E. Ruppin

Employing RNA editing to engineer personalized tumor-specific neoantigens (editopes)

This paper develops a method to generate tumor-specific neoantigens using RNA editing, demonstrating its ability to create immunogenic epitopes that activate T cells and enhance immunotherapy potential.

Identification of targetable vulnerabilities of PLK1-overexpressing cancers by synthetic dosage lethality

The paper identifies synthetic dosage lethality targets for PLK1-overexpressing cancers using genome-wide screens and validates key hits to show their therapeutic potential.

Chromosome 7 to the rescue: overcoming chromosome 10 loss in gliomas

The paper investigates the co-occurrence of chromosome 10 loss and chromosome 7 gain in gliomas, finding functional rescue interactions on chromosome 7 that may compensate for chromosome 10 loss.

Temporal genomic analysis of melanoma rejection identifies regulators of tumor immune evasion

The paper identifies Mif as a regulator of tumor immune evasion in low intra-tumor heterogeneity melanoma by analyzing single-cell RNA sequencing data and validating in patient data.

Charting the transcriptomic landscape of primary and metastatic cancers in relation to their origin and target normal tissues

The paper compares gene expression in primary and metastatic tumors to their origin and target tissues, finding metastases more resemble target tissues and show reduced cancer hallmark activity.

Robust prediction of patient outcomes with immune checkpoint blockade therapy for cancer using common clinical, pathologic, and genomic features

This study develops a logistic regression model to predict immune checkpoint blockade response and survival in cancer patients using common clinical and genomic features.

Fraction of copy-number alterations significantly predicts survival following immunotherapy in a few cancers

The paper reanalyzes data to assess if tumor aneuploidy score or related metrics predict immunotherapy survival, finding only limited predictive power in a few cancers.

High Density Domain-Focused CRISPR Screens Reveal Novel Epigenetic Regulators of HOX/MEIS Activation in Acute Myeloid Leukemia

The paper identifies SGF29 as a novel chromatin regulator of MEIS1 and AML oncogenes, showing its role in leukemogenesis and potential as a drug target.

Transcriptomic Profiling of Plasma Extracellular Vesicles Enables Reliable Annotation of the Cancer-specific Transcriptome and Molecular Subtype

This study uses deep learning on plasma extracellular vesicle RNA to predict cancer subtypes, monitor treatment effects, and identify gene fusions and neoepitopes without tissue sampling.

Deep characterization of cancer drugs mechanism of action by integrating large-scale genetic and drug screens

DeepTarget integrates genetic and drug screens to predict cancer drugs' mechanisms of action, including primary and secondary targets and specificity, with high accuracy.

Control of alveolar macrophage differentiation by Siah1a/2 ubiquitin ligases limits carcinogen-induced lung adenocarcinoma

This study shows that Siah1a/2 ubiquitin ligases regulate alveolar macrophage differentiation, and their loss promotes lung adenocarcinoma by increasing immature macrophages and pro-tumorigenic inflammation.

Prediction of cancer treatment response from histopathology images through imputed transcriptomics

ENLIGHT-DeepPT predicts cancer treatment response from H&E slides by first imputing transcriptomics and then using that data to predict response across multiple therapies and cancer types.

Transcriptomics based prediction of survival and response to therapy in malignant mesothelioma

The paper identifies a 48-gene prognostic signature and synthetic-lethality profiles predictive of survival and therapy response in mesothelioma using transcriptomic and exomic data from 122 patients.

Melanoma Addiction to GCDH is Mediated by NRF2 Tumor Suppressor Function

This study identifies melanoma addiction to GCDH, showing that GCDH controls NRF2 glutarylation, which limits apoptotic UPR signaling and tumor growth.

Sex biases in cancer and autoimmune disease incidence are strongly positively correlated with mitochondrial gene expression across human tissues

A landscape of synergistic drug combinations in non-small-cell lung cancer

The paper identifies synergistic drug combinations in non-small-cell lung cancer cell lines, finding that synergy often arises from sensitizing resistant models through dual pathway targeting.

Using a recently approved tumor mutational burden biomarker to stratify patients for immunotherapy may introduce a sex bias

The paper investigates if using a high tumor mutational burden (TMB) threshold for immunotherapy selection introduces sex bias, finding significant bias in melanoma but not in other cancers.

Immune determinants of the association between tumor mutational burden and immunotherapy response across cancer types

The paper investigates how immune factors influence the predictive power of tumor mutational burden (TMB) for immunotherapy response across cancer types.

Cross-species identification of cancer-resistance associated genes uncovers their relevance to human cancer risk

The paper identifies cancer-resistance associated genes across species and finds their relevance to human cancer risk through conservation analysis and functional studies.

RNF5 Regulation of RBBP4 Defines Acute Myeloid Leukemia Growth and Susceptibility to Histone Deacetylase Inhibitors

This study shows RNF5 promotes AML growth by regulating RBBP4 and epigenetic pathways, and its inhibition enhances sensitivity to HDAC inhibitors, suggesting it as a therapeutic target and biomarker.

Predicting cancer prognosis and drug response from the tumor microbiome

This study shows that tumor microbial abundances can predict cancer prognosis and drug response, though less effectively than gene expression data.

scRNA-seq analysis of colon and esophageal tumors uncovers abundant microbial reads in myeloid cells undergoing proinflammatory transcriptional alterations

The paper develops a computational pipeline to identify microbial reads in scRNA-seq data and finds that microbial reads are enriched in myeloid cells with proinflammatory transcriptional changes.

Synthetic lethality across normal tissues is strongly associated with cancer risk, onset, and tumor suppressor specificity

The paper quantifies synthetic lethality in normal tissues and links it to cancer risk, onset, and tumor suppressor specificity using GTEx transcriptomics data.

Whole exome precision oncology targeting synthetic lethal vulnerabilities across the tumor transcriptome

This paper predicts patient response to cancer therapies using computationally derived genetic interactions across multiple tumor transcriptomics datasets.

Division of labor between YAP and TAZ in non-small cell lung cancer

This study identifies distinct roles for YAP and TAZ in NSCLC, showing YAP regulates cell cycle and TAZ regulates extracellular matrix, with differential impacts on growth and migration.

Integrated computational and experimental identification of p53, KRAS and VHL mutant selection associated with CRISPR-Cas9 editing

The paper identifies p53, KRAS, and VHL mutations as being selected during CRISPR-Cas9 editing through computational and experimental analysis.

Higher prevalence of homologous recombination-deficiency in lung squamous carcinoma from African Americans

The paper compares genomic features between African American and European American lung cancers, finding higher genomic instability and homologous recombination-deficiency in African American tumors.

Cancer-type specific aneuploidies hard-wire chromosome-wide gene expression patterns of their tissue of origin

The paper shows cancer-type specific aneuploidies correlate with normal tissue gene expression patterns, suggesting they hard-wire chromosome-wide expression levels to support tumorigenesis.

Criticality in Tumor Evolution and Clinical Outcome

The paper analyzes mutation and selection in tumors to show a critical point where mutation load correlates with survival, revealing two opposing regimes and deviations from neutrality in extreme cases.

Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy

The paper predicts synthetic rescue mediators of resistance to targeted and immunotherapy using tumor transcriptomics and survival data from 10,000 TCGA patients, validating predictions through experimental screens.