H. Nakagawa

Extrinsic MMPs drive epithelial shape change via basal ECM disassembly in the Drosophila wing disc

The paper shows that extrinsic MMPs drive epithelial shape change via basal ECM disassembly in Drosophila wing discs during pupal development.

Adaptive evolution of sesquiterpene deoxyphomenone in mycoparasitism by Hansfordia pulvinata associated with horizontal gene transfer from Aspergillus species

This study identifies deoxyphomenone biosynthesis gene clusters in Hansfordia pulvinata and related Aspergillus species, showing horizontal gene transfer and adaptive evolution in mycoparasitism.

Cancer-associated DNA Hypermethylation of Polycomb Targets Requires DNMT3A Dual Recognition of Histone H2AK119 Ubiquitination and the Nucleosome Acidic Patch

The paper identifies a critical binding interface in DNMT3A1 that facilitates DNA hypermethylation at Polycomb target genes by recognizing H2AK119Ub and the nucleosome acidic patch.

ALDH2 dysfunction accelerates ESCC pathogenesis

This study shows that ALDH2 dysfunction accelerates ESCC pathogenesis by increasing CSCs, ROS, and DNA damage, and reduces response to cisplatin chemotherapy.

Tumor Niche Network-Defined Subtypes Predict Immunotherapy Response of Esophageal Squamous Cell Cancer

This study defines ESCC subtypes based on tumor microenvironment transcriptional networks and predicts immunotherapy response using single-cell transcriptomics.

Key Genetic Determinants Driving Esophageal Squamous Cell Carcinoma Initiation and Immune Evasion

This study identifies key genetic drivers of ESCC initiation and immune evasion using CRISPR/Cas9 in murine organoids and human scRNA-seq data.

Cell-surface protein YwfG of Lactococcus lactis binds to α-1,2-linked mannose

This study identifies YwfG as a cell-surface protein in Lactococcus lactis that binds α-1,2-linked mannose, revealing its role in interactions with yeast cells.

Human papilloma virus E6 regulates therapy responses in oropharyngeal cancer by repressing the PGC-1α/ERRα axis

This study shows that HPV E6 reduces mitochondrial antioxidant capacity and therapy resistance in oropharyngeal cancer by suppressing the PGC-1α/ERRα pathway.

Comprehensive analysis of full-length transcripts reveal aberrations of splicing variants in liver cancer

The paper develops a pipeline to analyze full-length transcripts using long-read sequencing and identifies splicing variants and fusion events in liver cancer.

Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture

The paper identifies a mutational mechanism in hepatocellular carcinoma driven by Hepatitis B virus DNA integration, leading to genomic restructuring and oncogenic rearrangements.

Adaptive fitness in APC-mutant cells requires chromosome rearrangements

The paper shows that APC-mutant cells gain adaptive fitness through chromosome rearrangements that restore AURKA activity and counteract mitotic defects.

Seasonal and annual fluctuations of deer populations estimated by a Bayesian state-space model

This study uses a Bayesian state-space model to estimate seasonal and annual fluctuations in sika deer populations in Japan, identifying factors like snowfall and nuisance control affecting population dynamics.

Identifying predictors of HPV-related head and neck squamous cell carcinoma progression and survival through patient-derived models

This study identifies predictors of HPV-related head and neck squamous cell carcinoma progression and survival using patient-derived models and finds associations between mutational burden and E2F target dysregulation with clinical outcomes.

Comprehensive Analysis of Indels in Whole-genome Microsatellite Regions and Microsatellite Instability across 21 Cancer Types

The paper analyzes microsatellite mutations across 21 cancer types, identifies MSI cancers, and finds factors influencing mutation rates and functional impacts.

In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors

This study identifies the mutational signature of cisplatin in human cell lines and tumors, enabling detection of cisplatin exposure in hepatocellular and esophageal cancers.