H. Y. Chang

CoRAL accurately resolves extrachromosomal DNA genomestructures with long-read sequencing

CoRAL improves ecDNA structure reconstruction using long-read sequencing, outperforming short-read methods in simulations and cell-line datasets.

Coordinated inheritance of extrachromosomal DNA species in human cancer cells

This study shows that multiple extrachromosomal DNA species are coordinately inherited in cancer cells through mitotic co-segregation, enabling oncogene cooperation and guiding therapeutic strategies.

Transcriptional immune suppression and upregulation of double stranded DNA damage and repair repertoires in ecDNA-containing tumors

The paper identifies transcriptional correlates of ecDNA in tumors, showing upregulation of DNA repair and downregulation of immune pathways.

Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells

This study investigates chromosome loss in CRISPR-Cas9-engineered T cells and shows a modified manufacturing process reduces it while preserving editing efficacy.

Consensus design and engineering of an efficient and high-yield Peptide Asparaginyl Ligase

The paper designs and engineers a high-yield, efficient recombinant peptide asparaginyl ligase (PAL) by modifying a consensus legumain sequence and applying the LAD hypothesis.

Enhanced Effector Activity of Mediator Kinase Module Deficient CAR-T Cells

This study identifies the Mediator kinase module as a regulator of T cell differentiation and shows that its inhibition enhances effector T cell potency.

Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH

This study introduces CRISPR-CATCH, a method to purify and analyze extrachromosomal DNA, revealing hypomethylation and structural details of ecDNA in cancer cells.

Macrophage inflammatory and regenerative response periodicity is programmed by cell cycle and chromatin state

This study shows that macrophage inflammatory and regenerative responses are phase-dependent on the cell cycle, with S-G2/M phases linked to tissue remodeling and reduced IFNG-induced repolarization.

Principles of ecDNA random inheritance drive rapid genome change and therapy resistance in human cancers

Distinct T cell chromatin landscapes in circulating lymphocytes from patients with systemic sclerosis

This study examines chromatin accessibility in CD4+ T cells from SSc patients on MMF, finding sex and autoantibody-associated epigenetic differences linked to Th2 activation.

EcDNA hubs drive cooperative intermolecular oncogene expression

The paper identifies ecDNA hubs as nuclear structures that drive cooperative oncogene expression through intermolecular enhancer-promoter interactions and shows BET inhibitors can disrupt these hubs and kill cancer cells.

The Autism Risk Factor CHD8 Is a Chromatin Activator and Functionally Dependent on the ERK-MAPK Pathway Effector ELK1

This study identifies CHD8 as a chromatin activator in human neurons that depends on the ERK-MAPK pathway effector ELK1 for its function.

Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection

This study identifies 309 host proteins interacting with SARS-CoV-2 RNA during infection and reveals their roles in virus-induced cell death and mitochondrial dysfunction.

Transient "rest" induces functional reinvigoration and epigenetic remodeling in exhausted CAR-T cells

This study shows that temporarily stopping CAR-T cell signaling can reverse exhaustion and improve their anti-tumor function through transcriptional and epigenetic changes.

Frequent extrachromosomal oncogene amplification drives aggressive tumors

This study shows that extrachromosomal DNA amplification of oncogenes is common in human cancers and is associated with worse patient outcomes.

Atlas of Subcellular RNA Localization Revealed by APEX-seq

APEX-seq maps subcellular RNA localization with nanometer resolution, revealing nuclear transcriptome organization and mitochondrial mRNA pathways.

Clonal replacement of tumor-specific T cells following PD-1 blockade

This study tracks T cell clonal dynamics before and after PD-1 blockade in cancer patients, finding that new T cell clones, not pre-existing ones, expand in response to treatment.