Single Base Polymorphism Research Articles

Genetic risk score for common obesity and anthropometry in Spanish schoolchildren

IntroductionCommon or non-syndromic obesity is a complex polygenic trait conditioned by biallelic or single-base polymorphisms called SNPs (Single-Nucleotide Polymorphisms) that present an additive effect and act synergistically. Most genotype-obese phenotype association studies include body mass index (BMI) or waist-to-height ratio (WtHR), and very few introduce a broad anthropometric profile.ObjectiveTo verify whether a genetic risk score (GRS) developed from 10 SNPs is associated with the obesity phenotype assessed from anthropometric measures indicative of excess weight, adiposity and fat distribution.Material and methodsA series of 438 Spanish schoolchildren (6–16 years old) were evaluated anthropometrically (weight, height, waist circumference, skinfold thickness, BMI, WtHR, body fat percentage [%BF]). Ten SNPs were genotyped from saliva samples, generating a GRS for obesity, establishing genotype-phenotype association.ResultsSchoolchildren categorised as obese by BMI, ICT and %BF had higher GRS than their non-obese peers. The prevalence of overweight and adiposity was higher in subjects with a GRS above the median. Similarly, between 11 and 16 years of age, all anthropometric variables presented higher averages.ConclusionsGRS estimated from the 10 SNPs can be a diagnostic tool for the potential risk of obesity in Spanish schoolchildren and could be useful from the preventive perspective.

Puntuación de riesgo genético para la obesidad común y antropometría en escolares españoles

IntroductionCommon or non-syndromic obesity is a complex polygenic trait conditioned by biallelic or single-base polymorphisms called SNPs (Single-Nucleotide Polymorphisms) that present an additive effect and act synergistically. Most genotype-obese phenotype association studies include body mass index (BMI) or waist-to-height ratio (WtHR), and very few introduce a broad anthropometric profile. ObjectiveTo verify whether a genetic risk score (GRS) developed from 10SNPs is associated with the obesity phenotype assessed from anthropometric measures indicative of excess weight, adiposity and fat distribution. Material and methodsA series of 438 Spanish schoolchildren (6 to 16years old) were evaluated anthropometrically (weight, height, waist circumference, skinfold thickness, BMI, WtHR, body fat percentage [%BF]). Ten SNPs were genotyped from saliva samples, generating a GRS for obesity, establishing genotype-phenotype association. ResultsSchoolchildren categorised as obese by BMI, ICT and %BF had higher GRS than their non-obese peers. The prevalence of overweight and adiposity was higher in subjects with a GRS above the median. Similarly, between 11 and 16years of age, all anthropometric variables presented higher averages. ConclusionsGRS estimated from the 10SNPs can be a diagnostic tool for the potential risk of obesity in Spanish schoolchildren and could be useful from the preventive perspective.

Cyt1Aa toxin gene frequency in Bacillus thuringiensis isolates and its relation with pathogenicity for vector mosquitoes

Bacillus thuringiensis produces several virulence factors, the main ones being the Cry and Cyt toxins, present in the parasporal body produced during sporulation. The Cyt toxins have mechanisms specific for mosquitoes and Cyt1Aa, the most studied cytolytic toxin, is effective for mosquito control by acting in synergism with Cry toxins. The goal of the present work was to study the frequency of the codifying gene for Cyt1Aa in B. thuringiensis native isolates acquired from samples of soil, insect and water, as well as to verify any possible genetic polymorphism. 1,448 B thuringiensis strains were used for DNA extraction and PCR technique, all with the use of a primer that amplifies a fragment of 300 pairs of the cyt1Aa gene. The strains that showed amplification in the PCR reaction were sequenced and compared to each other and to the sequences available at Genbank. 32 (2.3%) strains of B. thuringiensis showed positive amplification for the cyt1Aa gene. The highest frequency of isolates with cyt1Aa gene was acquired from samples coming from the Cerrado biome, both isolates from soil and from insects, equally with 3.4%. The cyt1Aa gene sequencing highlighted that, for that 300 bp region, the gene is conserved and there is no single-base polymorphism.

A large-scale population based organelle pan-genomes construction and phylogeny analysis reveal the genetic diversity and the evolutionary origins of chloroplast and mitochondrion in Brassica napus L.

