Multiancestry analysis of the HLA locus in Alzheimer's and Parkinson's diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes

Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson's disease (PD) and Alzheimer's disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, and intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased Aβ42. Protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1*04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues.

Empirical Bayes Estimation of Semi-parametric Hierarchical Mixture Models for Unbiased Characterization of Polygenic Disease Architectures

Genome-wide association studies (GWAS) suggest that the genetic architecture of complex diseases consists of unexpectedly numerous variants with small effect sizes. However, the polygenic architectures of many diseases have not been well characterized due to lack of simple and fast methods for unbiased estimation of the underlying proportion of disease-associated variants and their effect-size distribution. Applying empirical Bayes estimation of semi-parametric hierarchical mixture models to GWAS summary statistics, we confirmed that schizophrenia was extremely polygenic [~40% of independent genome-wide SNPs are risk variants, most within odds ratio (OR = 1.03)], whereas rheumatoid arthritis was less polygenic (~4 to 8% risk variants, significant portion reaching OR = 1.05 to 1.1). For rheumatoid arthritis, stratified estimations revealed that expression quantitative loci in blood explained large genetic variance, and low- and high-frequency derived alleles were prone to be risk and protective, respectively, suggesting a predominance of deleterious-risk and advantageous-protective mutations. Despite genetic correlation, effect-size distributions for schizophrenia and bipolar disorder differed across allele frequency. These analyses distinguished disease polygenic architectures and provided clues for etiological differences in complex diseases.

A functional SNP in FLT1 increases risk of coronary artery disease in a Japanese population

Coronary artery disease (CAD) including myocardial infarction is one of the leading causes of death in many countries. Similar to other common diseases, its pathogenesis is thought to result from complex interactions among multiple genetic and environmental factors. Recent large-scale genetic association analysis for CAD identified 15 new loci. We examined the reproducibility of these previous association findings with 7990 cases and 6582 controls in a Japanese population. We found a convincing association of rs9319428 in FLT1, encoding fms-related tyrosine kinase 1 (P=5.98 × 10(-8)). Fine mapping using tag single-nucleotide polymorphisms (SNPs) at FLT1 locus revealed that another SNP (rs74412485) showed more profound genetic effect for CAD (P=2.85 × 10(-12)). The SNP, located in intron 1 in FLT1, enhanced the transcriptional level of FLT1. RNA interference experiment against FLT1 showed that the suppression of FLT1 resulted in decreased expression of inflammatory adhesion molecules. Expression of FLT1 was observed in endothelial cells of human coronary artery. Our results indicate that the genetically coded increased expression of FLT1 by a functional SNP implicates activation in an inflammatory cascade that might eventually lead to CAD.

Performance comparison of four commercial human whole-exome capture platforms

Whole exome sequencing (WXS) is widely used to identify causative genetic mutations of diseases. However, not only have several commercial human exome capture platforms been developed, but substantial updates have been released in the past few years. We report a performance comparison for the latest release of four commercial platforms, Roche/NimbleGen’s SeqCap EZ Human Exome Library v3.0, Illumina’s Nextera Rapid Capture Exome (v1.2), Agilent’s SureSelect XT Human All Exon v5 and Agilent’s SureSelect QXT, using the same DNA samples. Agilent XT showed the highest target enrichment efficiency and the best SNV and short indel detection sensitivity in coding regions with the least amount of sequencing. Agilent QXT had slightly inferior target enrichment than Agilent XT. Illumina, with additional sequencing, detected SNVs and short indels at the same quality as Agilent XT, and showed the best performance in coverage of medically interesting mutations. NimbleGen detected more SNVs and indels in untranslated regions than the others. We also found that the platforms, which enzymatically fragment the genomic DNA (gDNA), detected more homozygous SNVs than those using sonicated gDNA. We believe that our analysis will help investigators when selecting a suitable exome capture platform for their particular research.

