Towards early prevention of lifestyle related diseases – a cohort study starting at the fetal stage
Dr. Kenichi Sakurai of the Center for Preventive Medical Sciences from Chiba University and Dr. Yoichiro Kamatani of the Graduate School of Frontier Sciences from The University of Tokyo have been investigating the causative factors of diabetes and obesity by using various samples collected through a cohort study beginning during the fetal stage.
We interviewed both about the details and progress of the research, the prospects of its social implementation, and the possibility of widening the scope of the study by combining the information about DNA methylation and single nucleotide polymorphism (SNP).
Q. (to Dr. Sakurai) Firstly, we would like to know about the cohort study in which the Center for Preventive Medical Sciences, Chiba University and you are involved.
A. We have been carrying out a cohort study from the fetal stage to childhood to investigate the effects of their environment on one’s health (Sakurai).
The Center for Preventive Medical Sciences, Chiba University was established with the objective of researching and raising awareness about “Preventive medical sciences” that prevent lifestyle-related disease, mental illness, and the effect of the environment on one’s health.
I have been working in the Nutrition and Metabolic Medicine Department since 2015. In that time, I have been involved in two cohort studies; the EcoChil study, and Chiba study of Mother and Child Health (C-MACH). These studies were implemented by the Center for Preventive Medical Sciences to investigate the association of nutrition with gut microbiota and health.
The EcoChil study is a country-wide study on children and their environment. Implemented by the Ministry of the Environment in 2011, it studies around 100,000 sets of children and parents, and got its name by combining “Ecology” and “Children”. A cohort study of this size is also unique. The study period is from the fetal stage until the child reaches the age of 13 years. During this period, the blood and urine of the mother during pregnancy and at the time of childbirth, the umbilical cord blood, the hair of the mother and child, the mother’s milk, the father’s blood, and the milk teeth of the child are all sampled and stored in a bank. Chemical substances are then measured, and a questionnaire survey is conducted.
C-MACH is an independent study carried out on children from the fetal stage up to 5 years of age and their parents. Blood, urine, the mother’s milk, child’s milk teeth, etc. are sampled and a questionnaire survey is conducted. Recently, the research plan has changed and the age limit has been extended to 15 years. The first phase of the study was started in 2014 and included 400 people, these participants were different from those of the EcoChil study. C-MACH samples are more varied including the umbilical cord, the stool of the mother and child etc. We hope that C-MACH would be a research tool that complements the EcoChil study.
Dr. Kenichi Sakurai, Center for Preventive Medical Services, Chiba University
Q. (to Dr. Sakurai) What research are you currently involved in?
A. I am investigating the association of the environment in the fetal stage and DNA methylation and how it can affect obesity and diabetes (Sakurai).
I am currently focusing on the association between DNA methylation in the fetal stage and childhood disease, using Infinium™ MethylationEPIC BeadChip
The concept that “Developmental Origins of Health and Disease” (DOHaD), where environmental factors during the fetal and early stages of development are contributors to the risk factors of disease in adulthood has been gathering attention. “Epigenome”, which includes DNA methylation, histone acetylation, and miRNA modification has become the buzzword. Initial results from the cohort study showed that a low birth weight was associated with various diseases such as coronary artery disease, respiratory disease, and kidney diseases in adulthood.
I specialize in metabolic diseases such as diabetes and obesity, and research how the environment in the fetal stage and methylation are connected to diabetes and obesity in adulthood. It has been suggested that not only nutrition, but also chemical substances play a role in the development of diabetes and obesity, and therefore, environmental factors also constitute an important area of research.
Prevention of diseases from the fetal stage is the objective of both the EcoChil study and C-MACH. If the relationship between methylation in the fetal stage or immediately after birth and childhood obesity is understood, there may be a possibility of preventing the development of obesity and diabetes in the future. This could eventually lead to prevention of these diseases before birth.
As for information on methylation with regard to diabetes, several reports are available on the umbilical cord blood and peripheral blood of adults. However, reports relating to the umbilical cord itself are currently unavailable. Moreover, the tissue of the umbilical cord includes many mesenchymal stem cells. Since adipocytes are also included in the mesenchyme, the utility of the umbilical cord is being focused upon.
