Exploration of microbiota targets for major depressive disorder and mood related traits.

Growing evidence suggests the link between gut microbiota and mood regulation. The current study aimed to identify microbiota targets for major depressive disorder (MDD) and mood-related traits in Taiwanese samples, while taking into account the influence of dietary patterns. We recruited 36 MDD patients and 37 healthy controls for 16S rRNA gene sequencing. We assessed nutrient content using food frequency questionnaire, and mood related phenotypes, including depressive severity, anxiety, and perceived stress. Analysis of composition of microbiomes (ANCOM) models were performed to evaluate microbiota compositions between patients and controls, while adjusted for fat intake% and sequencing platforms. We found 23 taxa (4 phyla, 7 families and 12 genera) to be associated with depression and beta diversity was differed between groups. Phylum Actinobacteria and Firmicutes were overrepresented in MDD patients. At genus level, Bifidobacterium (7%) and Blautia (8%) had relatively high abundance among MDD patients, while Prevotella (16%) had high abundance in controls. Holdemania exhibited moderate correlation with anxiety (r = 0.65) and perceived stress level (r = 0.49) mainly in MDD patients but not controls. Pathway analyses revealed that pentose phosphate and starch and sucrose metabolism processes were important pathways for depression via microbiota functions. In conclusion, our results revealed microbiota targets for depression that are independent of fat intake. It is worthwhile to conduct further studies to replicate the current findings and to integrate with biochemistry and metabolomics data to better understand the functions of identified targets.

Evaluation of the interaction between genetic variants of GAD1 and miRNA in bipolar disorders.

BACKGROUND: Glutamic acid dehydrogenase 1 (GAD1) serves as the rate-limiting enzyme for synthesizing GABA, and is reported to be associated with several psychiatric disorders. The present study examined the effects of GAD1 genetic variants on bipolar disorder (BD) and its subtypes. Moreover, we investigated functional interactions between genetic variants and miRNAs via algorithm prediction and experimental validation. METHODS: A case-control study was conducted with 280 BD patients and 200 healthy controls. Eight tag SNPs in GAD1 were genotyped. For associated markers, we performed in silico prediction for their potential functions through SNP-miRNA interactions by establishing a scoring system to combine information from several miRNA predictive algorithms. We then tested allelic expression differences using Dual-Glo luciferase reporter assays for the selected SNP-miRNA pair. Lastly, we examined the associations of the GAD1 gene and BD in two additional independent datasets with a few thousand samples for replication. RESULTS: Marker rs3749034 was associated with BD, in particular the BD-II subtype. According to our scoring system, several candidate miRNAs were predicted to interact with rs3749034, and hsa-miR-504 had the highest score. Findings from an in vitro experiment revealed a non-statistically significant trend for lower gene expression level with the A allele of rs3749034 compared with the G allele. The association between rs3749034 and BD was not replicated in either of the independent datasets. Instead, other rarer genetic variants in GAD1 showed suggestive signals (e.g. rs575441409, p-value = 3.8*10-4, D' = 1 with rs3749034) with BD in the Taiwanese dataset. LIMITATIONS: The present study considered common genetic variants only. In addition, we only used a 293T cell-line in conducting luciferase reporter assays, as no primary cell-lines from patient samples were available to differentiate the effects between BD subtypes. CONCLUSIONS: Our results demonstrate a weak effect of the GAD1 gene on the risk of bipolar illness, and the associated marker might represent a proxy for real signals of rare variants.

Building a genetic risk model for bipolar disorder from genome-wide association data with random forest algorithm.