The construction of risk prediction models using GWAS data and its application to a type 2 diabetes prospective cohort

Recent genome-wide association studies (GWAS) have identified several novel single nucleotide polymorphisms (SNPs) associated with type 2 diabetes (T2D). Various models using clinical and/or genetic risk factors have been developed for T2D risk prediction. However, analysis considering algorithms for genetic risk factor detection and regression methods for model construction in combination with interactions of risk factors has not been investigated. Here, using genotype data of 7,360 Japanese individuals, we investigated risk prediction models, considering the algorithms, regression methods and interactions. The best model identified was based on a Bayes factor approach and the lasso method. Using nine SNPs and clinical factors, this method achieved an area under a receiver operating characteristic curve (AUC) of 0.8057 on an independent test set. With the addition of a pair of interaction factors, the model was further improved (p-value 0.0011, AUC 0.8085). Application of our model to prospective cohort data showed significantly better outcome in disease-free survival, according to the log-rank trend test comparing Kaplan-Meier survival curves (p--value 2:09 x 10(-11)). While the major contribution was from clinical factors rather than the genetic factors, consideration of genetic risk factors contributed to an observable, though small, increase in predictive ability. This is the first report to apply risk prediction models constructed from GWAS data to a T2D prospective cohort. Our study shows our model to be effective in prospective prediction and has the potential to contribute to practical clinical use in T2D.

A genome-wide association study identifies 2 susceptibility Loci for Crohn's disease in a Japanese population

BACKGROUND & AIMS

Crohn's disease is an inflammatory bowel disease induced by multiple genetic and environmental factors. Genome-wide association studies have identified genetic factors that affect the risk for Crohn's disease in European populations, but information from other ethnic groups is scarce. We therefore investigated genetic factors associated with Crohn's disease in the Japanese population.

METHODS

We performed a genome-wide association study with 372 individuals with Crohn's disease (cases) and 3389 controls, all from the Japanese population. To confirm identified associations, we performed a replication study with an independent panel of 1151 Crohn's disease cases and 15,800 controls. We also performed an association analysis using genome-wide genotype imputation in the discovery cohort.

RESULTS

We confirmed associations of Crohn's disease with variants in MHC (rs7765379, P = 2.11 × 10(-59)), TNFSF15 (rs6478106, P = 3.87 × 10(-45)), and STAT3 (rs9891119, P = 2.24 × 10(-14)). We identified 2 new susceptibility loci: on chromosome 4p14 (rs1487630, P = 2.40 × 10(-11); odds ratio, 1.33), and in the SLC25A15-ELF1-WBP4 region on 13q14 (rs7329174 in ELF1, P = 5.12 × 10(-9); odds ratio, 1.27).

CONCLUSIONS

In a genome-wide association study, we identified 2 new susceptibility loci for Crohn's disease in a Japanese population. These findings could increase our understanding of the pathogenesis of Crohn's disease.

Reproducibility, performance, and clinical utility of a genetic risk prediction model for prostate cancer in Japanese

Prostate specific antigen (PSA) is widely used as a diagnostic biomarker for prostate cancer (PC). However, due to its low predictive performance, many patients without PC suffer from the harms of unnecessary prostate needle biopsies. The present study aims to evaluate the reproducibility and performance of a genetic risk prediction model in Japanese and estimate its utility as a diagnostic biomarker in a clinical scenario. We created a logistic regression model incorporating 16 SNPs that were significantly associated with PC in a genome-wide association study of Japanese population using 689 cases and 749 male controls. The model was validated by two independent sets of Japanese samples comprising 3,294 cases and 6,281 male controls. The areas under curve (AUC) of the model were 0.679, 0.655, and 0.661 for the samples used to create the model and those used for validation. The AUCs were not significantly altered in samples with PSA 1-10 ng/ml. 24.2% and 9.7% of the patients had odds ratio <0.5 (low risk) or >2 (high risk) in the model. Assuming the overall positive rate of prostate needle biopsies to be 20%, the positive biopsy rates were 10.7% and 42.4% for the low and high genetic risk groups respectively. Our genetic risk prediction model for PC was highly reproducible, and its predictive performance was not influenced by PSA. The model could have a potential to affect clinical decision when it is applied to patients with gray-zone PSA, which should be confirmed in future clinical studies.

