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Article
Open AccessLoss of Kmt2c or Kmt2d drives brain metastasis via KDM6A-dependent upregulation of MMP3
KMT2C and KMT2D, encoding histone H3 lysine 4 methyltransferases, are among the most commonly mutated genes in triple-negative breast cancer (TNBC). However, how these mutations may shape epigenomic and transcrip...
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Article
KDM6A epigenetically regulates subtype plasticity in small cell lung cancer
Small cell lung cancer (SCLC) exists broadly in four molecular subtypes: ASCL1, NEUROD1, POU2F3 and Inflammatory. Initially, SCLC subtypes were thought to be mutually exclusive, but recent evidence shows intra...
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Protocol
Universal NicE-Seq: A Simple and Quick Method for Accessible Chromatin Detection in Fixed Cells
Genome-wide accessible chromatin sequencing and identification has enabled deciphering the epigenetic information encoded in chromatin, revealing accessible promoters, enhancers, nucleosome positioning, transc...
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Article
Non-muscle-invasive micropapillary bladder cancer has a distinct lncRNA profile associated with unfavorable prognosis
Molecular subty** of bladder cancer has revealed luminal tumors generally have a more favourable prognosis. However, some aggressive forms of variant histology, including micropapillary, are often classified...
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Article
Open AccessMYC drives aggressive prostate cancer by disrupting transcriptional pause release at androgen receptor targets
c-MYC (MYC) is a major driver of prostate cancer tumorigenesis and progression. Although MYC is overexpressed in both early and metastatic disease and associated with poor survival, its impact on prostate tran...
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Protocol
High-Resolution ATAC-Seq Analysis of Frozen Clinical Tissues
The ATAC-seq method enables the genome-wide analysis of accessible chromatin revealing transcriptionally active and poised regulatory elements. The ATAC-seq analysis of clinical specimens at a single-cell reso...
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Article
FGFR-inhibitor-mediated dismissal of SWI/SNF complexes from YAP-dependent enhancers induces adaptive therapeutic resistance
How cancer cells adapt to evade the therapeutic effects of drugs targeting oncogenic drivers is poorly understood. Here we report an epigenetic mechanism leading to the adaptive resistance of triple-negative b...
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Article
Open AccessSubtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer
Neuroendocrine carcinomas (NEC) are tumors expressing markers of neuronal differentiation that can arise at different anatomic sites but have strong histological and clinical similarities. Here we report the c...
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Article
Reprogramming of the esophageal squamous carcinoma epigenome by SOX2 promotes ADAR1 dependence
Esophageal squamous cell carcinomas (ESCCs) harbor recurrent chromosome 3q amplifications that target the transcription factor SOX2. Beyond its role as an oncogene in ESCC, SOX2 acts in development of the squa...
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Article
Open AccessReprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer
Lineage plasticity, the ability of a cell to alter its identity, is an increasingly common mechanism of adaptive resistance to targeted therapy in cancer. An archetypal example is the development of neuroendoc...
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Article
CDK4/6 inhibition reprograms the breast cancer enhancer landscape by stimulating AP-1 transcriptional activity
Pharmacologic inhibitors of cyclin-dependent kinases 4 and 6 (CDK4/6) were designed to induce cancer cell cycle arrest. Recent studies have suggested that these agents also exert other effects, influencing can...
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Article
Open AccessTranscriptomic analysis of micropapillary high grade T1 urothelial bladder cancer
No consensus currently exist on the optimal treatment of patients with high-risk nonmuscle invasive (HGT1) micropapillary variant of bladder cancer (MPBC). Transcripsome analysis may allow stratification of MP...
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Article
Open AccessClonal tracing reveals diverse patterns of response to immune checkpoint blockade
Immune checkpoint blockade (ICB) therapy has improved patient survival in a variety of cancers, but only a minority of cancer patients respond. Multiple studies have sought to identify general biomarkers of IC...
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Article
Open AccessUniversal NicE-seq for high-resolution accessible chromatin profiling for formaldehyde-fixed and FFPE tissues
Accessible chromatin plays a central role in gene expression and chromatin architecture. Current accessible chromatin approaches depend on limited digestion/cutting and pasting adaptors at the accessible DNA, ...
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Article
Prostate cancer reactivates developmental epigenomic programs during metastatic progression
Epigenetic processes govern prostate cancer (PCa) biology, as evidenced by the dependency of PCa cells on the androgen receptor (AR), a prostate master transcription factor. We generated 268 epigenomic dataset...
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Article
FiTAc-seq: fixed-tissue ChIP-seq for H3K27ac profiling and super-enhancer analysis of FFPE tissues
Fixed-tissue ChIP-seq for H3K27 acetylation (H3K27ac) profiling (FiTAc-seq) is an epigenetic method for profiling active enhancers and promoters in formalin-fixed, paraffin-embedded (FFPE) tissues. We previous...
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Article
Open AccessChromatin accessibility promotes hematopoietic and leukemia stem cell activity
Chromatin organization is a highly orchestrated process that influences gene expression, in part by modulating access of regulatory factors to DNA and nucleosomes. Here, we report that the chromatin accessibil...
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Article
Publisher Correction: Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Article
Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors
Most pancreatic neuroendocrine tumors (PNETs) do not produce excess hormones and are therefore considered ‘non-functional’1–3. As clinical behaviors vary widely and distant metastases are eventually lethal2,4, bi...
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Article
Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles
Fixed-tissue chromatin immunoprecipitation sequencing (FiT-seq) enables accurate detection of histone marks on chromatin extracted from formalin-fixed paraffin-embedded (FFPE) tissue samples.