A genetic risk score could be beneficial in assisting clinical diagnosis for complex diseases with high heritability. With large-scale genome-wide association (GWA) data, the current study constructed a genetic risk model with a machine learning approach for bipolar disorder (BPD). The GWA dataset of BPD from the Genetic Association Information Network was used as the training data for model construction, and the Systematic Treatment Enhancement Program (STEP) GWA data were used as the validation dataset. A random forest algorithm was applied for pre-filtered markers, and variable importance indices were assessed. 289 candidate markers were selected by random forest procedures with good discriminability; the area under the receiver operating characteristic curve was 0.944 (0.935-0.953) in the training set and 0.702 (0.681-0.723) in the STEP dataset. Using a score with the cutoff of 184, the sensitivity and specificity for BPD was 0.777 and 0.854, respectively. Pathway analyses revealed important biological pathways for identified genes. In conclusion, the present study identified informative genetic markers to differentiate BPD from healthy controls with acceptable discriminability in the validation dataset. In the future, diagnosis classification can be further improved by assessing more comprehensive clinical risk factors and jointly analysing them with genetic data in large samples.

Identification of Susceptible Loci and Enriched Pathways for Bipolar II Disorder Using Genome-Wide Association Studies.

BACKGROUND: This study aimed to identify susceptible loci and enriched pathways for bipolar disorder subtype II. METHODS: We conducted a genome-wide association scan in discovery samples with 189 bipolar disorder subtype II patients and 1773 controls, and replication samples with 283 bipolar disorder subtype II patients and 500 controls in a Taiwanese Han population using Affymetrix Axiom Genome-Wide CHB1 Array. We performed single-marker and gene-based association analyses, as well as calculated polygeneic risk scores for bipolar disorder subtype II. Pathway enrichment analyses were employed to reveal significant biological pathways. RESULTS: Seven markers were found to be associated with bipolar disorder subtype II in meta-analysis combining both discovery and replication samples (P<5.0×10-6), including markers in or close to MYO16, HSP90AB3P, noncoding gene LOC100507632, and markers in chromosomes 4 and 10. A novel locus, ETF1, was associated with bipolar disorder subtype II (P<6.0×10-3) in gene-based association tests. Results of risk evaluation demonstrated that higher genetic risk scores were able to distinguish bipolar disorder subtype II patients from healthy controls in both discovery (P=3.9×10-4~1.0×10-3) and replication samples (2.8×10-4~1.7×10-3). Genetic variance explained by chip markers for bipolar disorder subtype II was substantial in the discovery (55.1%) and replication (60.5%) samples. Moreover, pathways related to neurodevelopmental function, signal transduction, neuronal system, and cell adhesion molecules were significantly associated with bipolar disorder subtype II. CONCLUSION: We reported novel susceptible loci for pure bipolar subtype II disorder that is less addressed in the literature. Future studies are needed to confirm the roles of these loci for bipolar disorder subtype II.

Genome-Wide Association Study for Autism Spectrum Disorder in Taiwanese Han Population.

BACKGROUND: Autism spectrum disorder (ASD) is a neurodevelopmental disorder with strong genetic components. Several recent genome-wide association (GWA) studies in Caucasian samples have reported a number of gene regions and loci correlated with the risk of ASD--albeit with very little consensus across studies. METHODS: A two-stage GWA study was employed to identify common genetic variants for ASD in the Taiwanese Han population. The discovery stage included 315 patients with ASD and 1,115 healthy controls, using the Affymetrix SNP array 6.0 platform for genotyping. Several gene regions were then selected for fine-mapping and top markers were examined in extended samples. Single marker, haplotype, gene-based, and pathway analyses were conducted for associations. RESULTS: Seven SNPs had p-values ranging from 3.4~9.9*10-6, but none reached the genome-wide significant level. Five of them were mapped to three known genes (OR2M4, STYK1, and MNT) with significant empirical gene-based p-values in OR2M4 (p = 3.4*10(-5)) and MNT (p = 0.0008). Results of the fine-mapping study showed single-marker associations in the GLIS1 (rs12082358 and rs12080993) and NAALADL2 (rs3914502 and rs2222447) genes, and gene-based associations for the OR2M3-OR2T5 (olfactory receptor genes, p = 0.02), and GLIPR1/KRR1 gene regions (p = 0.015). Pathway analyses revealed important pathways for ASD, such as olfactory and G protein-coupled receptors signaling pathways. CONCLUSIONS: We reported Taiwanese Han specific susceptibility genes and variants for ASD. However, further replication in other Asian populations is warranted to validate our findings. Investigation in the biological functions of our reported genetic variants might also allow for better understanding on the underlying pathogenesis of autism.