A single-nucleotide polymorphism in ANK1 is associated with susceptibility to type 2 diabetes in Japanese populations

To identify a novel susceptibility locus for type 2 diabetes, we performed an imputation-based, genome-wide association study (GWAS) in a Japanese population using newly obtained imputed-genotype data for 2 229 890 single-nucleotide polymorphisms (SNPs) estimated from previously reported, directly genotyped GWAS data in the same samples (stage 1: 4470 type 2 diabetes versus 3071 controls). We directly genotyped 43 new SNPs with P-values of <10(-4) in a part of stage-1 samples (2692 type 2 diabetes versus 3071 controls), and the associations of validated SNPs were evaluated in another 11 139 Japanese individuals (stage 2: 7605 type 2 diabetes versus 3534 controls). Combined meta-analysis using directly genotyped data for stages 1 and 2 revealed that rs515071 in ANK1 and rs7656416 near MGC21675 were associated with type 2 diabetes in the Japanese population at the genome-wide significant level (P < 5 × 10(-8)). The association of rs515071 was also observed in European GWAS data (combined P for all populations = 6.14 × 10(-10)). Rs7656416 was in linkage disequilibrium to rs6815464, which had recently been identified as a top signal in a meta-analysis of East Asian GWAS for type 2 diabetes (r(2) = 0.76 in stage 2). The association of rs7656416 with type 2 diabetes disappeared after conditioning on rs6815464. These results indicate that the ANK1 locus is a new, common susceptibility locus for type 2 diabetes across different ethnic groups. The signal of association was weaker in the directly genotyped data, so the improvement in signal indicates the importance of imputation in this particular case.

Ototoxicity of Povidone-Iodine applied to the middle ear cavity of guinea pigs

OBJECTIVE

Povidone-Iodine preparation is used as a disinfectant in otological surgeries. The ototoxicity of Povidone-Iodine preparation was evaluated using infant, young and adult guinea pigs. The effects of different concentrations and of different exposure durations on compound action potentials were also studied.

MATERIALS & METHODS

Povidone-Iodine was used to fill one middle ear cavity of the guinea pig, and the compound action potential (CAP) was measured from the round window membrane at 24h, 7 days, and 28 days. The contralateral side was filled with saline as control. Test sounds used were clicks and tone bursts of 2, 4, and 8 kHz.

RESULTS

At 24h, Povidone-Iodine solution showed a significant toxic effect in the infant group. In the young animal group, no toxic effect was seen. In the adult group, a mild degree of deafness for 2 kHz was found. At 7 days, the young group showed significant hearing loss for all frequencies, but the adult group did not show any hearing loss. With a half strength solution, both young and adult group did not show hearing loss. At 28 days, with a full strength solution, hearing loss became prominent for all sound stimulation. With 1/8th dilution, the young group showed a moderate hearing loss, but the adult group did not.

CONCLUSION

The thicker round window membrane in human is expected to provide more protection to the human cochlea than in the guinea pig model that we have studied. Mild hearing loss at 24h and 7 days using 10% solution, but no hearing loss with 5% solution at 7 days may indicate that rinsing of the middle ear cavity with saline during surgery should minimize the ototoxic effect of this product. The age of the animals does influence the outcome of the ototoxicity experiment. From this experiment, Povidone-Iodine preparations in the infant should be used with caution. Povidone scrub should not be used for otologic surgery.

Variation in the DEPDC5 locus is associated with progression to hepatocellular carcinoma in chronic hepatitis C virus carriers

Chronic viral hepatitis is the most important risk factor for progression to hepatocellular carcinoma (HCC). To identify genetic risk factors for progression to HCC in individuals with chronic hepatitis C virus (HCV), we analyzed 467,538 SNPs in 212 Japanese individuals with chronic HCV with HCC and 765 individuals with chronic HCV without HCC. We identified one intronic SNP in the DEPDC5 locus on chromosome 22 associated with HCC risk and confirmed the association using an independent case-control population (710 cases and 1,625 controls). The association was highly significant when we analyzed the stages separately as well as together (rs1012068, P(combined) = 1.27 × 10(-13), odds ratio = 1.75). The significance level of the association further increased after adjustment for gender, age and platelet count (P = 1.35 × 10(-14), odds ratio = 1.96). Our findings suggest that common variants within the DEPDC5 locus affect susceptibility to HCC in Japanese individuals with chronic HCV infection.