BackgroundAllotetraploid oilseed rape (Brassica napus L.) is an important worldwide oil-producing crop. The origin of rapeseed is still undetermined due to the lack of wild resources. Despite certain genetic architecture and phylogenetic studies have been done focus on large group of Brassica nuclear genomes, the organelle genomes information under global pattern is largely unknown, which provide unique material for phylogenetic studies of B. napus. Here, based on de novo assemblies of 1,579 B. napus accessions collected globally, we constructed the chloroplast and mitochondrial pan-genomes of B. napus, and investigated the genetic diversity, phylogenetic relationships of B. napus, B. rapa and B. oleracea.ResultsBased on mitotype-specific markers and mitotype-variant ORFs, four main cytoplasmic haplotypes were identified in our groups corresponding the nap, pol, ole, and cam mitotypes, among which the structure of chloroplast genomes was more conserved without any rearrangement than mitochondrial genomes. A total of 2,092 variants were detected in chloroplast genomes, whereas only 326 in mitochondrial genomes, indicating that chloroplast genomes exhibited a higher level of single-base polymorphism than mitochondrial genomes. Based on whole-genome variants diversity analysis, eleven genetic difference regions among different cytoplasmic haplotypes were identified on chloroplast genomes. The phylogenetic tree incorporating accessions of the B. rapa, B. oleracea, natural and synthetic populations of B. napus revealed multiple origins of B. napus cytoplasm. The cam-type and pol-type were both derived from B. rapa, while the ole-type was originated from B. oleracea. Notably, the nap-type cytoplasm was identified in both the B. rapa population and the synthetic B. napus, suggesting that B. rapa might be the maternal ancestor of nap-type B. napus.ConclusionsThe phylogenetic results provide novel insights into the organelle genomic evolution of Brassica species. The natural rapeseeds contained at least four cytoplastic haplotypes, of which the predominant nap-type might be originated from B. rapa. Besides, the organelle pan-genomes and the overall variation data offered useful resources for analysis of cytoplasmic inheritance related agronomical important traits of rapeseed, which can substantially facilitate the cultivation and improvement of rapeseed varieties.

Improvement of base editors and prime editors advances precision genome engineering in plants.

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein (Cas)-mediated gene disruption has revolutionized biomedical research as well as plant and animal breeding. However, most disease-causing mutations and agronomically important genetic variations are single base polymorphisms (single-nucleotide polymorphisms) that require precision genome editing tools for correction of the sequences. Although homology-directed repair of double-stranded breaks (DSBs) can introduce precise changes, such repairs are inefficient in differentiated animal and plant cells. Base editing and prime editing are two recently developed genome engineering approaches that can efficiently introduce precise edits into target sites without requirement of DSB formation or donor DNA templates. They have been applied in several plant species with promising results. Here, we review the extensive literature on improving the efficiency, target scope, and specificity of base editors and prime editors in plants. We also highlight recent progress on base editing in plant organellar genomes and discuss how these precision genome editing tools are advancing basic plant research and crop breeding.

PSIII-11 Effect of Breast cancer metastasis-suppressor 1-like (BRMS1L) genotype on teat number traits in Jeju native pigs (JNP) and Landrace

Abstract The purpose of this study was to compare the changes of teat number traits of Jeju native pig (JNP) and Landrace varieties according to the breast cancer metastasis-suppressor 1-like (BRMS1L) genotype. The number of teat varies according to the single-base polymorphism with a G or A base 1,087 from the start codon ATG in the exon 1 region of the BRMS1L gene. The total teat number was examined at birth for 28 JNPs and 72 Landraces, and the BRMS1L genotype was analyzed by Pyrosequencing. As a result, the genotyping frequency of JNP was 1 A / A type, 9 A / G type, and 18 G / G type, whereas, on the contrary, Landrace had 70 A / A type, 2 A / C type, and C / C was identified as 0 heads. The total teat number was between the two varieties was 13.32 ± 0.95 and 14.51 ± 1.03, respectively (P < 0.001). According to genotypes in Jeju native pig breeds, the total number of nipples was 15 A / A, 14.0 ± 0.82 A / G, and 12.89 ± 0.74 G / G (P < 0.018). Conversely, Landrace was 14.54 ± 1.02 A / A and 13.5 ± 0.5 A / G. As a result of the above study, the frequency of varieties and genotypes was found to have a significant effect on the difference in nipple count. Based on the results of this study, if the improvement of Jeju native pigs is to be carried out, it is expected that the number of nipples will increase and the mammalian capacity will increase.

Rapid and sensitive detection of Mycobacterium tuberculosis based on strand displacement amplification and magnetic beads.