Risk and information evaluation of prioritized genes for complex traits: application to bipolar disorder.

Many susceptibility genes for complex traits were identified without conclusive findings. There is a strong need to integrate rapidly accumulated genomic data from multi-dimensional platforms, and to conduct risk evaluation for potential therapeutic and diagnostic usages. We set up an algorithm to computationally search for optimal weight-vector for various data sources, while minimized potential noises. Through gene-prioritization framework, combined scores for the resulting prioritized gene-set were calculated using a genome-wide association (GWA) dataset, following with evaluation using weighted genetic risk score and risk-attributed information using an independent GWA dataset. The significance of association of GWA data was corrected for gene length. Enriched functional pathways were identified for the prioritized gene-set using the Gene Ontology analysis. We illustrated our framework with bipolar disorder. 233 prioritized genes were identified from 10,830 candidates that curated from six platforms. The prioritized genes were significantly enriched (P(adjusted) < 1 × 10(-5)) in 18 biological functions and molecular mechanisms including membrane, synaptic transmission, transmission of nerve impulse, integral to membrane, and plasma membrane. Our risk evaluation demonstrated higher weighted genetic risk score in bipolar patients than controls (P-values ranged from 0.002 to 3.8 × 10(-6)). Substantial risk-information (71%) was extracted from prioritized genes for bipolar illness than other candidate-gene sets. Our evidence-based prioritized gene-set provides opportunity to explore the complex network and to conduct follow-up basic and clinical studies for complex traits.

Exploring the associations between genetic variants in genes encoding for subunits of calcium channel and subtypes of bipolar disorder.

BACKGROUND: Associations of two voltage-gated calcium channel (Cav) genes, CACNA1C and CACNB2, were identified for bipolar disorder (BP) in different ethnic groups in recent genome-wide association studies. The current study aimed to evaluate the associations of several Cav genes and subtypes of BP in genetically more homogeneous Taiwanese samples. Additionally, we tested interaction effects among genes that encode for α1, ß and γ-subunits of calcium channel. METHODS: 8 Cav genes were selected based on evidence in prior association studies and significant linkage regions for BP. 280 BP patients and 200 controls were recruited. Multifactor dimensionality reduction was performed for interaction testing in these discovery samples. Replication was conducted for two markers using additional 495 Taiwanese cases and 1341 controls. RESULTS: Weak associations for CACNA1C (rs10848635), CACNA1E (rs10848635), CACNB2 (rs11013860), and CACNG2 (rs2284018) genes were observed. Joint analysis of four markers revealed higher accumulative risk with increasing numbers of risk genotypes an individual endorsed for BP-I (Ptrend=0.006) and BP-II (Ptrend=0.017) disorders. Combined analysis with independent replication samples further supported the association of rs11013860 in CACNB2 with BP subtype I (P=1×10(-6)). Suggestive interactions were found between genes encoded for different subunits of calcium channel (α1, ß, and γ). LIMITATIONS: Moderate sample size and incomplete markers coverage for the chosen Cav genes. CONCLUSIONS: Our results support the involvement of different calcium channel genes in bipolar illness, in particular the beta-subunit in the Asian population. Further investigation of functional property of these genes can contribute on understanding the etiological mechanisms of bipolar illness.

Pathway analysis using information from allele-specific gene methylation in genome-wide association studies for bipolar disorder.