Association of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility

Recent genome-wide association studies reported strong and reproducible associations of multiple genetic variants in a large "gene-desert" region of chromosome 8q24 with susceptibility to prostate cancer (PC). However, the causative or functional variants of these 8q24 loci and their biological mechanisms associated with PC susceptibility remain unclear and should be investigated. Here, focusing on its most centromeric region (so-called Region 2: Chr8: 128.14-128.28 Mb) among the multiple PC loci on 8q24, we performed fine mapping and re-sequencing of this critical region and identified SNPs (single nucleotide polymorphisms) between rs1456315 and rs7463708 (chr8: 128,173,119-128,173,237 bp) to be most significantly associated with PC susceptibility (P = 2.00 × 10(-24) , OR = 1.74, 95% confidence interval = 1.56-1.93). Importantly, we show that this region was transcribed as a ∼13 kb intron-less long non-coding RNA (ncRNA), termed PRNCR1 (prostate cancer non-coding RNA 1), and PRNCR1 expression was upregulated in some of the PC cells as well as precursor lesion prostatic intraepithelial neoplasia. Knockdown of PRNCR1 by siRNA attenuated the viability of PC cells and the transactivation activity of androgen receptor, which indicates that PRNCR1 could be involved in prostate carcinogenesis possibly through androgen receptor activity. These findings could provide a new insight in understanding the pathogenesis of genetic factors for PC susceptibility and prostate carcinogenesis.

Variation in TP63 is associated with lung adenocarcinoma susceptibility in Japanese and Korean populations

Lung cancer is the most common cause of death from cancer worldwide, and its incidence is increasing in East Asian and Western countries. To identify genetic factors that modify the risk of lung adenocarcinoma, we conducted a genome-wide association study in a Japanese cohort, with replication in two independent studies in Japanese and Korean individuals, in a total of 2,098 lung adenocarcinoma cases and 11,048 controls. The combined analyses identified two susceptibility loci for lung adenocarcinoma: TERT (rs2736100, combined P = 2.91 × 10⁻¹¹), odds ratio (OR) = 1.27) and TP63 (rs10937405, combined P = 7.26 × 10⁻¹²), OR = 1.31). Fine mapping of the region containing TP63 showed that a SNP (rs4488809) in intron 1 of TP63 showed the most significant association. Our results suggest that genetic variation in TP63 may influence susceptibility to lung adenocarcinoma in East Asian populations.

Production of a human antibody fragment against the insulin-like growth factor І receptor as a fusion protein

The aim of this study was to isolate single-chain variable fragments (scFvs) against human insulin-like growth factor I receptor (IGFIR) from a phage library displaying human scFvs. Isolated scFvs-displaying phages showed affinity for IGF-IR in comparison to the control. Expression of scFv proteins in Escherichia coli for further characterization, however, proved extremely difficult. Alternatively, the scFv protein was expressed as a fusion protein with a maltose-binding protein (MBP) that is a highly soluble E. coli protein. The MBPscFv fusion protein expressed in a soluble form in E. coli was purified to homogeneity by two-step affinity chromatography. The resulting MBP-scFv exhibited affinity for IGF-IR and structurally-related insulin receptor (IR). These results suggest both that MBPscFv fusion proteins are practical alternatives to isolating scFv proteins for further characterization and that successful isolation of human scFvs against a specific protein of interest requires vigorous screening in the early stages. Such screening is accomplished by using two independent screening methods such as measuring binding to IGF-IR but not to IR by ELISA or measuring competitive binding by IGF-I in addition to binding to IGF-IR alone.

A second generation human haplotype map of over 3.1 million SNPs

We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations.

Safety of ofloxacin (OFLX) and fosfomycin sodium (FOM) ear drops

OBJECTIVE

The objective of this study is to evaluate the safety of two ear drops, Ofloxacin (OFLX: Taribid Otic Solution, Daiichi Seiyaku) and Fosfomycin sodium (FOM: Fosmicin S, Meiji Seiyaku).

