R. Beroukhim

A compendium of Amplification-Related Gain Of Sensitivity (ARGOS) genes in human cancer

The paper identifies ARGOS genes, which are amplified in cancer, have low expression relative to copy number, and are toxic when overexpressed, and validates several as pan-cancer targets.

Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries

The paper identifies ancestry-related biases in CRISPR experiments caused by germline variants, showing disproportionate effects in cell models from recent African descent.

Aberrant DNA repair is a vulnerability in histone H3.3-mutant brain tumors

The paper identifies aberrant DNA repair as a vulnerability in H3.3-mutant brain tumors, showing that PNKP-mediated repair is specific to mutant cells and offers therapeutic potential.

Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

This study characterizes intra-tumor heterogeneity across 2,658 human cancer genomes, identifying subclonal mutations and evolutionary patterns across 38 cancer types.

DNA-based copy number analysis confirms genomic evolution of PDX models

The paper reassesses genomic evolution in PDX models using DNA-based copy number profiles, finding significant genomic divergence between primary tumors and PDXs across passages.

Selective vulnerability of aneuploid human cancer cells to inhibition of the spindle assembly checkpoint

This study identifies aneuploid cancer cells as more vulnerable to spindle assembly checkpoint (SAC) inhibition and explores the underlying mechanisms.

Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities

The paper identifies LOH of essential genes as a class of non-driver cancer vulnerabilities by showing allele-specific inactivation can selectively kill cancer cells.

The UTX Tumor Suppressor Directly Senses Oxygen to Control Chromatin and Cell Fate

The paper shows that KDM6A, an H3K27 histone demethylase, is oxygen-sensitive and its inactivation under hypoxia affects chromatin and cell fate.

Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition

This study identifies SMARCB1 loss as critical for RMC survival and shows proteasome inhibition as a potential therapeutic strategy.

The evolutionary history of 2,658 cancers

This study uses whole-genome sequencing of cancer samples to reconstruct the evolutionary history of 39 cancer types, identifying early and late-stage mutational patterns and driver genes.

Patient-derived xenografts undergo murine-specific tumor evolution

This study shows that PDX tumors acquire new genomic changes over passages, differ from human tumors, and affect drug responses.