Update on Osaka University Twin Registry: An Overview of Multidisciplinary Research Resources and Biobank at Osaka University Center for Twin Research

Heritability of bone mineral density among Japanese women: A twin study

BACKGROUND

Osteoporosis is a major risk factor for fractures among the older population. Despite osteoporosis being a significant concern in super-aged societies such as Japan, the heritability of bone mineral density within the Japanese populace remains unexplored. Therefore, we conducted a twin study among Japanese women to determine the extent of genetic and environmental influences on bone mineral density.

METHODS

The bone area ratio of 298 healthy, female Japanese twins (comprising 149 pairs, 136 monozygotic and 13 dizygotic twin pairs) registered in the Osaka University Twin Registry was measured using quantitative ultrasound. Classical twin analysis was employed to ascertain the heritability of bone mineral density.

RESULTS

The heritability of bone mineral density for the entire cohort was 0.51 (95 % confidence interval 0.38-0.63). For the women younger than 50 years, the effects of menopause were adjusted, and the best-fit model was also found to be the additive genetics and unique environment (AE) model, with a heritability estimate of 0.53 (95 % confidence interval 0.34-0.72).

CONCLUSIONS

Compared with women from other countries, Japanese women appear to have a lower heritability of bone mineral density. Consequently, environmental factors may exert a larger influence on osteoporosis among Japanese women than among women of other races and ethnicities.

Genetic and epigenetic factors affecting carotid intima-media thickness in monozygotic twins

BACKGROUND AND AIMS

The intima-media thickness (IMT) of the carotid artery, an indicator of subclinical atherosclerosis, varies in close association with various factors such as diabetes and immune response. The extent of changes in IMT varies among individuals owing to both genetic and epigenetic factors. In this study, we aimed to identify single nucleotide polymorphisms (SNPs) and DNA methylation patterns that affect carotid IMT in monozygotic (MZ) twins.

METHODS

We measured the maximum IMT (IMT-Cmax) and the mean IMT in the common carotid artery wall using ultrasonography in 107 pairs of MZ twins recruited from the Osaka University Twin Registry. The genotyping of SNPs and the measurement of methylation levels were performed using a beads array, and the expression of each gene was determined by RNA sequencing. Linear regression analysis was performed on each of the two groups: one group consisted of twins randomly selected from each pair, and the other group consisted of co-twins.

RESULTS

We identified a CpG site (cg02432467) on HS3ST6 as a significant epigenetic factor in both IMT-Cmax and mean IMT analyses. The methylation level at another site (cg07927379) was negatively correlated with LINC01006 expression and IMT-Cmax. Furthermore, there were significant differences in AP2A2 expression and mean IMT among individuals with each genotype of the rs10902263 polymorphism.

CONCLUSIONS

We identified genetic and epigenetic factors associated with carotid IMT that may be useful for individualized assessments.

Environmental Factor Index (EFI): A Novel Approach to Measure the Strength of Environmental Influence on DNA Methylation in Identical Twins

BACKGROUND/OBJECTIVES

The dynamic interaction between genomic DNA, epigenetic modifications, and phenotypic traits was examined in identical twins. Environmental perturbations can induce epigenetic changes in DNA methylation, influencing gene expression and phenotypes. Although DNA methylation mediates gene-environment correlations, the quantitative effects of external factors on DNA methylation remain underexplored. This study aimed to quantify these effects using a novel approach.

METHODS

A cohort study was conducted on healthy monozygotic twins to evaluate the influence of environmental stimuli on DNA methylation. We developed the Environmental Factor Index (EFI) to identify methylation sites showing statistically significant changes in response to environmental stimuli. We analyzed the identified sites for associations with disorders, DNA methylation markers, and CpG islands.

RESULTS

The EFI identified methylation sites that exhibited significant associations with genes linked to various disorders, particularly cancer. These sites were overrepresented on CpG islands compared to other genomic features, highlighting their regulatory importance.