Tuberculosis is one of the main infectious diseases threatening public health, and the development of simple, rapid, and cost-saving methods for tuberculosis diagnosis is of profound importance for tuberculosis prevention and treatment. The bacterium Mycobacterium tuberculosis (MTB) is the pathogen that causes tuberculosis, and assaying for MTB is the only criterion for tuberculosis diagnosis. A new enzyme-free method based on strand displacement amplification and magnetic beads was developed for simple, rapid, and cost-saving MTB detection. Under optimum conditions, a good linear relationship could be observed between fluorescence and MTB specific DNA concentration ranging from 0.05 to 150 nM with a correlation coefficient of 0.993 (n = 8) and a detection limit of 47 pM (3σ/K). The present method also distinguished a one base mismatch from MTB specific DNA, showing great promise for MTB genome single base polymorphism analysis. MTB specific DNA content in polymerase chain reaction samples was successfully detected using the new method, and recoveries were 97.8-100.8%, indicating that the present method had high accuracy and shows good potential for the early diagnosis of tuberculosis.

Severe toxicity in adult patients with lung cancer under treatment with pemetrexed: a prospective cohort study

Pemetrexed is an antimetabolite approved for treatment of non-small cell lung cancer. Harbouring interindividual variability in both the pharmacokinetic and pharmacogenetic profiles may lead to life-threatening toxicities. A prospective cohort study of adult patients initiating treatment with pemetrexed in combination with platinum between 2013 and 2015 were follow up. Primary exposure were the methylenetetrahydrofolate reductase (MTHFR) single base polymorphisms in exon 4 and 7 and 5'-UTR- thymidylate synthase (TYMS) VNTR genotypes, in addition to baseline clinical and demographic variables. We used a Cox regression model to evaluate patient's survival and toxicity experience and its association with both baseline characteristics, and a-priori determined genetic polymorphisms. Seventy two patients were included, 52.7% developed severe hematologic toxicity during follow-up. None of the tested genotypes were significantly associated with the main outcome on multivariate analysis, nor other basal clinical variables. Overall survival between patients experiencing the outcome was not different from those without it, but hospital admissions were more frequent. MTHFR and 5'-UTR-TYMS genotypes were not useful for predicting high grade toxicity events in patients under treatment with pemetrexed.

Mannose-Binding Lectin2 Gene Polymorphism and IgG4 in Membranous Nephropathy

Background: Idiopathic membranous nephropathy (IMN) has been linked to the lectin pathway, IgG4 and genetic susceptibility. We investigated the frequency of mannose-binding lectin2 (MBL2) gene polymorphisms and the serum ratio of IgG4 in patients with membranous nephropathy (MN). Methods: Polymorphisms in the exon 1 of the MBL2 gene (codons 52, 54, and 57) and single base polymorphisms at positions –550 (HL) and –221 (XY) in the promoter region were evaluated in 60 patients compared to a control group (CG) of 101 blood donors. It established the frequency of polymorphisms and the serum ratio of IgG4 comparing 2 etiologies of MN: idiopathic (35 patients) and secondary to systemic lupus erythematosus (25 patients). Results: Patients with MN had a 2.54-fold higher probability (95% CI 1.51–4.31) of carrying the O alelle, exon 1 variant, and 11.16-fold higher probability (95% CI 4.77–28.41) of having A/O genotype when compared to CG. The frequency of polymorphisms in the promoter region was similar between the groups. Combined genotypes generally related to the defective production of MBL (YA/O, XA/O and O/O) were more frequent in patients with MN (OR 7.11; 95% CI 2.69–21.27), when compared to controls. The median of serum ratio IgG4 was 5% for idiopathic MN and 3% for lupus MN patients (p = 0.016). Conclusions: Our data suggests that MBL2 polymorphisms may be associated with the activation of the lectin pathway by IgG4 subclass antibodies in MN.

A Novel Ultrasensitive In Situ Hybridization Approach to Detect Short Sequences and Splice Variants with Cellular Resolution

