J. S. Boehm

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.

Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal

This study compares CRISPR-Cas9 and RNAi screens to identify cancer vulnerabilities, finding that RNAi better detects pan-dependencies while CRISPR identifies more dependencies overall.

Targeting TRIP13 in Wilms Tumor with Nuclear Export Inhibitors

This study identifies XPO1 inhibition with selinexor as a potential therapy for favorable histology Wilms tumors, showing synergy with doxorubicin in preclinical models.

Cell Painting predicts impact of lung cancer variants

The paper uses Cell Painting to predict the functional impact of lung cancer variants by analyzing cell morphology at the single-cell level.

Phosphate dysregulation via the XPR1:KIDINS220 protein complex is a therapeutic vulnerability in ovarian cancer

The paper identifies XPR1 and KIDINS220 as therapeutic targets in ovarian cancer by showing their role in phosphate dysregulation leading to cell death.

Global computational alignment of tumor and cell line transcriptional profiles

The paper develops an unsupervised alignment method to compare tumor and cell line transcriptional profiles, revealing differences in similarity across cancer types and identifying cell lines with distinct transcriptional states.

Gene expression has more power for predicting in vitro cancer cell vulnerabilities than genomics

This study compares DNA- and expression-based models for predicting cancer cell viability and finds expression models are more accurate and interpretable.

Non-oncology drugs are a source of previously unappreciated anti-cancer activity

The paper identifies non-oncology drugs with anti-cancer activity across 578 cancer cell lines using PRISM, finding that many drugs selectively inhibit cancer cells based on molecular features.

Agreement between two large pan-cancer CRISPR-Cas9 gene dependency datasets

This study compares two large pan-cancer CRISPR-Cas9 screens, finding high concordance in gene dependencies despite differences in protocols and reagents.

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.

Expanding discovery from cancer genomes by integrating protein network analyses with in vivo tumorigenesis assays

The paper develops a method to identify new cancer genes by integrating protein network analysis with in vivo tumorigenesis assays, finding 62 new candidates and validating two in patient data.

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.