimeric mice were then generated by bone marrow (BM) transplantation to identify IL7Rα+ cellular compartments contributing to EAE. Rag-/- mice engrafted with IL7RTgIL7R-/- or WT BM display equivalent disease severity, suggesting that IL7Rα on non-hematopoietic cells contributes to EAE. Lymphodeplete IL7R-/- mice reconstituted with WT or IL7RTgIL7R-/- BM showed dramatic reductions in EAE only with IL7RTgIL7R-/- engraftment and not WT, suggesting that IL7Rα signaling on lymphocytes contributes to disease. Taken together, IL7Rα signaling blockade in multiple cell types is necessary for marked reductions in EAE, and should be considered as a new therapeutic target for MS.

A Large-Scale Population-Based Analysis of Common Genetic Variation in the Thyroid Hormone Receptor Alpha Locus and Bone

ThyroidVol. 22, No. 2 Letters to the EditorA Large-Scale Population-Based Analysis of Common Genetic Variation in the Thyroid Hormone Receptor Alpha Locus and BoneMarco Medici, Fernando Rivadeneira, Wendy M. van der Deure, Albert Hofman, Joyce B.J. van Meurs, Unnur Styrkársdottir, Cornelia M. van Duijn, Timothy Spector, Douglas P. Kiel on behalf of The GEFOS Consortium, André G. Uitterlinden, Theo J. Visser, and Robin P. PeetersMarco MediciDepartment of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.Search for more papers by this author, Fernando RivadeneiraDepartment of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Rotterdam, The Netherlands.Search for more papers by this author, Wendy M. van der DeureDepartment of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.Search for more papers by this author, Albert HofmanDepartment of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.Search for more papers by this author, Joyce B.J. van MeursDepartment of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Rotterdam, The Netherlands.Search for more papers by this author, Unnur StyrkársdottirdeCODE Genetics, Reykjavik, Iceland.Search for more papers by this author, Cornelia M. van DuijnDepartment of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Rotterdam, The Netherlands.Search for more papers by this author, Timothy SpectorDepartment of Twin Research and Genetic Epidemiology, Kings College London, London, United Kingdom.Search for more papers by this author, Douglas P. Kiel on behalf of The GEFOS ConsortiumHebrew SeniorLife, Harvard Medical School, Boston, Massachusetts.Search for more papers by this author, André G. UitterlindenDepartment of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA), Rotterdam, The Netherlands.Search for more papers by this author, Theo J. VisserDepartment of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.Search for more papers by this author, and Robin P. PeetersDepartment of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.Search for more papers by this authorPublished Online:1 Feb 2012https://doi.org/10.1089/thy.2011.0245AboutSectionsView articleView Full TextSupplemental MaterialPDF/EPUBView Supplemental Data Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"A Large-Scale Population-Based Analysis of Common Genetic Variation in the Thyroid Hormone Receptor Alpha Locus and Bone." , 22(2), pp. 223–224FiguresReferencesRelatedDetailsCited byThyroid hormone, thyroid medication, and the skeletonThyroid Hormone in Bone and Joint DisordersRole of Thyroid Hormones in Skeletal Development and Bone MaintenanceEndocrine Reviews, Vol. 37, No. 2Genetic Determination of the Hypothalamic-Pituitary-Thyroid Axis: Where Do We Stand?9 March 2015 | Endocrine Reviews, Vol. 36, No. 2THRA and DIO2 mutations are unlikely to be a common cause of increased bone mineral density in euthyroid post-menopausal womenEuropean Journal of Endocrinology, Vol. 170, No. 4Emerging Lipoprotein-Related Therapeutics for Patients with Diabetes17 July 2013 Volume 22Issue 2Feb 2012 InformationCopyright 2012, Mary Ann Liebert, Inc.To cite this article:Marco Medici, Fernando Rivadeneira, Wendy M. van der Deure, Albert Hofman, Joyce B.J. van Meurs, Unnur Styrkársdottir, Cornelia M. van Duijn, Timothy Spector, Douglas P. Kiel on behalf of The GEFOS Consortium, André G. Uitterlinden, Theo J. Visser, and Robin P. Peeters.A Large-Scale Population-Based Analysis of Common Genetic Variation in the Thyroid Hormone Receptor Alpha Locus and Bone.Thyroid.Feb 2012.223-224.http://doi.org/10.1089/thy.2011.0245Published in Volume: 22 Issue 2: February 1, 2012Online Ahead of Print:January 6, 2012PDF download

A remarkable effect of alemtuzumab in a patient suffering from narcolepsy with cataplexy