Investigating the expression of RNAs that differ by short or single nucleotide sequences at a single-cell level in tissue has been limited by the sensitivity and specificity of in situ hybridization (ISH) techniques. Detection of short isoform-specific sequences requires RNA isolation for PCR analysis—an approach that loses the regional and cell-type-specific distribution of isoforms. Having the capability to distinguish the differential expression of RNA variants in tissue is critical because alterations in mRNA splicing and editing, as well as coding single nucleotide polymorphisms, have been associated with numerous cancers, neurological and psychiatric disorders. Here we introduce a novel highly sensitive single-probe colorimetric/fluorescent ISH approach that targets short exon/exon RNA splice junctions using single-pair oligonucleotide probes (~ 50 bp). We use this approach to investigate, with single-cell resolution, the expression of four transcripts encoding the neuregulin (NRG) receptor ErbB4 that differ by alternative splicing of exons encoding two juxtamembrane (JMa/JMb) and two cytoplasmic (CYT-1/CYT-2) domains that alter receptor stability and signaling modes, respectively. By comparing ErbB4 hybridization on sections from wild-type and ErbB4 knockout mice (missing exon 2), we initially demonstrate that single-pair probes provide the sensitivity and specificity to visualize and quantify the differential expression of ErbB4 isoforms. Using cell-type-specific GFP reporter mice, we go on to demonstrate that expression of ErbB4 isoforms differs between neurons and oligodendrocytes, and that this differential expression of ErbB4 isoforms is evolutionarily conserved to humans. This single-pair probe ISH approach, known as BaseScope, could serve as an invaluable diagnostic tool to detect alternative spliced isoforms, and potentially single base polymorphisms, associated with disease.

Genetic association of NAD(P)H quinone oxidoreductase (NQO1*2) polymorphism with NQO1 levels and risk of diabetic nephropathy.

NAD(P)H quinone oxidoreductase 1 (NQO1) catalyzes reactions having a cyto-protective effect against redox cycling and oxidative stress. A single base polymorphism (C/T) at nucleotide 609 of the NQO1 gene impairs the stability and function of its protein. Its role in the development of diabetic nephropathy (DN) has not been deciphered. Therefore, this study aimed to evaluate the association of NQO1*2 (rs1800566) polymorphism with plasma NQO1 levels and DN. This study screened 600 participants including healthy controls (HC), type 2 diabetes mellitus without complications (T2DM) and diabetic nephropathy (DN): 200 each for studying NQO1*2 gene polymorphism using the PCR-RFLP. Plasma NQO1 levels were measured by ELISA. Analysis of variance and logistic regression were used to evaluate the association of NQO1 polymorphism with plasma NQO1 levels and DN. The allelic frequencies of NQO1*1/NQO1*2 were 0.88/0.12 in HC, 0.765/0.235 in T2DM and 0.65/0.35 in DN. Carriers of the NQO1*2 allele had significantly lower plasma NQO1 levels (p<0.05) and revealed higher risk towards the development of DN (OR=1.717, p=0.010). NQO1*2 SNP is a functional polymorphism having a significant effect on NQO1 levels. Our results indicate that NQO1*2 genotype may increase susceptibility to DN in north Indian subjects with T2DM.

Association between two single base polymorphisms of intercellular adhesion molecule 1 gene and inflammatory bowel disease.

The present study evaluated the association between G241R and K469E polymorphisms of intercellular adhesion molecule 1 gene and inflammatory bowel disease in Iranian population. Inflammatory bowel disease including ulcerative colitis and Crohn's disease, is a chronic idiopathic inflammatory disease of the gastrointestinal tract. There are two single base polymorphisms of intercellular adhesion molecule 1gene, G241R and K469E, reported to be associated with inflammatory disorders. In this case-control study, 156 inflammatory bowel disease patients (110 ulcerative colitis and 46 Crohn's disease patients) and 131 healthy controls were enrolled. Two polymorphisms of intercellular adhesion molecule 1 gene, including G241R and K469E, were assessed by polymerase chain reaction followed by restriction fragment length polymorphism. The E469 allele of K469E polymorphism was significantly more frequent in Crohn's disease patients compared to controls (P< 0.05, OR= 1.83; 95% CI: 1.13 to 2.96). The mutant homozygote genotype of K469E polymorphism (E/E) was also significantly more frequent in Crohn's disease patients compared to controls (P< 0.05, OR= 4.23; 95% CI: 1.42 to 12.59). No difference was observed in the frequency of K469E polymorphism among ulcerative colitis patients compared to controls. There were no significant differences in genotype and allele frequencies of G241R polymorphism among ulcerative colitis and Crohn's disease patients compared to control subjects. According to our findings, K469E polymorphism of intercellular adhesion molecule 1 gene may probably participate in the pathogenesis of Crohn's disease in Iran.

Oxidative stress in susceptibility to breast cancer: study in Spanish population.