CONCLUSIONS

The EFI is a valuable tool for understanding the molecular mechanisms underlying disease pathogenesis. It provides insights into the development of preventive and therapeutic strategies and offers a new perspective on the role of environmental factors in epigenetic regulation.

Twin Study: The Factors Affecting the Serum LDL-C and HDL-C Levels and an RNA-Seq Analysis in Mononuclear Cells in Monozygotic Twins

AIM

A twin study is a valuable tool for elucidating the acquired factors against lifestyle diseases such as dyslipidemia, diabetes mellitus, and obesity. We aimed 1. to investigate the factors that affect low-density lipoprotein cholesterol (LDL-C) and high-density lipoprotein cholesterol (HDL-C) in monozygotic (MZ) twins, and 2. to identify genes which expression levels changed in pairs with large differences in LDL-C or HDL-C levels.

METHODS

The registered database at the Center for Twin Research, Osaka University, containing 263 pairs of MZ twins, was analyzed. 1. The effects of smoking, exercise, nutritional factors, and anthropometric and biochemical parameters on LDL-C or HDL-C levels were examined in MZ twins. 2. RNA sequencing in the peripheral blood mononuclear cells of 59 pairs was analyzed for large differences of LDL-C or HDL-C groups.

RESULTS

1. The ΔLDL-C levels were significantly associated with an older age, the ΔTG levels, and ΔBMI. ΔHDL-C levels were associated with the ΔBMI, ΔTG, ΔTP, and ΔLDL-C levels. The HDL-C levels were affected by smoking and exercise habits. The intakes of cholesterol and saturated fatty acids were not associated with the LDL-C or HDL-C levels. 2. An RNA sequencing analysis revealed that the expression of genes related to the TLR4 and IFNG pathways was suppressed in accordance with the HDL-C levels in the larger ΔHDL-C group among the 59 pairs.

CONCLUSION

We identified the factors affecting the LDL-C or HDL-C levels in monozygotic twins. In addition, some types of inflammatory gene expression in peripheral blood mononuclear cells were suppressed in accordance with the HDL-C levels, thus suggesting the importance of weight management and exercise habits in addition to dietary instructions to control the LDL-C or HDL-C levels.

Functional landscape of genome-wide postzygotic somatic mutations between monozygotic twins

Monozygotic (MZ) twins originate from a single fertilized egg, making them genetically identical at the time of conception. However, postzygotic somatic mutations (PZMs) can introduce genetic differences after separation. Although whole-genome sequencing (WGS) sheds light on somatic mutations in cancer genomics, its application in genomic studies of MZ twins remains limited. In this study, we investigate PZMs in 30 healthy MZ twin pairs from the Osaka University Center for Twin Research using WGS (average depth = 23.8) and a robust germline-calling algorithm. We find high genotype concordance rates (exceeding 99%) in MZ twins. We observe an enrichment of PZMs with variant allele frequency around 0.5 in twins with highly concordant genotypes. These PZMs accumulate more frequently in non-coding regions compared with protein-coding regions, which could potentially influence gene expression. No significant association is observed between the number of PZMs and age or sex. Direct sequencing confirms a missense mutation in the ANKRD35 gene among the PZMs. By applying a genome-wide mutational signature pattern technique, we detect an age-related clock-like signature in these early postzygotic somatic mutations in MZ twins. Our study provides insights that contribute to a deeper understanding of genetic variation in MZ twins.

Rigorous evaluation of genetic and epigenetic effects on clinical laboratory measurements using Japanese monozygotic twins

The investigation of environmental effects on clinical measurements using individual samples is challenging because their genetic and environmental factors are different. However, using monozygotic twins (MZ) makes it possible to investigate the influence of environmental factors as they have the same genetic factors within pairs because the difference in the clinical traits within the MZ mostly reflect the influence of environmental factors. We hypothesized that the within-pair differences in the traits that are strongly affected by genetic factors become larger after genetic risk score (GRS) correction. Using 278 Japanese MZ pairs, we compared the change in within-pair differences in each of the 45 normalized clinical measurements before and after GRS correction, and we also attempted to correct for the effects of genetic factors to identify Cytosine-phosphodiester-Guanine (CpG) sites in DNA sequences with epigenetic effects that are regulated by genetic factors. Five traits were classified into the high heritability group, which was strongly affected by genetic factors. CpG sites could be classified into three groups: regulated only by environmental factors, regulated by environmental factors masked by genetic factors, and regulated only by genetic factors. Our method has the potential to identify trait-related methylation sites that have not yet been discovered.

