SMuRF: portable and accurate ensemble prediction of somatic mutations.

SUMMARY: Somatic Mutation calling method using a Random Forest (SMuRF) integrates predictions and auxiliary features from multiple somatic mutation callers using a supervised machine learning approach. SMuRF is trained on community-curated matched tumor and normal whole genome sequencing data. SMuRF predicts both SNVs and indels with high accuracy in genome or exome-level sequencing data. Furthermore, the method is robust across multiple tested cancer types and predicts low allele frequency variants with high accuracy. In contrast to existing ensemble-based somatic mutation calling approaches, SMuRF works out-of-the-box and is orders of magnitudes faster. AVAILABILITY AND IMPLEMENTATION: The method is implemented in R and available at https://github.com/skandlab/SMuRF. SMuRF operates as an add-on to the community-developed bcbio-nextgen somatic variant calling pipeline. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A pan-cancer metabolic atlas of the tumor microenvironment.

Tumors are heterogeneous cellular environments with entwined metabolic dependencies. Here, we use a tumor transcriptome deconvolution approach to profile the metabolic states of cancer and non-cancer (stromal) cells in bulk tumors of 20 solid tumor types. We identify metabolic genes and processes recurrently altered in cancer cells across tumor types, highlighting pan-cancer upregulation of deoxythymidine triphosphate (dTTP) production. In contrast, the tryptophan catabolism rate-limiting enzymes IDO1 and TDO2 are highly overexpressed in stroma, raising the hypothesis that kynurenine-mediated suppression of antitumor immunity may be predominantly constrained by the stroma. Oxidative phosphorylation is the most upregulated metabolic process in cancer cells compared to both stromal cells and a large atlas of cancer cell lines, suggesting that the Warburg effect may be less pronounced in cancer cells in vivo. Overall, our analysis highlights fundamental differences in metabolic states of cancer and stromal cells inside tumors and establishes a pan-cancer resource to interrogate tumor metabolism.

Pan-Cancer Analysis of Ligand-Receptor Cross-talk in the Tumor Microenvironment.

Signaling between cancer and nonmalignant (stromal) cells in the tumor microenvironment (TME) is a key to tumor progression. Here, we deconvoluted bulk tumor transcriptomes to infer cross-talk between ligands and receptors on cancer and stromal cells in the TME of 20 solid tumor types. This approach recovered known transcriptional hallmarks of cancer and stromal cells and was concordant with single-cell, in situ hybridization and IHC data. Inferred autocrine cancer cell interactions varied between tissues but often converged on Ephrin, BMP, and FGFR-signaling pathways. Analysis of immune checkpoints nominated interactions with high levels of cancer-to-immune cross-talk across distinct tumor types. Strikingly, PD-L1 was found to be highly expressed in stromal rather than cancer cells. Overall, our study presents a new resource for hypothesis generation and exploration of cross-talk in the TME. SIGNIFICANCE: This study provides deconvoluted bulk tumor transcriptomes across multiple cancer types to infer cross-talk in the tumor microenvironment.