Bipolar disorder (BPD) is a complex psychiatric trait with high heritability. Despite efforts through conducting genome-wide association (GWA) studies, the success of identifying susceptibility loci for BPD has been limited, which is partially attributed to the complex nature of its pathogenesis. Pathway-based analytic strategy is a powerful tool to explore joint effects of gene sets within specific biological pathways. Additionally, to incorporate other aspects of genomic data into pathway analysis may further enhance our understanding for the underlying mechanisms for BPD. Patterns of DNA methylation play important roles in regulating gene expression and function. A commonly observed phenomenon, allele-specific methylation (ASM) describes the associations between genetic variants and DNA methylation patterns. The present study aimed to identify biological pathways that are involve in the pathogenesis of BPD while incorporating brain specific ASM information in pathway analysis using two large-scale GWA datasets in Caucasian populations. A weighting scheme was adopted to take ASM information into consideration for each pathway. After multiple testing corrections, we identified 88 and 15 enriched pathways for their biological relevance for BPD in the Genetic Association Information Network (GAIN) and the Wellcome Trust Case Control Consortium dataset, respectively. Many of these pathways were significant only when applying the weighting scheme. Three ion channel related pathways were consistently identified in both datasets. Results in the GAIN dataset also suggest for the roles of extracellular matrix in brain for BPD. Findings from Gene Ontology (GO) analysis exhibited functional enrichment among genes of non-GO pathways in activity of gated channel, transporter, and neurotransmitter receptor. We demonstrated that integrating different data sources with pathway analysis provides an avenue to identify promising and novel biological pathways for exploring the underlying molecular mechanisms for bipolar disorder. Further basic research can be conducted to target the biological mechanisms for the identified genes and pathways.

Incorporating Information of microRNAs into Pathway Analysis in a Genome-Wide Association Study of Bipolar Disorder.

MicroRNAs (miRNAs) are known to be important post-transcriptional regulators that are involved in the etiology of complex psychiatric traits. The present study aimed to incorporate miRNAs information into pathway analysis using a genome-wide association dataset to identify relevant biological pathways for bipolar disorder (BPD). We selected psychiatric- and neurological-associated miRNAs (N = 157) from PhenomiR database. The miRNA target genes (miTG) predictions were obtained from microRNA.org. Canonical pathways (N = 4,051) were downloaded from the Molecule Signature Database. We employed a novel weighting scheme for miTGs in pathway analysis using methods of gene set enrichment analysis and sum-statistic. Under four statistical scenarios, 38 significantly enriched pathways (P-value < 0.01 after multiple testing correction) were identified for the risk of developing BPD, including pathways of ion channels associated (e.g., gated channel activity, ion transmembrane transporter activity, and ion channel activity) and nervous related biological processes (e.g., nervous system development, cytoskeleton, and neuroactive ligand receptor interaction). Among them, 19 were identified only when the weighting scheme was applied. Many miRNA-targeted genes were functionally related to ion channels, collagen, and axonal growth and guidance that have been suggested to be associated with BPD previously. Some of these genes are linked to the regulation of miRNA machinery in the literature. Our findings provide support for the potential involvement of miRNAs in the psychopathology of BPD. Further investigations to elucidate the functions and mechanisms of identified candidate pathways are needed.

Baseline human papillomavirus infection, high vaginal parity, and their interaction on cervical cancer risks after a follow-up of more than 10 years.

OBJECTIVES: Human papillomavirus (HPV) has been recognized as a major factor for cervical cancer causation. Other factors, relating to reproduction, are also important. This study aims to disentangle the roles of baseline HPV infection, high vaginal parity (defined as having ≥4 vaginal deliveries), and the interaction between the two in predicting cervical cancer risk. METHODS: The authors apply a newly developed causal-pie modeling technique to analyze a cohort of more than 10,000 women conducted in Taiwan with more than 10 years of follow-up. The rate ratios adjusted by age and menopausal status were further modeled by an additive Poisson regression with non-negative parameters. The index of causal-pie weight (CPW) was calculated to indicate the proportion of cervical cancer cases attributable to a particular class of causal pies. RESULTS: It was found that the CPWs are 36.3 % for baseline HPV infection, 35.6 % for baseline HPV infection and high vaginal parity, and 28.1 % for other factors. CONCLUSIONS: A causal-pie modeling based on a women cohort in Taiwan successfully disentangles the roles of virus factors and reproductive factors at study entry, independently or interactively, on subsequent cervical cancer risk.

