Alex Kentsis

Recurrent non-canonical proteoforms in acute myeloid leukemia identified by integrative proteogenomics

The paper identifies recurrent non-canonical proteoforms in AML using integrative proteogenomics, revealing 5,849 unannotated proteoforms, including 1,987 with no homology to annotated proteins.

Histone deacetylase activity limits the response to EZH2 inhibition-based therapy in epithelioid sarcoma and is targetable by epigenetic combination

This paper identifies HDAC inhibition as a strategy to overcome resistance to EZH2 inhibitors in INI1-deficient epithelioid sarcoma by restoring H3K27 acetylation and enhancing therapeutic response.

ER-tethering directs TREX1 penetration of a BAF-dependent barrier at micronuclei

The paper identifies BAF as a barrier that restricts TREX1 access to micronuclei, explaining the need for ER-tethering to enable TREX1 entry and suppress cGAS activation.

A transposase-derived gene required for human brain development

This study identifies PGBD5 as a transposase-derived gene essential for brain development in humans and mice, with deficiency causing intellectual disability and seizures.

Modular platform for therapeutic drug delivery using trifunctional bio-orthogonal macromolecular conjugates

The paper develops a modular platform for synthesizing bio-orthogonal macromolecular conjugates (BMCs) to enable targeted delivery of macromolecular therapeutics with improved efficiency and specificity.

End-to-end proteogenomics for discovery of cryptic and non-canonical cancer proteoforms using long-read transcriptomics and multi-dimensional proteomics

The paper introduces ProteomeGenerator3, an end-to-end proteogenomics method that detects non-canonical proteoforms in cancer using long-read transcriptomics and multi-dimensional proteomics.

Epigenetic targeting of PGBD5-dependent DNA damage in SMARCB1-deficient sarcomas

The paper identifies ATR as a target for combination EZH2 epigenetic therapy in SMARCB1-deficient sarcomas, showing that EZH2 inhibition promotes DNA damage via PGBD5, and that ATR inhibition enhances therapeutic responses.

The piggyBac derived transposase 5 (PGBD5) can interact with human piggyBac-like elements

This paper shows human PGBD5 can interact with four species of piggyBac-like elements and promote their chromosomal integration, similar to insect PB.

MOZ and HBO1 Histone Acetyltransferase Complexes Are Molecular Dependencies and Therapeutic Targets in NUP98-Rearranged Acute Myeloid Leukemia

This study identifies MOZ and HBO1 as molecular dependencies in NUP98-rearranged AML, showing their inhibition reduces leukemic burden and synergizes with Menin inhibitors.

Integrative proteogenomics using ProteomeGenerator2

The paper introduces ProteomeGenerator2, a tool that integrates genomic and transcriptomic data to generate proteomes including non-canonical variants, and benchmarks it using synthetic and biological data.

Analysis of DNA transposition by DNA transposases in human cells

The paper investigates DNA transposition activity of PGBD5 in human cells, showing that overexpression causes DNA damage and challenges previous findings of transposition.

Integrative analysis reveals unique features of the Smc5/6 complex

The paper presents an integrative structural analysis of the Smc5/6 complex in budding yeast, revealing unique structural features and functional interactions among its subunits.

Optimized cross-linking mass spectrometry for in situ interaction proteomics

This paper optimizes cross-linking mass spectrometry (XL-MS) for in situ protein interaction mapping using DSSO cross-linkers, CSM score calibration, and protease combinations, improving interaction density and coverage.

ProteomeGenerator: A framework for comprehensive proteomics based on de novo transcriptome assembly and high-accuracy peptide mass spectral matching

ProteomeGenerator enables sample-specific proteome discovery by integrating transcriptome sequencing and high-accuracy mass spectrometry, identifying non-canonical protein isoforms and improving proteogenomic analysis.

High sensitivity quantitative proteomics using accumulated ion monitoring and automated multidimensional nano-flow chromatography

This paper develops a high-sensitivity quantitative proteomics method using accumulated ion monitoring and automated multidimensional nano-flow chromatography, achieving sub-attomolar detection limits and accurate quantification of protein abundance and phosphorylation.

Towards comprehensive and quantitative proteomics for diagnosis and therapy of human disease

The paper discusses how high-resolution mass spectrometry and chromatography can improve proteomics for diagnosing and treating diseases, with a focus on phosphorylation analysis.

Forward genetic screen of human transposase genomic rearrangements

This study uses a forward genetic screen to identify genomic rearrangements caused by the human transposase PGBD5, revealing specific signal sequences that serve as substrates for genomic remodeling.

Genomics of primary chemoresistance and remission induction failure in pediatric and adult acute myeloid leukemia

The paper investigates genetic factors contributing to primary chemoresistance in AML using targeted sequencing of 670 genes in 107 AML cases, identifying mutations and overexpressed genes but finding they only partially explain resistance.

Genomic DNA transposition induced by human PGBD5

This study identifies PGBD5 as a human gene capable of inducing DNA transposition in human cells, with specific sequence preferences and conserved transposase activity.