PRCGAP provides a haplotype-resolved analysis of cancer genomes, detecting variants missed by standard references and revealing new insights into structural variants and fusion events in leukemia.

bioRxiv · Jul 9, 2026 · PreprintBioinformatics

HTLV-1-Induced Neuroimmunome Correlates with Disease Progression and Severity

Fernando Yuri Nery do Vale, Carlota Miranda-Solé, Adriel Leal Nóbile, Júlia Nakanishi Usuda, Dennyson Leandro M. Fonseca, Lena F. Schimke, Mauro César Cafundó Morais, Débora Gomes de Albuquerque Freitas, Anny Silva Adri, Roseane Galdioli Nava, Yohan Lucas Gonçalves Corrêa, Hugo Fernando Nery do Vale, Adriana Simizo, Niels Olsen Saraiva Câmara, Gustavo Cabral‐Miranda, , Otávio Cabral-Marques

The paper identifies a neuroimmune signature in HTLV-1 infection that correlates with disease progression and severity using bulk and single-cell transcriptomic data.

bioRxiv · Mar 12, 2026 · PreprintMolecular Biology

FDXR Upregulation by p63/p73 is a Prognostic and Therapeutic Marker of HTLV-1-Associated Adult T Cell Leukemia/Lymphoma

Lara Gallucci, Maria Josephine, Yasunori Kogure, Alex Ap. Rosini Silva, Vincent Cantaloube-Ferrieu, Marcos Eduardo Souza Abreu, Trusha Ramteke, Phoebe Kibble, Guilherme Lucchesi D Angelo Braz, Rubens de Assis Santos Sebastiao, Luiza Amoroso Lambaz, Aijun Lin, Beth Hoare, Felipe Custodio Carvalho dos Santos, Sophie Shackley, , Iart Luca Shytaj

This study identifies FDXR upregulation as a prognostic marker and therapeutic target in HTLV-1-associated ATL, showing its link to disease severity and sensitivity to fluorouracil.

bioRxiv · Feb 25, 2026 · PreprintMicrobiology

Hyperactive PLCG1 drives non-canonical signaling to promote cell survival

Longhui Zeng, Xinyan Zhang, Yiwei Xiong, K. Satoh, Nicole Hajicek, Yasunori Kogure, Keisuke Kataoka, Seishi Ogawa, John Sondek, Xiaolei Su

This study identifies hyperactive PLCG1 mutations in T-cell leukemia/lymphoma that drive non-canonical signaling, enhancing cell survival and drug resistance.

EMBO Reports · Aug 12, 2025Peer-reviewedCell Biology

Precise characterization of somatic complex structural variations from paired long-read sequencing data with nanomonsv

Yuichi Shiraishi, Junji Koya, Kenichi Chiba, Ai Okada, Yasuhito Arai, Yuki Saito, Tatsuhiro Shibata, Keisuke Kataoka

nanomonsv detects somatic structural variations from long-read sequencing data with high precision and recall, revealing complex SV features in cancer.

Nucleic Acids Research · Jun 8, 2023Peer-reviewedBioinformatics

The viral oncoproteins Tax and HBZ reprogram the cellular mRNA splicing landscape

Charlotte Vandermeulen, Tina M. O’Grady, Jérôme Wayet, Bartimée Galvan, Sibusiso B. Maseko, Majid Cherkaoui, Alice Desbuleux, Georges Coppin, Julien Olivet, Lamya Ben Ameur, Keisuke Kataoka, Seishi Ogawa, Olivier Hermine, Ambroise Marçais, Marc Thiry, , Jean‐Claude Twizere

This study shows that Tax and HBZ, viral oncoproteins, alter mRNA splicing in T-cells by interacting with spliceosome components, leading to changes in cancer-related genes.

PLoS Pathogens · Sep 20, 2021Peer-reviewedSystems Biology

A comprehensive characterization of cis-acting splicing-associated variants in human cancer

Yuichi Shiraishi, Keisuke Kataoka, Kenichi Chiba, Ai Okada, Yasunori Kogure, Hiroko Tanaka, Seishi Ogawa, Satoru Miyano

The paper identifies and characterizes splicing-associated variants in cancer using a statistical framework applied to 8,976 samples across 31 cancer types, revealing 14,438 SAVs and their association with smoking and tumor suppressors.

Genome Research · Aug 1, 2018Peer-reviewedGenomics