Yutaka Suzuki

SPATNIC enables H&E-grounded cancer-cell identification across spatial and single-cell transcriptomic modalities in colorectal cancer

SPATNIC is a variational autoencoder that identifies cancer cells from spatial and single-cell transcriptomic data in colorectal cancer, outperforming existing tools and identifying a rare cancer stem cell population.

NECTIN4 defines a subtype-dependent tumor state coupling enfortumab vedotin targetability to antitumor immunity in bladder cancer

The paper identifies NECTIN4 as a subtype-dependent determinant of tumor state and antitumor immunity in bladder cancer, linking its expression to response to enfortumab vedotin and checkpoint inhibitors.

Aqp1aa and Aqp4a mediate collecting duct water permeability in a marine teleost

This study identifies Aqp1aa and Aqp4a as key aquaporins mediating water permeability in the collecting ducts of marine teleosts, with Aqp1aa expression reduced in hypoosmotic conditions.

Calmodulin controls the tempo of HSV-1 gene-expression cascade to reshape infection heterogeneity

This study identifies calmodulin as a host factor that accelerates HSV-1 gene-expression tempo, increasing virus-producing cells and protecting mice from lethal infection.

An APOC1+ inflammatory CAF-like state drives a senescent, treatment-resistant niche in rheumatoid arthritis

The paper identifies a treatment-resistant fibroblast state in RA synovitis that drives chronic inflammation through senescence-associated mechanisms and highlights therapeutic targets beyond cytokine inhibition.

Pathway-Centric Integration of CRISPR Fitness with Molecular Features Draws Cancer State Maps

StateMap integrates CRISPR fitness and gene expression data to map cancer pathway states, identifying therapeutic vulnerabilities in the Hippo pathway.

Experimental SARS-CoV-2 infection using horseshoe bats

This study experimentally infects horseshoe bats with SARS-CoV-2, showing low-level persistent viral replication without disease, and identifies host mechanisms that enable viral coexistence.

Transcriptome comparison between the cultured and in vivo Chick Primordial Germ Cells by SMART-seq-based single cell RNA sequencing

This study compares transcriptomes of cultured and in vivo chicken primordial germ cells using single-cell RNA sequencing, revealing shifts in gene regulatory networks and new intermediate cell states.

In vivo transition in chromatin accessibility during differentiation of deep-layer excitatory neurons in the neocortex

The paper tracks chromatin accessibility changes in mouse embryonic deep-layer excitatory neurons during differentiation using RNA-seq and DNase-seq.

Muc6-expressing gastric isthmus progenitors contribute to regeneration and metaplasia supported by myeloid-mesenchymal interactions

This study identifies Muc6-expressing isthmus progenitors as key contributors to gastric regeneration and metaplasia through myeloid-mesenchymal interactions.

Priming Epigenetic Landscape at Gene Promoters through Transcriptional Activation in Mammalian Germ Cells

The paper shows that in mouse male germ cells, promoter chromatin states are shaped by H3K4me3 density and H3K27me3 dynamics, influencing gene expression during development.

Enhanced functional divergence of duplicate genes several million years after gene duplication in the Arabidopsis lineage

The paper investigates gene duplication and selective pressures in Arabidopsis species, finding that functional divergence of duplicated genes accelerates several million years post-duplication.

Identification of physical interactions between genomic regions by enChIP-Seq

This paper introduces enChIP-Seq, a method to detect physical genomic interactions using engineered DNA-binding complexes and NGS, and demonstrates its application in identifying interactions involving the 5HS5 locus in K562 cells.