Another factor associated with DOHaD is the gut microbiota. The gut microbiota is transmitted from the mother to the child at the time of birth, and since families eat similar food, the influence of the parents can also be seen on the gut microbiota. As such, stool samples collected in C-MACH are used to also conduct research on the gut microbiota as well as on diabetes and obesity.
Q. (to Dr. Kamatani) What are the focuses of your research?
A. I am analyzing the traits of the complex association between multiple factors by using big data (Kamatani).
Kamatani: I am analyzing complex traits, the characteristics (traits) of association of multiple factors such as diseases through big data like genomes, by using genetics, statistics, AI, and machine learning.
For a long time now, I have been dealing with the Genome Wide Association Study (GWAS) that investigates single-nucleotide polymorphism using an SNP array and analyzes genetic factors of diseases. However in order to view complex traits, it is necessary to combine the rare variants and omics data. The development of an analysis method is currently being researched.
One of the complex traits researched are lifestyle-related diseases that develop as a result of an accumulation of several genetic factors concerning obesity, fats, blood pressure, blood sugar control, lifestyle and environmental risk factors. For example, the association between cerebrovascular diseases such as cerebral infarction or brain aneurysm and DNA polymorphism is being studied by an international joint research team. While brain dock is performed as preventive screening for brain aneurysm, an MRI scan cannot be performed every year for all citizens. If research can show from the DNA that a brain aneurysm is likely to occur, the high-risk group of individuals for whom an MRI scan must be performed can be identified, which will likely result in effective prevention. As a researcher who was originally a doctor, I would like the outcomes of this research to eventually be linked with medical care.
Dr. Yoichiro Kamatani, Graduate School of Frontier Sciences, The University of Tokyo
Q. (to Dr. Kamatani) You have been involved in the design of the SNP array which has been optimized for genome analysis in Japanese populations "Infinium Japanese Screening Array（JSA)” I believe you are currently conducting a study, together with Dr. Sakurai, by using this microarray.
A. I investigated the association between DNA methylation and SNP in some of the samples of C-MACH (Kamatani).
Kamatani: I was invited by Prof. Matsuda Fumihiko of the Graduate School of Medicine, Kyoto University, and worked with him in improving the imputation performance on polymorphisms in Japanese populations by modifying a part of the Infinium Asian Screening Array（ASA) Genome data forms the basis of the multi-layered omics research, and by combining various types of data, the interpretation range of research results becomes extremely vast. It is therefore important that a low-cost array with high accuracy is used. I think that the genome data of the Japanese will appear sharper by JSA.
Through a joint study with Dr. Sakurai, we are investigating the association between methylation of the samples of C-MACH and the genome information using EPIC and JSA. From the umbilical cord tissue of 91 people, we have identified the loci influencing the DNA methylation condition and have obtained results by which we can make an interpretation. Generally, it is difficult to obtain effective analysis results through analysis of the SNP array of 100 people, however, by combining with methylation, it is possible to achieve statistical significance even if the sample size is small.
Q. What do you think about the importance of combining the genome information, DNA methylation information, and the results of cohort study?
A. By combining the information about the genome, epigenome, disease, and the cohort study, the origin of the disease can be better understood (Sakurai).
Sakurai: Some people will get sick and others will not regardless of genetic predisposition. To understand this process, the genome information that forms the basis is of utmost importance. Information of environmental exposure, and the epigenome such as DNA methylation are also important factors. Since methylated DNA is retained for a longer time, if the tendency of onset of disease can be found from DNA methylation in the fetal stage, immediately after birth, or in childhood, it may be possible to prevent the disease. I think that by combining information about the genome and epigenome, environmental factors, and tracking this information through a cohort study over an extended period of time, we can get a better understanding of the prognosis.
Kamatani: A genome is complete at the time of fertilization. However that genomes are related to adult illness imply that the various stages from fertilization to adulthood can contribute to clinical conditions. Generally, adult data is collected in human genome research targeting adult illnesses. For example, even if specific methylation known from the umbilical cord blood is related to an illness, it cannot be seen in the adult genome research. Through the comparison between the genome analysis after reaching adulthood and the genome analysis of the umbilical cord blood, the relationship between the effect of the environment in the fetal stage or immediately after birth and the illness is better understood.