BackgroundAlterations in the redox balance are involved in the origin, promotion and progression of cancer. Inter-individual differences in the oxidative stress regulation can explain a part of the variability in cancer susceptibility.The aim of this study was to evaluate if polymorphisms in genes codifying for the different systems involved in oxidative stress levels can have a role in susceptibility to breast cancer.MethodsWe have analyzed 76 single base polymorphisms located in 27 genes involved in oxidative stress regulation by SNPlex technology. First, we have tested all the selected SNPs in 493 breast cancer patients and 683 controls and we have replicated the significant results in a second independent set of samples (430 patients and 803 controls). Gene-gene interactions were performed by the multifactor dimensionality reduction approach.ResultsSix polymorphisms rs1052133 (OGG1), rs406113 and rs974334 (GPX6), rs2284659 (SOD3), rs4135225 (TXN) and rs207454 (XDH) were significant in the global analysis. The gene-gene interactions demonstrated a significant four-variant interaction among rs406113 (GPX6), rs974334 (GPX6), rs105213 (OGG1) and rs2284659 (SOD3) (p-value = 0.0008) with high-risk genotype combination showing increased risk for breast cancer (OR = 1.75 [95% CI; 1.26-2.44]).ConclusionsThe results of this study indicate that different genotypes in genes of the oxidant/antioxidant pathway could affect the susceptibility to breast cancer. Furthermore, our study highlighted the importance of the analysis of the epistatic interactions to define with more accuracy the influence of genetic variants in susceptibility to breast cancer.

An efficient DNA-fueled molecular machine for the discrimination of single-base changes.

A new strategy for single-base polymorphism (SNP) detection based on the assembly of DNA-AuNPs (gold nanoparticles) driven by a DNA-fueled molecular machine, is established and optimized. It is highly efficient, works at room temperature, and is easy to handle. A single-base change on an oligonucleotide strand is unambiguously discriminated for either SNPs or insertions and deletions (indels). The strategy is demonstrated to detect a mutation in the breast cancer gene BRCA1 in homogeneous solution at room temperature.

Single Base Extension and Fourier-Transform Infra-Red Spectroscopy Techniques; Further Approaches in Discriminating Hazelnut-Adulterated Olive Oil

Background:Confirmation of olive oil authenticity and particularly virgin olive oil has a great importance. Several advanced chemical and genetic analyses have been used to monitor especial components; however each has its limitations especially when detecting hazelnut-adulterated olive oil. Objectives:The objective of this research is to assess the presence of trace amount of hazelnut oil in olive oil (less than 10%) by Single Base Extension (SBE) and Fourier Transform InfraRed Spectroscopy (FTIR). Materials and Methods:The study was based on the analysis of chloroplast DNA sequences using SBE to detect Single Base Polymorphism (SNPs) in highly preserved DNA regions among species to differentiate pure and adulterated olive oil by means of two parallel tools; ABI PRISM automatic sequencer and the SNaPshot lit (APPLERA). Fourier -Transform InfraRed technique has been used for FTIR spectrum comparisons of pure olive oil and hazelnut-adulterated one as well. Results:Total DNA was extracted successfully from pure and hazelnut-adulterated olive oil, and it provided properly acceptable amplification with the primers designed on chloroplast region of both species and admixture oil of them in different ratios; 50: 50, 70: 30, and vice versa. However, for lesser than 10% hazelnut oil in olive oil only SBE analysis provided recognizable results. FTIR spectra of oil samples were assessed at frequency regions of 4000 - 700 cm-1. Eight wave numbers (3007, 1373, 1237, 1120, 1098, 1032, 965, and 722 cm-1) out of eleven differentiating ones were selected as candidate wave-numbers to distinguish pure and adulterated olive oil. Conclusions:SBE technique proved to be an effective strategy to verify olive oil authenticity, especially from hazelnut-adulterated olive oil. However, FTIR technique provided trustable results only when higher than 10% hazelnut oil is present in olive oil.

Oligonucleotide Delivery by Nucleofection Does Not Rescue the Reduced Proliferation Phenotype of Gene-Edited Cells

