RIKEN Center for Integrative Medical Sciences Laboratory for Cancer Genomics

Team Director: Hidewaki Nakagawa (M.D., Ph.D)

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Research Summary

Cancer is a disease driven by genomic abnormalities, and various molecular-targeted therapies have been developed to specifically address these abnormalities. Additionally, cancer risk prediction based on genomic mutations and polymorphisms is advancing, promoting personalized approaches in treatment, diagnosis, and prevention. As demonstrated by the success of immunotherapy, cancer is also recognized as an immune-related disease.
Our team utilizes next-generation sequencing, single-cell analysis, and spatial transcriptomics to investigate the genomics and immunology of various human diseases, including cancer and hereditary disorders. We are actively building genomic databases to elucidate the relationship between genomic alterations and disease or treatment response and conducting functional analyses to assess their biological, immunological, and clinical significance.
Furthermore, we participate in the development of global genomic databases, such as those managed by the International Cancer Genome Consortium (ICGC), contributing to the infrastructure for genome-based research. Our ultimate goal is to enable personalized medicine through the integration and application of genomic information.

Main Research Fields

Medicine, Dentistry & Pharmacy

Related Research Fields

Informatics
Biological Sciences
Biology

Keywords

Cancer genomics
Precision Medicine
Next generation sequencer
Cancer immunogenomics

Selected Publications

1. Sasagawa S, Ono A, Arihiro K, Miura R, Maejima K, Osawa-Tatsuguchi A, Tanaka Y, Tsuge M, Oka S, and Nakagawa H*.
"Spatial profiling of chronic liver disease: a pilot case series."
Sci Rep. 16: 18223 (2026)
2. Jikuya R, Johnson AT, Muraoka E, Noguchi G, Maekawa S, Obara W, Numakura K,　Habuchi T, Maejima K, Sasaagwa S, Kanazashi Y, Lee HW, 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, Muira Y, Kimura G, Imoto S, Momozawa Y, Fujii S, Makiyama K, Shuch BM, Ricketts CJ, Schmidt LS, Linehan WM, Nakagawa H*, and Hasumi H*
"Comprehensive transcriptome atlas as an assistive modality for complex classification of rare kidney cancers."
Nat Commun. 16(1): 10340 (2025)
3. Sasagawa S, Honnma Y, Peng X, Maejima K, Nagaoka K, Kobayashi Y, Johnson TA, Okawa Y, Oosawa A, Liang H, Kakimi K, Yamada Y, and Nakagawa H*.
"Predicting chemotherapy responsiveness in gastric cancer through machine learning analysis of genome, immune, and neutrophil signatures."
Gastric Cancer 28(2): 228-244 (2025)
4. Wang H, Chen L, Xue R, Lie M, Bai J, Bao J, Wang Y, Li Z, Wang W, Wang R, Zheng B, Yang A, Hu J, Lie K, Shen S, Wang Y, Zhu Y, Gu J, Gao D, Wng XW, Nakagawa H, Zang N, Wu L, Rozen SG, Bai F, and Wang H.
"Deep whole genome analysis of 494 hepatocellular carcinomas."
Nature. 627(8004):586-593 (2024)
5. Okawa Y, Iwasaki Y, Johnson TA, Ebata N, Inai C, Endo M, Maejima K, Sasagawa S,　Fujita M, Matsuda K, Murakami Y, Nakamura T, Hirano S, Momozawa Y and Nakagawa H.
"Hereditary cancer variants and homologous recombination deficiency in biliary tract cancers."
J Hepatol. 78(2): 333-342 (2023)
6. Shima Y, Sasagawa S, Ohta N, Oyama R, Sogawa C, Kim Y, Sakashita-Kubota M, Kawakami H, Naemura K, Takubo N, Kobayashi M, Ozeki A, Nakaki R, Tanaka M, Kamatani Y, Matsuda K, Kurihara H, Furihata T, Takahashi S, Rikitake Y, Kozaki K, Nakafuku M, Mataga N, Ohtsuka N, Akimitsu N, Wada Y, Kamiguchi H, Okabe S, Kato T, Nakagawa H, Saito N, and Nakatomi H.:
"Increased PDGFRB and NF-κB signaling caused by highly prevalent somatic mutations in intracranial aneurysms."
Science Trans Med. 15(700): eabq77218 (2023)
7. Fujita M, Chen MM, Siwak DR, Sasagawa S, Arihiro M, Arihiro K, Ono A, Miura R, Osawa-Tatsuguchi A,　Maejima K, Aikata H, Ueno M, Hayami S, Yamaue H, Chayama K, Lu Y, Liang H, Nishizuka SS, and Nakagawa H.:
"Proteogenomic characterization of virus-associated liver cancers reveals potential subtypes and therapeutic targets."
Nat Commun. 13(1): 6481 (2022)
8. Sasagawa S, Kato H, Nagaoka K, Sun C, Imano M, Sato T, Johnson TA, Fujita M, Maejima K, Okawa Y, Kakimi K, Yasuda T, and Nakagawa H.:
"Immuno-genomic profiling of biopsy specimens predicts neoadjuvant chemotherapy response in esophageal squamous cell carcinoma."
Cell Rep Med. 3(8): 100705 (2022)
9. The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium.:
"Pan-cancer analysis of whole genomes."
Nature 578(7793): 82-93 (2020)
10. Fujimoto A, Furuta M, Totoki Y, Tsunoda T, Kato M, Shiraishi Y, Tanaka H, Taniguchi H, Kawakami Y, Ueno M, Gotoh K, Ariizumi S, Wardell CP, Hayami S, Nakamura T, Aikata H, Arihiro K, Boroevich KA, Abe T, Nakano N, Maejima K, Sasaki-Oku A, Ohsawa A, Shibuya T, Nakamura H, Hama N, Hosoda F, Arai Y, Ohashi S, Urushidate T, Nagae G, Yamamoto S, Ueda H, Tatsuno K, Ojima H, Hiraoka N, Okusaka T, Kubo M, Marubashi S, Yamada T, Hirano S, Yamamoto M, Ohdan H, Shimada K, Ishikawa O, Yamaue H, Chayama K, Miyano S, Aburatani H, Shibata T, and Nakagawa H.:
"Whole genome mutational landscape and characterization of non-coding and structural mutations in liver cancer."
Nat Genet 48: 500-509 (2016)