Sakurai: In the birth cohort study being conducted currently, the chemical substances of the samples of children and parents and various other types of information is gathered and accumulated in a database. Since we can investigate the combination between the genome and the exposome elements that deal with the exposures that a human being experiences including food, medicines, ultraviolet rays, noise, chemical substances, proceeding with the genome research through the birth cohort study is a huge achievement.
Kamatani: There are some historical genetic variants that provide different levels of reactivity to some environmental substances that can affect human beings. It is highly possible that such genetic variations may be rare among human populations as a result of natural selection. On the other hand, there may be genetic factors that react intensely to new substances. If such genetic factors are found, a person having those genetic factors can observe caution when dealing with such substances. If the genome can be investigated, we can get the sharper results from epidemiology, and that would make it easier to implement the results in society.
Q. What are your views on the social implementation of the results of genome research?
A. It is important to make progress in social understanding of the genome itself and build a social system without discrimination (Kamatani).
Kamatani: Social implementation has several stages. In terms of making use of the genome data in medical care, the data is almost in the implementation stage for cancer and monogenic diseases. Cancer and genetic diseases are special in the sense that cancer is a disease in which the genome changes at a later stage and genetic diseases occur when an extremely large genetic mutation occurs at the time of birth.
Therefore, diagnosis and treatment using genomes are in the process of implementation. In addition, the genetic factors for diseases involving a large number of genes are also being understood. What is left is the need to make some progress in the technological and cost aspects, and I can see that we have reached the stage where we are devising the specific means of actual usage in the society.
It is often said that there isn’t enough awareness in society with regard to genomes, and therefore we must also put in efforts to bring about this awareness.
Sakurai: If the relationship between the genome, epigenome, and traits can be understood, it would be useful in preventing diseases, and if this knowledge can be applied to education, it would lead to good health for all citizens of the country.
Kamatani: Currently, due to the progress of science, the understanding of human beings has been changing in a fundamental manner, and what exactly a genome is needs to be understood not only by researchers, but also by society. Otherwise, we would be unable to figure out what we are doing in the clinical environment. It is also important to build a social system in which discrimination is not caused by the genome.
Q. What kind of research would you be carrying out in the future?
A. I plan to add the analysis of environmental factors, such as analysis of the air inside a room, and genomes, and believe that single-cell analysis would also be interesting (Sakurai).
Sakurai: In the second phase of C-MACH that will start this year, we will investigate the chemical substances and allergens by sampling the air inside one’s house, performing adsorption of the organic substances in the air, and collecting dust. We will analyze the data to assess whether they are associated with DNA methylation of blood from the mother and child or umbilical cord. We also plan on performing genome analysis.
We are currently examining whether or not to continue with the EcoChil study. Entries to this study started right before the Great East Japan earthquake, and since we are going through the COVID-19 pandemic, we should be able to follow the effect of various environmental changes on the children. I sincerely hope that this study gets extended as much as possible.
In the future, I would like to investigate the metabolic syndrome in children. There are diagnostic criteria for the metabolic syndrome in children and blood sample needs to be collected on an empty stomach. Although collection of blood samples on an empty stomach is not included in the EcoChil study or C-MACH, it may be possible to do so once a child reaches around the junior high school age. Therefore, the percentage of children who could be suffering from the metabolic syndrome, and the past data can be analyzed.
Kamatani: The fusion of information about the genome and epigenome with single-cell analysis is also interesting.
Sakurai: For example, we found differences upon comparing the DNA methylation of the umbilical cord and the umbilical cord blood of a single new-born by using Reduced Representation Bisulfite Sequencing (RRBS). It would be fascinating to know how such differences in methylation of each tissue could become a marker for some disease or trait in the future.
In the future, we may be able to see more details through analysis of the pattern of DNA methylation by sampling specific cells. For example, by investigating macrophage or monocytes that have been reported to have a strong relationship with obesity, we may be able to predict the onset of obesity in the future.
From left, Dr. Tomoko Takahashi, Dr. Yoichiro Kamatani and Dr. Kenichi Sakurai in the laboratory of the Medical Science Building, Chiba University Inohana Campus.
Learn more about the products and systems mentioned in this article:
DNA methylation analysis tool Infinium MethylationEPIC BeadChip and SNP array optimized for genome analysis in Japanese populations Infinium Japanese Screening Array（JSA)