We made a remarkable clinical observation in a patient suffering from narcolepsy with cataplexy that may add to the understanding of the pathophysiology of this disorder. Our patient, born in 1929, developed all classical symptoms of narcolepsy in 1946, and came to our attention in 1997. Cataplectic attacks were present on a daily basis, mostly partial, involving the face, neck and knees. Typical triggers were making witty remarks and laughter. He was overweight and used no medication because various treatments in the past had been ineffective or not tolerated. Nocturnal polysomnography showed fragmentation but no co-morbid disorders, and the multiple sleep latency test gave a mean sleep latency of 2.1 min and two SOREMs. He was HLA DQB1-0602*positive, and hypocretin-1 was undetectable in the cerebrospinal fluid. He refused to try any newly available treatment. We contacted him irregularly for participation in research protocols. In 2008, he developed a low grade T-cell lymphoma. A year later, he informed us that he had started treatment with alemtuzumab several months before, after which he had observed a complete absence of his cataplectic attacks, whereas prior to this treatment they had been present on a daily basis. The diagnosed lymphoma and initial therapy with methotrexate had not had any influence on the frequency, duration or pattern of his cataplectic attacks. He stated that as far as joking and witty remarks were concerned, his life had not changed. His wife who had observed his attacks for decades confirmed this. All other narcoleptic symptoms remained unchanged with alemtuzumab. His cataplexy did not return during the 1.5 years he was treated with alemtuzumab, until his death. Narcolepsy with cataplexy is considered to be an autoimmune disorder with T-cell involvement, although there is no final proof for this hypothesis. The main arguments are: the tight association with HLA (Mignot et al., 2001); the presence of HLA DQB1*0602 that is almost conditional; and a trans DRB1*1301-DQB1*0603 haplotype that is highly protective (Hor et al., 2010); the identification of Trib2 reactive autoantibodies; the association with polymorphisms in the T-cell receptor alpha locus in a genome-wide association study

HIF-1α in Epidermis: Oxygen Sensing, Cutaneous Angiogenesis, Cancer, and Non-Cancer Disorders

Besides lung, postnatal human epidermis is the only epithelium in direct contact with atmospheric oxygen. Skin epidermal oxygenation occurs mostly through atmospheric oxygen rather than tissue vasculature, resulting in a mildly hypoxic microenvironment that favors increased expression of hypoxia-inducible factor-1α (HIF-1α). Considering the wide spectrum of biological processes, such as angiogenesis, inflammation, bioenergetics, proliferation, motility, and apoptosis, that are regulated by this transcription factor, its high expression level in the epidermis might be important to HIF-1α in skin physiology and pathophysiology. Here, we review the role of HIF-1α in cutaneous angiogenesis, skin tumorigenesis, and several skin disorders.

MHC mediated resistance to Piscirickettsia salmonis in salmonids farmed in Chile

Piscirickettsia salmonis is the most persistent and threatening pathogen for Chilean aquaculture. In our search for alternatives to control the disease, we analyzed class II polymorphic genes of the Major Histocompatibility Complex (MHC) in juvenile fish trying to find alleles that may confer resistance or susceptibility to the agent in the three major salmonid species cultured in Chile: Salmo salar, Oncorhynchus mykiss and Oncorhynchus kisutch. DNA from farmed fish naturally exposed to the pathogen in different aquaculture centers in Chile were analyzed via PCR for the MHC class II alpha and beta loci ( DAA and DAB), and characterized by denaturant gradient gel electrophoresis (DGGE) followed by DNA sequencing. The comparison between alleles present in either healthy or diseased individuals clearly demonstrated allelic differences between the two populations, specifically for the DAB locus in the three species and only for the DAA locus in S. salar. We conclude that a thorough analysis of the allelic differences identified between fish naturally susceptible/resistant to P. salmonis could potentiate MHC to become a powerful genetic marker for both prophylactic and breeding purposes.

Revisiting the T-cell receptor alpha/delta locus and possible associations with multiple sclerosis

A role for T cells in the pathogenesis of multiple sclerosis (MS) is well supported, evidenced by myriad immunological studies, as well as the unequivocal genetic influence of the major histocompatibility complex (MHC). Despite many attempts, no convincing genetic associations have been made between T-cell receptor (TCR) gene loci and MS. However, these studies may not be definitive because of small sample sizes and under-representative marker coverage of the chromosomal regions being investigated. To explore potential roles between the TCR alpha locus and MS, we have genotyped a large family-based cohort, including 1360 affected individuals and 1659 of their unaffected first-degree relatives, at 40 single-nucleotide polymorphism (SNP) markers within the TCR alpha/delta locus. This represents the largest TCR alpha-MS study to date. From this screen, we identified three potential loci of interest in TCR alpha variable and constant gene regions using the transmission disequilibrium test. Although SNPs implicating each of these regions of interest will require genotyping in independent replication cohorts, these findings suggest a role for TCR gene polymorphisms in MS susceptibility. In the context of these findings we review the evidence.