Twin study: genotype-dependent epigenetic factors affecting free thyroxine levels in the normal range

Aim: To explore the clinical application of DNA methylation affecting thyroid function, we evaluated the association of DNA methylation with free thyroxine (FT4) and TSH measurements in monozygotic twins. Materials & methods: Discordant pairs for FT4 or TSH levels were examined for the relationship between the within-pair difference of each measurement and the DNA methylation levels using epigenome-wide association studies. The contribution of polymorphisms to the methylation sensitivity was also examined. Results: We found two CpG sites significantly associated with FT4 levels, and also some CpG sites showing significant differences in their methylation levels within FT4-discordant pairs depending on the polymorphism in EPHB2. Conclusion: The FT4 level may be associated with a combination of methylation and polymorphisms in the EPHB2 gene.

Twin Study: Genetic and Epigenetic Factors Affecting Circulating Adiponectin Levels

CONTEXT

Clarification of the association among phenotypes, genetic, and environmental factors with clinical laboratory traits can reveal the cause of diseases and assist in developing methods for the prediction and prevention of diseases. It is difficult to investigate the environmental effect on phenotypes using individual samples because their genetic and environmental factors differ, but we can easily investigate the influence of environmental factors using monozygotic (MZ) twins because they have the same genetic factors.

OBJECTIVE

We aimed to examine the methylation level of CpG sites as an environmental factor affecting adiponectin levels on the basis of the same genetic background using MZ twins and to identify the epigenetic factors related to adiponectin levels and the genetic factors associated with sensitivity to acquired changes in adiponectin.

METHODS

Using 2 groups built from each twin of 232 MZ twin pairs, we performed a replicated epigenome-wide association study to clarify the epigenetic factors affecting adiponectin levels adjusted by genetic risk score. Moreover, we divided twin pairs into concordant and discordant for adiponectin levels. We conducted a genome-wide association study to identify a genetic background specific for discordance.

RESULTS

Methylation levels at 38 CpG sites were reproducibly associated with adjusted adiponectin levels, and some of these CpG sites were in genes related to adiponectin, including CDH13. Some genes related to adiponectin or insulin resistance were found to be genetic factors specific for discordance.

CONCLUSION

We clarified specific epigenetic factors affecting adiponectin levels and genetic factors associated with sensitivity to acquired changes in adiponectin.

Lobular Difference in Heritability of Brain Atrophy among Elderly Japanese: A Twin Study

Background and Objectives: Brain atrophy is related to cognitive decline. However, the heritability of brain atrophy has not been fully investigated in the Eastern Asian population. Materials and Methods: Brain imaging of 74 Japanese twins registered in the Osaka University Twin Registry was conducted with voxel-based morphometry SPM12 and was processed by individual voxel-based morphometry adjusting covariates (iVAC) toolbox. The atrophy of the measured lobes was obtained by comparing the focal volume to the average of healthy subjects. Classical twin analysis was used to measure the heritability of its z-scores. Results: The heritability of brain atrophy ranged from 0.23 to 0.97, depending upon the lobes. When adjusted to age, high heritability was reported in the frontal, frontal-temporal, and parietal lobes, but the heritability in other lobes was lower than 0.70. Conclusions: This study revealed a relatively lower heritability in brain atrophy compared to other ethnicities. This result suggests a significant environmental impact on the susceptibility of brain atrophy the Japanese. Therefore, environmental factors may have more influence on the Japanese than in other populations.