METHODS

Albino guinea pigs were used as experimental animals, and the ototoxicity was evaluated by means of threshold changes in the compound action potentials (CAP), when topically applied to the middle ear cavity of the guinea pig. The sound stimuli applied were; click sound, with tone bursts of 8 kHz, 4 kHz, and 2 kHz. In one group of animals, after one application of the ear drops in the right middle ear cavity, the change in CAP was compared with a contralateral saline control at 24h, one week, and four weeks. In other group of animals, the ear drops were applied into the middle ear cavity for seven consecutive days and the CAP was measured at 24h.

RESULTS

At 24h the CAP threshold for click, 8 and 4 kHz elevated significantly for both the saline and ear drop treatment, but the threshold returned to normal when measured at 7 days and 28 days. Seven consecutive days of ear drops administration resulted in no reduction in the CAP for either ear drops.

CONCLUSIONS

Based on the lack of changes in the CAP, these two ear drops studied did not show any significant ototoxicities.

Role of dorsal neck proprioceptive inputs to vestibular compensation in humans

To investigate the role of cervical proprioceptive inputs in the process of vestibular compensation, we performed static posturography in patients with acute and compensated unilateral vestibular dysfunction, by applying vibratory stimulation to the dorsal neck muscles. Neck vibration induced disequilibrium in both groups of patients, but was more pronounced in the compensated patients. These results indicate that manipulation of the neck afferents causes discompensation in subjects whose vestibular dysfunction has already been compensated by multisensory inputs including neck afferents.

A 'neural' response with 3-ms latency evoked by loud sound in profoundly deaf patients

A large negative deflection with a latency of 3 ms was observed in the auditory brainstem response (ABR) waveforms of some patients with peripheral profound deafness. This deflection was termed the N3 potential. In this paper, we review patients with the N3 potential and discuss the characteristics of abnormal ABR waveforms. The origin of the N3 potential was also discussed, especially with respect to vestibular evoked potentials. In most of the patients, audiograms showed no response to the maximum output of an audiometer in the high-frequency range and a residual response in the low-frequency range. The N3 potentials were noted at intensities of 80 dB nHL or greater. As the stimulus intensity increased, the amplitude of the potential increased and the latency decreased. A high repetition rate (83.3/s) of the click stimulus influenced the latency and amplitude of the N3 potential. The potential was replicated on retest within less than a month, and had a consistent latency and amplitude over the scalp. The results indicate that the N3 potential is not an electrical artifact but a physiological neural response evoked by a loud sound. The N3 potential is most likely not an auditory evoked response from cochlear or a response from a semicircular canal, because it has a 3-ms latency, a sharp waveform, and is unassociated with vertigo. The results suggest that the N3 potential may be a saccular acoustic response.

Developmental anatomy of the supratubal recess in temporal bones from fetuses and children

The supratubal recess (STR), located superior to the bony eustachian tube and anterior to the attic and often the site of disease, is clearly separated from the attic by the presence of a bony partition. Its anatomic development in childhood, however, remains nuclear. We reviewed serial horizontal sections of fetal and children's temporal bones from the collection of the Otopathology Laboratory, University of Minnesota. Apparently, upward expansion of the bony eustachian tube begins at a late fetal stage and continues throughout childhood, thus forming the STR. Our finding that the STR had already developed in temporal bones without pneumatization of petrous bone suggests that its formation is independent of the air-cell system. Absorption of mesenchymal tissue in the STR tends to be slower than elsewhere in the temporal bone. Surrounded solely by petrous bone, the STR seems, both developmentally and anatomically, a distinctive compartment of the middle ear.

Three-component analysis of benign paroxysmal positional nystagmus

Three-component analysis of Benign Paroxysmal Positional Nystagmus (BPPN), focusing on the horizontal, vertical, and torsional, using a computerized eye movement analysis system, was carried out in 10 patients. Using a pendular rotation stimulus, we also measured three components of eye movement elicited from the vertical semicircular canals in normal subjects. We compared two components (vertical and torsional) of BPPN with that of eye movements elicited from the vertical semicircular canals. In BPPN, the torsional component of eye movements was larger than that of the vertical component. Conversely, the vertical component from the vertical semicircular canals was larger than that of the torsional component. From these results, by analysing the vestibulo-ocular reflex of the vertical semicircular canals, it is difficult to support the idea that the pathology of the BPPV is localized in the posterior semi-circular canal alone.