Dual Functions of Nbs1 in the Repair of DNA Breaks and Proliferation Ensure Proper V(D)J Recombination and T-Cell Development

Immunodeficiency and lymphoid malignancy are hallmarks of the human disease Nijmegen breakage syndrome (NBS; OMIM 251260), which is caused by NBS1 mutations. Although NBS1 has been shown to bind to the T-cell receptor alpha (TCRα) locus, its role in TCRβ rearrangement is unclear. Hypomorphic mutations of Nbs1 in mice and patients result in relatively mild T-cell deficiencies, raising the question of whether the truncated Nbs1 protein might have clouded a certain function of NBS1 in T-cell development. Here we show that the deletion of the entire Nbs1 protein in T-cell precursors (Nbs1(T-del)) results in severe lymphopenia and a hindrance to the double-negative 3 (DN3)-to-DN4 transition in early T-cell development, due to abnormal TCRβ coding and signal joints as well as the functions of Nbs1 in T-cell expansion. Chromatin immunoprecipitation (ChIP) analysis of the TCR loci reveals that Nbs1 depletion compromises the loading of Mre11/Rad50 to V(D)J-generated DNA double-strand breaks (DSBs) and thereby affects resection of DNA termini and chromatin conformation of the postcleavage complex. Although a p53 deficiency relieves the DN3→DN4 transition block, neither a p53 deficiency nor ectopic expression of TCRαβ rescues the major T-cell loss in Nbs1(T-del) mice. All together, these results demonstrate that Nbs1's functions in both repair of V(D)J-generated DSBs and proliferation are essential for T-cell development.

Genetic variations at loci involved in the immune response are risk factors for hepatocellular carcinoma

Primary liver cancer is the third most common cause of cancer-related death worldwide, with a rising incidence in Western countries. Little is known about the genetic etiology of this disease. To identify genetic factors associated with hepatocellular carcinoma (HCC) and liver cirrhosis (LC), we conducted a comprehensive, genome-wide variation analysis in a population of unrelated Asian individuals. Copy number variation (CNV) and single nucleotide polymorphisms (SNPs) were assayed in peripheral blood with the high-density Affymetrix SNP6.0 microarray platform. We used a two-stage discovery and replication design to control for overfitting and to validate observed results. We identified a strong association with CNV at the T-cell receptor gamma and alpha loci (P < 1 × 10(-15)) in HCC cases when contrasted with controls. This variation appears to be somatic in origin, reflecting differences between T-cell receptor processing in lymphocytes from individuals with liver disease and healthy individuals that is not attributable to chronic hepatitis virus infection. Analysis of constitutional variation identified three susceptibility loci including the class II MHC complex, whose protein products present antigen to T-cell receptors and mediate immune surveillance. Statistical analysis of biologic networks identified variation in the "antigen presentation and processing" pathway as being highly significantly associated with HCC (P = 1 × 10(-11)). SNP analysis identified two variants whose allele frequencies differ significantly between HCC and LC. One of these (P = 1.74 × 10(-12)) lies in the PTEN homolog TPTE2. Combined analysis of CNV, individual SNPs, and pathways suggest that HCC susceptibility is mediated by germline factors affecting the immune response and differences in T-cell receptor processing.

Utilization of Molecular Phenotypes to Detect Relapse and Optimize the Management of Acute Promyelocytic Leukemia

Acute promyelocytic leukemia (APL) is characterized by a unique genetic aberration, the t(15;17) chromosome translocation. Translocation breakpoints are located within the promyelocytic leukemia (PML) locus on chromosome 15 and the retinoic acid receptor alpha (RARA) locus on chromosome 17. In the past 2 decades, critical advances have been made in understanding the molecular pathogenesis of APL. APL represents a paradigm for molecularly targeted therapy in cancer and an extraordinary model for translational research in medicine. In fact, the release of differentiation block upon treatment of APL with all-trans-retinoic acid (ATRA) has represented the first example of targeted therapy in human cancer. More recently, the advent of arsenic trioxide (ATO) has allowed further progress in the management of this disease through improved outcomes in patients receiving this agent in combination with ATRA. Finally, optimization of therapy and minimization of toxicity is feasible in this disease through careful monitoring of residual disease using polymerase chain reaction-based approaches targeting the PML-RARA fusion gene.

T cells expressing two different T cell receptors form a heterogeneous population containing autoreactive clones

During T cell development both alleles of the T cell receptor (TCR) alpha locus are rearranged. As a result, a sizeable proportion of T cells can express two distinct TCRs, but the functional significance of this phenomenon remains controversial. Studies on transgenic mice with two TCRs have focused on the risk of immunopathology that such cells may pose, while some have suggested that most dual-specific T cells are nonfunctional or even protective. We tracked the fate and TCR repertoire of single- and dual-specific T cells within a normal polyclonal population undergoing lymphopenia-induced proliferation, a setting which has been shown to cause immunopathology and autoimmunity. After the expansion the repertoire of dual-specific T cells had become highly biased, with both prominent clonal expansions and the complete disappearance of other clones. Our results suggest that the normal repertoire of dual-specific T cells contains both nonfunctional cells and a small, 5% fraction of clones which display a much higher than average affinity to antigens normally tolerated as harmless. This heterogeneity may also help in reconciling some of the earlier, conflicting results.