Remarkable progress has recently been made in molecular profiling tech-19nologies, including genome-wide technologies developed at RIKEN, and their effective use is one of the major interests in life science research, in partic-ular to solve medical problems. The RIKEN Preventive Medicine and Diagnosis Innovation Program (RIKEN PMI) coordinates translational studies that utilize RIKEN technologies to solve clinical problems. Our unit was established to conduct or support such studies with PMI funding, in particular from the per-spective of information sciences or computational genomics. Our projects are roughly classified into three categories: identification of cell markers required for regenerative medicine, exploration of diagnostic markers useful in patient treatment and our own advances to assist in such translational as well as basic science research.Our collaborative research with RIKEN PMI led to several biomedical re-search publications: Molecular characterization of cancer-associated fibroblasts in non-small cell lung cancers (Iwai M., et al. Mol Oncol. 2021), Gene expres-sion signatures of patient-derived mononuclear cells cultured for vasculogenic wound healing (Tanaka R., Stem Cells Transl Med. 2021), Single-cell profiling of patient-derived multiple myeloma cells (Hirabayashi S. et al. Biochem Bio-phys Res Commun. 2021), and Potential diagnostic biomarkers of myelopro-liferative neoplasms (Morishita S., et al. Cancer Sci. 2021). Furthermore, we uncovered more than 200 mRNA isoforms derived from a single gene locus, TACC2, by using a long-read sequencer (Ito Y., et al. Sci Rep. 2021). This level of isoform variety has not been seen before, which motivates further explora-tion of transcriptome complexity. We also provided an important foundation for safety assessment of oligonucleotide therapeutics in a pre-clinical study, i.e., a high-quality genome assembly of the crab-eating macaque (Jayakumar V., et al. Sci Data. 2021). This has been employed as the reference genome assembly of the species and is also a major contribution to basic science as well as bio-medical studies.Figure: Integrated view of transcriptome and epigenetic marks provided by the FANTOM5 web resourceA partial listing of the TACC2 mRNA isoforms discovered by using a long-read sequencer. Gray squares and lines listing indicate exons and introns, respectively, and the adjacent boxplots indicate frequencies of individual exons and isoforms. Only the top 50 isoforms are shown. (The figure is from Sci. Rep. 11:16835, 2021).Recent Major PublicationsJayakumar V, Nishimura O, Kadota M, Hirose N, Sano H, Murakawa Y, Yamamoto Y, Nakaya M, Tsukiyama T, Seita Y, Nakamura S, Kawai J, Sasaki E, Ema M, Kuraku S, Kawaji H, Sakakibara Y. Chromosomal-scale de novo genome assemblies of Cynomolgus Macaque and Com-mon Marmoset. Sci Data 8, 159 (2021)Ito Y, Terao Y, Noma S, Tagami M, Yoshida E, Hayashizaki Y, Itoh M, Kawaji H. Nanopore sequencing reveals TACC2 locus complexity and diversity of isoforms transcribed from an intronic promoter. Sci Rep 11, 9355 (2021)Abugessaisa I, Ramilowski JA, Lizio M, Severin J, Hasegawa A, Harshbarger J, Kondo A, Noguchi S, Yip CW, Ooi JLC, Tagami M, Hori F, Agrawal S, Hon CC, Cardon M, Ikeda S, Ono H, Bono H, Kato M, Hashimoto K, Bonetti A, Kato M, Kobayashi N, Shin J, de Hoon M, Hayashizaki Y, Carninci P, Kawaji H, Kasukawa T. FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs. Nucleic Acids Res 49, D892-D898 (2021)Preventive Medicine and Applied Genomics UnitUnit Leader: Hideya Kawaji
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