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Three-dimensional genome landscape of primary human cancers

This study characterizes the three-dimensional (3D) genome architecture of 15 primary human cancer types from The Cancer Genome Atlas. The analyses identify different archetypes of enhancer usage and enhancer rewiring events due to different classes of mutations and structural variants.

Kathryn E. Yost
Yanding Zhao
Howard Y. Chang
ResearchOpen Access12 May 2025
Nature Genetics

Volume: 57, P: 1189-1200
Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes

The mechanism controlling SWI/SNF chromatin remodeler targeting is incompletely understood. This study demonstrates that AP-1 transcription factors guide SWI/SNF to genomic regions, resulting in 3D genomic architecture alterations.

Bennett K. Wolf
Yanding Zhao
Xiaofeng Wang
Research15 Dec 2022
Nature Structural & Molecular Biology

Volume: 30, P: 10-21
Enhancing transcription–replication conflict targets ecDNA-positive cancers

Extrachromosomal DNA makes cancerous tumours resistant to treatment, but this research demonstrates that increasing transcription–replication conflict allows for targeted elimination of cancer cells containing extrachromosomal DNA, and thus sustained tumour regression in mice.

Jun Tang
Natasha E. Weiser
Howard Y. Chang
ResearchOpen Access06 Nov 2024
Nature

Volume: 635, P: 210-218
Resident and circulating memory T cells persist for years in melanoma patients with durable responses to immunotherapy

Turk and colleagues analyze exceptional responders to checkpoint blockade for melanoma, and detect tissue-resident memory and effector memory T-cell clonotypes in skin and blood, respectively, up to 9 years after treatment.

Jichang Han
Yanding Zhao
Christina V. Angeles
Research24 Mar 2021
Nature Cancer

Volume: 2, P: 300-311
Comparative Analysis of Mutant Huntingtin Binding Partners in Yeast Species

Yanding Zhao
Ashley A. Zurawel
Surachai Supattapone
ResearchOpen Access22 Jun 2018
Scientific Reports

Volume: 8, P: 1-14
Computational STAT3 activity inference reveals its roles in the pancreatic tumor microenvironment

Evelien Schaafsma
Yiwei Yuan
Chao Cheng
ResearchOpen Access03 Dec 2019
Scientific Reports

Volume: 9, P: 1-12
Whole transcriptome signature for prognostic prediction (WTSPP): application of whole transcriptome signature for prognostic prediction in cancer

We propose a statistical framework named WTSPP to generate prognostic gene signatures. Using ovarian cancer and lung adenocarcinoma as examples, they provide evidence that our prognostic signatures overperform previous reported signatures, capture prognostic features not explained by clinical variables and expose biologically relevant prognostic pathways.

Evelien Schaafsma
Yanding Zhao
Chao Cheng
Research06 Mar 2020
Laboratory Investigation

Volume: 100, P: 1356-1366

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Three-dimensional genome landscape of primary human cancers

Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes

Enhancing transcription–replication conflict targets ecDNA-positive cancers

Resident and circulating memory T cells persist for years in melanoma patients with durable responses to immunotherapy

Comparative Analysis of Mutant Huntingtin Binding Partners in Yeast Species

Computational STAT3 activity inference reveals its roles in the pancreatic tumor microenvironment

Whole transcriptome signature for prognostic prediction (WTSPP): application of whole transcriptome signature for prognostic prediction in cancer

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