Associations of human leukocyte antigen class II genotypes with human papillomavirus 18 infection and cervical intraepithelial neoplasia risk.

BACKGROUND: Only a small proportion of women infected with human papillomavirus type 18 (HPV18) may progress to persistent infection and cervical neoplasia. This community-based cohort study aimed to assess associations with human leukocyte antigen (HLA) class II genotypes for natural infection of HPV18 and subsequent risk of cervical neoplasia. METHODS: Among 10,190 cytologically normal participants, 125 with HPV18 infection were identified by HPV blot kit. HPV18 viral load at study entry was examined by real-time polymerase chain reaction; persistent infection was defined as HPV18 infection at 2 consecutive examinations. RESULTS: There was a significant association between HLA-DRB1*0403 allele and high HPV18 viral load (>1000 copies in 50 ng of total DNA) at study entry (odds ratio [OR], 7.2; 95% confidence interval [CI], 2.0-25.2). After adjustment for age and viral load at study entry, haplotype HLA-DRB1*0405-DQA1*0301-DQB1*0302 was significantly associated with persistent HPV18 infection (OR, 13.3; 95% CI, 1.7-105.9). HLA-DRB1*0403 allele was also associated with a significantly increased risk of high-grade squamous intraepithelial lesion or cancer, showing a multivariate-adjusted hazard ratio (95% CI) of 18.1 (2.6-128.5). CONCLUSIONS: HLA-DRB1*0403 allele and HLA-DRB1*0405-DQA1*0301-DQB1*0302 haplotype may play important roles in determination of high viral load and persistent infection of HPV18 and subsequent cervical neoplasia risk.

Persistence of type-specific human papillomavirus infection and increased long-term risk of cervical cancer.

BACKGROUND: Human papillomavirus (HPV) persistence is the pivotal event in cervical carcinogenesis. We followed a large-scale community-based cohort for 16 years to investigate the role of genotype-specific HPV persistence in predicting cervical cancer including invasive and in situ carcinoma. METHODS: At the baseline examination in 1991-1992, 11,923 participants (aged 30-65 years) consented to HPV testing and cytology; 6923 participants were reexamined in 1993-1995. For HPV testing, we used a polymerase chain reaction-based assay that detected 39 HPV types. Women who developed cervical cancer were identified from cancer and death registries. Cumulative risks for developing cervical cancer among infected and persistently infected women were calculated by the Kaplan-Meier method. RESULTS: Of 10,123 women who were initially cytologically normal, 68 developed cervical cancer. The 16-year cumulative risks of subsequent cervical cancer for women with HPV16, HPV58 (without HPV16), or other carcinogenic HPV types (without HPV16 or HPV58) were 13.5%, 10.3%, and 4.0%, respectively, compared with 0.26% for HPV-negative women. Women with type-specific persistence of any carcinogenic HPV had greatly increased risk compared with women who were HPV-negative at both visits (hazard ratio = 75.4, 95% confidence interval = 31.8 to 178.9). The cumulative cervical cancer risks following persistent carcinogenic HPV infections increased with age: The risks were 5.5%, 14.4%, and 18.1% for women aged 30-44 years, 45-54 years, and 55 years and older, respectively. However, newly acquired infections were associated with a low risk of cervical cancer regardless of age. CONCLUSIONS: HPV negativity was associated with a very low long-term risk of cervical cancer. Persistent detection of HPV among cytologically normal women greatly increased risk. Thus, it is useful to perform repeated HPV testing following an initial positive test.

Association between human papillomavirus and adenocarcinoma of rectum and recto-sigmoid junction: a cohort study of 10,612 women in Taiwan.