India's Opportunities and Challenges in Establishing a Twin Registry: An Unexplored Human Resource for the World's Second-Most Populous Nation

Nature and nurture have always been a prerogative of evolutionary biologists. The environment's role in shaping an organism's phenotype has always intrigued us. Since the inception of humankind, twinning has existed with an unsettled parley on the contribution of nature (i.e. genetics) versus nurture (i.e. environment), which can influence the phenotypes. The study of twins measures the genetic contribution and that of the environmental influence for a particular trait, acting as a catalyst, fine-tuning the phenotypic trajectories. This is further evident because a number of human diseases show a spectrum of clinical manifestations with the same underlying molecular aberration. As of now, there is no definite way to conclude just from the genomic data the severity of a disease or even to predict who will get affected. This greatly justifies initiating a twin registry for a country as diverse and populated as India. There is an unmet need to set up a nationwide database to carefully curate the information on twins, serving as a valuable biorepository to study their overall susceptibility to disease. Establishing a twin registry is of paramount importance to harness the wealth of human information related to the biomedical, anthropological, cultural, social and economic significance.

Bridging gaps between images and data: a systematic update on imaging biobanks

BACKGROUND AND OBJECTIVE

The systematic collection of medical images combined with imaging biomarkers and patient non-imaging data is the core concept of imaging biobanks, a key element for fuelling the development of modern precision medicine. Our purpose is to review the existing image repositories fulfilling the criteria for imaging biobanks.

METHODS

Pubmed, Scopus and Web of Science were searched for articles published in English from January 2010 to July 2021 using a combination of the terms: "imaging" AND "biobanks" and "imaging" AND "repository". Moreover, the Community Research and Development Information Service (CORDIS) database ( https://cordis.europa.eu/projects ) was searched using the terms: "imaging" AND "biobanks", also including collections, projects, project deliverables, project publications and programmes.

RESULTS

Of 9272 articles retrieved, only 54 related to biobanks containing imaging data were finally selected, of which 33 were disease-oriented (61.1%) and 21 population-based (38.9%). Most imaging biobanks were European (26/54, 48.1%), followed by American biobanks (20/54, 37.0%). Among disease-oriented biobanks, the majority were focused on neurodegenerative (9/33, 27.3%) and oncological diseases (9/33, 27.3%). The number of patients enrolled ranged from 240 to 3,370,929, and the imaging modality most frequently involved was MRI (40/54, 74.1%), followed by CT (20/54, 37.0%), PET (13/54, 24.1%), and ultrasound (12/54, 22.2%). Most biobanks (38/54, 70.4%) were accessible under request.

CONCLUSIONS

Imaging biobanks can serve as a platform for collecting, sharing and analysing medical images integrated with imaging biomarkers, biological and clinical data. A relatively small proportion of current biobanks also contain images and can thus be classified as imaging biobanks.

KEY POINTS

• Imaging biobanks are a powerful tool for large-scale collection and processing of medical images integrated with imaging biomarkers and patient non-imaging data. • Most imaging biobanks retrieved were European, disease-oriented and accessible under user request. • While many biobanks have been developed so far, only a relatively small proportion of them are imaging biobanks.

An information-based framework for development national twin registry: Scoping review and focus group discussion

BACKGROUND

Registries in various clinical domains have been established in the last decades. The specific genetic structure of twins has enabled researchers to find answers to the role of genetics and the environment in medical sciences. Thus, twin registries were developed across the world to support twin studies. Our main objective was to devise a conceptual model for developing the national twin registry to ensure the success of this registry.

METHODS

In this descriptive and qualitative study, the combination of literature review and focus group discussions was applied to achieve suitable models for developing a national twin registry based on lessons learned from founded registries. The qualitative synthesis and reporting results were conducted based on the COREQ checklist.

RESULTS

According to a systematic literature review, the characteristics and employed strategies employed by established twin registries were recognized. Moreover, based on our objectives, suitable models for registry development were defined. The source of information, the different levels of data, and the information flow were determined based on this model.

CONCLUSION

Suggesting a conceptual framework for twin registry development at the national level based on the experiences of other countries could contribute to a greater understanding of twin registry implementation efficiently.