Gene editing using single-stranded oligonucleotides (ODNs) can be used to reverse or create a single base mutation in mammalian cells. This approach could be used to treat genetic diseases caused, at least in part, by a nucleotide substitution. The technique could also be used as a tool to establish single base polymorphisms at multiple sites and thus aid in creating cell lines that can be used to define the basis for drug resistance in human cells. A troubling outcome of the gene-editing reaction is the effect on normal growth of cells that have undergone nucleotide exchange. In this work, we attempt to overcome this reduced proliferation phenotype by changing the method by which the ODN is introduced into the target cell. Using a series of assays that measure gene editing, DNA damage response, and cell viability, we report that chemically modified ODNs, the most active form of ODN for gene editing, can be used successfully if introduced into the cell by the method of nucleofection. Unlike electroporation, which has been used as the standard mode of ODN delivery, one new result is that nucleofection does not induce a dramatic loss of viability within the first 24 hours after the start of gene editing. In addition, and importantly, ODNs introduced to the cell by nucleofection do not activate the DNA damage response pathway as dramatically as ODNs introduced by electroporation. These 2 novel findings are encouraging for the application of gene editing in other systems. However, reduced proliferation phenotype is still observed when the population of corrected cells is monitored out to 8 days, and thus, delivery by nucleofection does not solve the proliferation problem encountered by cells bearing an edited gene.

Dynamics of a Recurrent Buchnera Mutation That Affects Thermal Tolerance of Pea Aphid Hosts

Mutations in maternally transmitted symbionts can affect host fitness. In this study we investigate a mutation in an obligate bacterial symbiont (Buchnera), which has dramatic effects on the heat tolerance of pea aphid hosts (Acyrthosiphon pisum). The heat-sensitive allele arises through a single base deletion in a homopolymer within the promoter of ibpA, which encodes a universal small heat-shock protein. In laboratory cultures reared under cool conditions (20°), the rate of fixation (1.4 × 10(-3) substitutions per Buchnera replication) is much higher than the previously estimated mutation rate for single base deletions in homopolymers in the Buchnera genome, implying a strong selective benefit. This mutation recurs in natural populations, but seldom reaches high frequencies, implying that it is only rarely favored by selection. Another potential source of physiological stress in pea aphids is infection by other microorganisms, including facultative bacterial symbionts, which occur in a majority of pea aphids in field populations. Frequency of the heat-sensitive Buchnera allele is negatively correlated with presence of facultative symbionts in both laboratory colonies and field populations, suggesting that these infections impose stress that is ameliorated by ibpA expression. This single base polymorphism in Buchnera has the potential to allow aphid populations to adapt quickly to prevailing conditions.

Einzelbasenpaarpolymorphismen und erektile Dysfunktion

The risk for erectile dysfunction is closely linked to cardiovascular morbidities such as coronary heart disease, arterial hypertension, hypercholesterolemia, and diabetes. Molecular analysis revealed an association between the genotypes in single base polymorphisms and the risk for these cardiovascular morbidities. In this review the current knowledge of association studies of single nucleotide polymorphisms and erectile dysfunction and the response to the PDE-5 inhibitor sildenafil is described.

Expression of CETP and of splice variants induces the same level of ER stress despite secretion efficiency differences

The cholesteryl ester transfer protein (CETP) gene has been associated with a variety of phenotypes, including HDL-cholesterol levels and, more sporadically, with cardiovascular disease, obesity, and extreme longevity. Alterations of CETP activity levels can be caused by single-base polymorphisms as well as by alternative splicing. In addition to the previously characterized alternative splicing that skips exon 9, we found additional minor variants and characterized the activity of the resultant proteins. The novel variants skipped exon 9 sequences and inserted one of two in-frame exons from Alu-derived intronic sequences. None of the alternatively spliced variants are efficiently secreted, and coexpression of them inhibits wild-type CETP secretion. Expression of the alternative spliced variants causes an induction of genes linked to the endoplasmic reticulum (ER) stress response, including the neighboring HERPUD1 (homocysteine- and ER stress-inducible protein, ubiquitin-like domain-containing) gene. Unexpectedly, even though wild-type CETP is secreted much more efficiently than spliced variants, it induces the same degree of stress response as spliced variants, whereas a control secreted protein does not. CETP plays a complex role in modulating ER stress, with its expression inducing the response and its cholesteryl ester transfer activity and differential splicing modulating the response in other ways.

Polymorphism of tumour necrosis factor-alpha (TNF-alpha) at position -308 in relation to ankylosing spondylitis.

In addition to HLA-B27, other genetic factors are thought to be involved in the pathogenesis of ankylosing spondylitis (AS). Because of the localization, in the proximity of the HLA-B locus, and the biological activities of TNF-alpha, we investigated the association between AS and a single base polymorphism located at position -308 of the TNF-alpha gene. An allele-specific polymerase chain reaction was developed to monitor this polymorphism. The frequency of the TNF-alpha alleles was determined in 66 AS patients and 37 healthy controls. The TNF-alpha allele frequency was not significantly different between AS patients and controls.