This study aimed at assessing the association between the type-specific human papillomavirus (HPV) infection and the risk of adenocarcinoma of the rectum and recto-sigmoid junction. A total of 10,612 women aged 30-65 years old were enrolled from seven townships in Taiwan. Cervical cells collected at study entry were tested for 39 types of HPV infection by polymerase chain reactions and HPV blot kit. Newly developed adenocarcinomas of rectum and recto-sigmoid junction were ascertained through computerized linkage with national cancer registry profiles. An increased risk of adenocarcinomas of the rectum and recto-sigmoid junction was observed with HPV infection, showing a hazard ratio [HR] (95% confidence interval [CI]) of 1.99 (0.98-4.04) after adjustment for age and body mass index. The adjusted HR (95% CI) for the infection of HPV types other than 6 and 11 was 2.18 (1.04-4.60). Women with cervical infection of HPV types other than 6 and 11 at study entry may have an increased risk of adenocarcinomas of the rectum and recto-sigmoid junction, which deserves further validation by large-scale studies.

Quality assurance of genotyping array for detection and typing of human papillomavirus.

The aim of this study was to evaluate the sensitivity, specificity, reliability and reproducibility of the EasyChip HPV blot for human papillomavirus (HPV) genotyping. Type-specific sensitivity and specificity for 39 types of HPV (HPV 6, 11, 16, 18, 26, 31, 32, 33, 35, 37, 39, 42, 43, 44, 45, 51, 52, 53, 54, 55, 56, 58, 59, 61, 62, 66, 67, 68, 69, 70, 72, 74, 82, CP8061, CP8304, L1AE5, MM4, MM7 and MM8) were examined. The operating environment, reliability, reproducibility and blot interpretation were assessed by a quality assurance system. Each batch experiment contained samples from 89 cervical specimens and 7 extrinsic controls. Caski, HeLa and Jurkat cells, male human blood cell DNA and sterile water were used to assess reliability. Furthermore, pairs of sibling controls were used to assess reproducibility. The overall sensitivity of HPV detection was 1-50 copies of HPV genome equivalent. There was no cross-reactivity with amplicons of other HPV genotypes. One hundred batch experiments demonstrated that the reliability was excellent. The intra-batch and inter-batch reproducibility was 98 and 97%, respectively. It was concluded that the EasyChip HPV blot is a highly sensitive, reliable and reproducible tool for detection and identification of HPV genotypes.

The modulatory role of transforming growth factor beta1 and androstenedione on follicle-stimulating hormone-induced gelatinase secretion and steroidogenesis in rat granulosa cells.

To investigate the potential roles of matrix metalloproteinases (MMPs) in ovarian granulosa cell differentiation, we studied the interactive effects of FSH and local ovarian factors, transforming growth factor beta1 (TGFbeta1) and androstenedione, on gelatinase secretion and progesterone production in rat ovarian granulosa cells. Granulosa cells of eCG-primed immature rats were treated once with various doses of FSH and TGFbeta1 and androstenedione alone or in combinations for 2 days. Conditioned media were analyzed for gelatinase activity using gelatin-zymography/densitometry and progesterone levels using enzyme immunoassay. Cell lysates were analyzed for steroidogenic acute regulatory (StAR) and cholesterol side-chain-cleavage (P450scc) enzyme protein levels. This study demonstrates for the first time that FSH dose-dependently increased the secretion of a major 63-kDa gelatinase and minor 92- and 67-kDa gelatinases. TGFbeta1 also dose-dependently increased the secretion of 63-kDa gelatinase, while androstenedione alone had no effect. The 92-kDa gelatinase was identified as the pro-MMP9 that could be cleaved by aminophenylmercuric acetate into the 83-kDa active form. Importantly, we show that TGFbeta1 and androgen act in an additive manner to enhance FSH stimulatory effects both on the secretion of gelatinases and the production of progesterone. We further show by immunoblotting that the enhancing effect of TGFbeta1 and androstenedione on FSH-stimulated steroidogenesis is partly mediated through the increased level of StAR protein and/or P450scc enzyme. In conclusion, this study indicates that, during antral follicle development, TGFbeta1 and androgen act to enhance FSH promotion of granulosa cell differentiation and that the process may involve the interplay of modulating cell- to-matrix/cell-to-cell interaction and steroidogenic activity.