Identification of Dominant Transcripts in Oxidative Stress Response by a Full-Length Transcriptome Analysis

jMorp: Japanese Multi-Omics Reference Panel update report 2023

Modern medicine is increasingly focused on personalized medicine, and multi-omics data is crucial in understanding biological phenomena and disease mechanisms. Each ethnic group has its unique genetic background with specific genomic variations influencing disease risk and drug response. Therefore, multi-omics data from specific ethnic populations are essential for the effective implementation of personalized medicine. Various prospective cohort studies, such as the UK Biobank, All of Us and Lifelines, have been conducted worldwide. The Tohoku Medical Megabank project was initiated after the Great East Japan Earthquake in 2011. It collects biological specimens and conducts genome and omics analyses to build a basis for personalized medicine. Summary statistical data from these analyses are available in the jMorp web database (https://jmorp.megabank.tohoku.ac.jp), which provides a multidimensional approach to the diversity of the Japanese population. jMorp was launched in 2015 as a public database for plasma metabolome and proteome analyses and has been continuously updated. The current update will significantly expand the scale of the data (metabolome, genome, transcriptome, and metagenome). In addition, the user interface and backend server implementations were rewritten to improve the connectivity between the items stored in jMorp. This paper provides an overview of the new version of the jMorp.

Induction of Nrf2-EpRE-mediated gene expression by hydroxyanthraquinones present in extracts from traditional Chinese medicine and herbs

Hydroxyanthraquinones that can be present in traditional Chinese medicine (TCM) and herbal extracts have claimed beneficial intestinal effects. We examined the ability of a panel hydroxyanthraquinones, and methanolic extracts from selected TCM and herbal granules to activate Nrf2-EpRE mediated gene expression using a reporter-gene assay. The results indicate that purpurin, aloe-emodin, 2-hydroxy-3-methylanthraquinone and rhein induced Nrf2 mediated gene expressions with a high induction factor (IFs>10), with BMCL₁₀ values (the lower confidence limit of the concentration giving 10% added response above background) of 16 μM, 1.1 μM, 23 μM and 2.3 μM, respectively, while aurantio-obtusin, obtusifolin, rubiadin 1-methyl ether and emodin were less potent (IFs<5), with BMCL₁₀ values for added response above background level of 4.6 μM, 15 μM, 9.8 μM and 3.8 μM, respectively. All TCM extracts and the herbal extracts of Aloe Vera, Polygonum multiflorum, Rubia (cordifolia) and Rheum officinale activated the Nrf2-EpRE pathway. Of the TCM extracts, Chuan-Xin-Lian-Kang-Yan-Pian was the most potent Nrf2-inducer. LC-MS/MS analysis indicated the presence of selected hydroxyanthraquinones in the extracts and herbs, in part explaining their Nrf2-EpRE mediated activity. In conclusion, different hydroxyanthraquinones have different potencies of Nrf2 activation. The Nrf2 activation by extracts from TCM and herbs can be partially explained by the presence of selected hydroxyanthraquinones.

Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long-read sequencing technology

Long-read sequencing technology enable better characterization of structural variants (SVs). To adapt the technology to population-scale analyses, one critical issue is to obtain sufficient amount of high-molecular-weight genomic DNA. Here, we propose utilizing activated T lymphocytes, which can be established efficiently in a biobank to stably supply high-grade genomic DNA sufficiently. We conducted nanopore sequencing of 333 individuals constituting 111 trios with high-coverage long-read sequencing data (depth 22.2x, N50 of 25.8 kb) and identified 74,201 SVs. Our trio-based analysis revealed that more than 95% of the SVs were concordant with Mendelian inheritance. We also identified SVs associated with clinical phenotypes, all of which appear to be stably transmitted from parents to offspring. Our data provide a catalog of SVs in the general Japanese population, and the applied approach using the activated T-lymphocyte resource will contribute to biobank-based human genetic studies focusing on SVs at the population scale.

Long-read sequencing on activated T-cells from a sample of 333 Japanese individuals (representing 111 parent-offspring trios) provides a useful reference dataset of structural variation in the Japanese population.