Lab Activities
Laboratory for Cancer Genomics
Research Activities
Team Director
Hidewaki Nakagawa
Understanding of the genetic diversity in cancer is likely to increase the success of new cancer treatment modalities. Our DNA/RNA sequencing and bioinformatics analyses enable us to characterize each type of cancer at the molecular level and to identify biomarkers and new therapeutic targets. As cancer genome profiling (CGP) has been implemented clinically, we have focused on cancer RNA profiling now. For kidney cancer, where pathological diagnosis is challenging, we performed RNA profiling on preserved clinical specimens. This demonstrated that it could assist pathological diagnosis and suggests higher clinical utility than CGP, and we are pursuing the clinical implementation of this method and exploring its potential applicability to other cancer types. We also adopted a machine learning or AI algorithm to predict the clinical outcome of cancer patients by using cancer genome, transcriptome, and multi-omics data. Furthermore, cancer has proven to be an “immune disease”, with a variety of features of immune reactions, and immune therapies targeting immune checkpoints and neo-antigens derived from somatically mutated proteins are also treatment realities. To explore immuno-genomic alterations in human cancer, we have been utilizing WGS and RNA-seq data from cancer tissues. These approaches, combined with state-of-art single-cell RNAseq (scRNAseq) and spatial transcriptome (ST) analysis of cancer tissues and immune cells, can clarify the underlying carcinogenesis and cancer immunology and achieve a molecular sub-classification of cancer, which will facilitate the discovery of drug-targets and personalized cancer medicine.
In 2025, ASTRA (Asia-Pacific Space Translational Research Alliance) embarked on an ambitious mission to construct a comprehensive cancer spatial atlas for the Asia-Pacific region, featuring high resolution and over 2,000 cancer tissues. This groundbreaking collaborative research by Japan and Australia is currently underway, establishing the foundational data necessary to decipher the complexity and heterogeneity of the tumor tissues and the tumor microenvironment at scale.
Classification and diagnosis of kidney cancers by whole transcriptome analysis
(A) t-SNE plot for whole transcriptome classified five classes of kidney cancers. (B) Kaplan-Meier curves show overall survival of patients in five clusters. Poor prognostic kidney cancer cases were clustered in a specific site of comparative transcriptome atlas, named Cluster X.
Recent Major Publications
Jikuya R, Johnson TA, Muraoka E, Noguchi G, Maekawa S, Obara W, Numakura K, Habuchi T, Maejima K, Sasagawa S, Kanazashi Y, Lee H, Song WJ, Sasagawa H, Mitome T, Ohtake S, Kawaura S, Iribe Y, Aomori K, Nagasaka H, Tatenuma T, Ueno D, Komeya M, Ito H, Ito Y, Muraoka K, Kawahara T, Furuya M, Kato I, Hamanoue H, Nishiyama A, Tamura T, Baba M, Suda T, Kodama T, Ogawa T, Uemura H, Yao M, Tsuzuki T, Nagashima Y, Miura Y, Kimura G, Imoto S, Momozawa Y, Fujii S, Makiyama K, Hasegawa T, Shuch BM, Ricketts CJ, Schmidt LS, Linehan WM, Nakagawa H, Hasumi H. Comparative transcriptome atlas as an assistive modality for complex classification of rare kidney cancers. Nat Commun 16, 10340 (2025)
Noguchi G, Baba M, Ohtake S, Jikuya R, Mitome T, Kawaura S, Aomori K, Iribe Y, Nagasaka H, Wilan K, Funasaki S, Muraoka E, Fujii S, Tsuzuki T, Kato I, Furuya M, Nagashima Y, Nishizawa H, Kamba T, Kuraoka S, Kawagoe T, Mizuki N, Tatenuma T, Ueno D, Kawahara T, Ito H, Komeya M, Ito Y, Muraoka K, Uemura H, Tamura T, Ogawa T, Suda T, Yao M, Makiyama K, Nakagawa H, Shuch BM, Ricketts CJ, Schmidt LS, Linehan WM, Nishinakamura R, Hasumi H. Genetically engineered human iPS cell-derived kidney organoid recapitulates an early stage of ALK fusion gene-associated renal tumorigenesis. Mol Cancer Res (2025)
Kobayashi T, Hachiya T, Lu Y, Ikehata Y, China T, Kawano H, Nagata M, Ide H, Isotani S, Nojiri S, Iwami T, Uchiyama S, Okazaki Y, Nakagawa H, Morisaki T, Matsuda K, Kamatani Y, Terao C, Horie S. Local radiotherapy for cancer patients is associated with mosaic loss of chromosome Y, a hallmark of male aging. NPJ Aging 11, 69 (2025)
Yoshida N, Stewart DR, Uchimura A, Arita K, Bombard Y, Frone M, Hinoi T, Kamiya K, Katamine S, Kayukawa J, Kodama K, Miller DT, Miura K, Muto K, Nagami F, Nakagawa H, Noda A, Ohishi W, Tanabe O, Terao C, Rajaraman P, Kato K, Biesecker LG. Symposium report—ethical and social considerations regarding return of secondary findings in atomic bomb survivors. Carcinogenesis 46, bgaf059 (2025)
Takehara Y, Usui Y, Stolařová L, Kleiblova P, Iwasaki Y, Johnson TA, Hirata M, Kamatani Y, Murakami Y, Endo M, Shiraishi K, Kohno T, Sugano K, Matsuda K, Yoshida T, Spurdle AB, Nakagawa H, Macurek L, Kleibl Z, Momozawa Y. Case-Control Study for 23 Cancer Types With Functional Analysis of CHEK2: Risk Estimation and Clinical Recommendations in East Asia. JCO Precis Oncol 9, e2400945 (2025)
Sasaki T, Iwaya T, Yaegashi M, Idogawa M, Hiraki H, Abe M, Koizumi Y, Sasaki N, Yashima-Abo A, Fujisawa R, Endo F, Tange S, Otsuka K, Sasaki A, Masuda M, Fujita M, Nakagawa H, Takahashi F, Sasaki Y, Tokino T, Nishizuka SS. Impact of Sensitive Circulating Tumor DNA Monitoring on CT Scan Intervals During Postoperative Colorectal Cancer Surveillance. Annals of Surgery Open 6, e549 (2025)
Invited Presentations
Nakagawa H. "Liver cancer genomics and its translation research” The 46th Meeting of West Branch of the Japan Society of Hepatology. The 46th Meeting of West Branch of the Japan Society of Hepatology, Japan, December 4 (2025)
Nakagawa H. "Cancer immunogenomics by cell signature, single-cell transcriptomics and spatial transcriptomics." ASTRA (Asia-Pacific Spatial Translational Research Alliance) 1st meeting, Sydney, Australia, November 19 (2025)
Nakagawa H. "Cancer Immuno-Genomics and Precision Medicine by Single-Cell Analysis and Machine Learning." EMBL Conference for Cancer Genomics, Heidelberg, Germany, November 11 (2025)
Nakagawa H. "Multi-omics analysis of liver cancers indicates therapeutic strategies and new drug therapies." KCA (Korean Cancer Association) Annual Meeting AOS session, Seoul, Korea, July 3 (2025)
Nakagawa H. "Population-based Screening for Hereditary Cancer Variants in Japan." NCCS (National Cancer Centre Singapore) Symposium, Singapore, Singapore, Singapore, January 16 (2025)