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Open AccessAuthor Correction: Liquid biopsy epigenomic profiling for cancer subty**
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Open AccessAuthor Correction: Comprehensive genomic characterization of HER2-low and HER2-0 breast cancer
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Open AccessComprehensive genomic characterization of HER2-low and HER2-0 breast cancer
The molecular underpinnings of HER2-low and HER2-0 (IHC 0) breast tumors remain poorly defined. Using genomic findings from 1039 patients with HER2-negative metastatic breast cancer undergoing next-generation ...
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Open AccessLiquid biopsy epigenomic profiling for cancer subty**
Although circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes...
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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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Open AccessAndrogen receptor reprogramming demarcates prognostic, context-dependent gene sets in primary and metastatic prostate cancer
The androgen receptor (AR) is a prostate master transcription factor. It binds to genetic enhancers, where it regulates gene activity and plays a fundamental role in prostate pathophysiology. Previous work has...
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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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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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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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Open AccessIntegrative analyses of single-cell transcriptome and regulome using MAESTRO
We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO), a comprehensive open-source computational workflow (http://github.com/liulab-dfci/MAESTRO)...
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Open AccessTargetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models
T- and NK-cell lymphomas (TCL) are a heterogenous group of lymphoid malignancies with poor prognosis. In contrast to B-cell and myeloid malignancies, there are few preclinical models of TCLs, which has hampere...
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Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity
A study investigating the mechanisms underlying lateral inhibition and lineage plasticity in the mouse small intestine crypts in vivo finds that crypt cells maintain a permissive chromatin state upon which a tran...
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Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification
Detailed analysis of DNase-seq protocols reveals the importance of choosing the right enzyme concentration and fragment length and cautions that many transcription factor footprints may represent cutting bias.
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Open AccessA closer look into DNase I hypersensitivity
