Resources

Mitsiades and colleagues utilize functional genomics data in over 700 cancer cell lines, to identify genes with preferentially essential functions in multiple myeloma, which may represent targets for precision medicine strategies.

Joyce and colleagues use bulk and single-cell profiling of T cell phenotypes in human samples from primary brain tumors and brain metastases as a resource for understanding the biology and therapeutic relevance of the brain tumor microenvironment.

Snijder and colleagues use ex vivo pharmacoscopy and bone marrow composition profiling in a cohort of patients with multiple myeloma to identify tailored therapeutic sensitivities and stratify the cohort into three microenvironmental PhenoGroups.

Perou and colleagues perform genomic, transcriptomic and epigenetic analyses on pairs of primary and metastatic breast tumors, detecting subtype switching and changes in immune signatures and DNA methylation patterns associated with metastasis.

Baek and colleagues present a proteogenomic analysis of 196 patients with pancreatic adenocarcinoma in an Asian population, identifying subtypes with invasive and proliferative features or immunogenic features, as a resource for future studies.

Wang et. al. perform single-cell and spatial analyses of paired primary and recurrent samples from patients receiving standard-of-care therapy for GBM and find changes in tumor signaling pathways and the microenvironment with targetable potential.

Dubois and colleagues assemble a large cohort of human pediatric high-grade glioma samples, identifying patterns of simple and complex structural variants and characterizing their role in tumor development and evolution.

Skokos and colleagues characterize human early-stage clear cell renal cell carcinoma with single-cell ATAC-seq and RNA-seq, identifying a spectrum of NFκB-promoted T cell dysfunction in the microenvironment and defining a pro-apoptotic signature.

Using genome-wide bisulfite sequencing of acute lymphoblastic leukemia subtypes, cell lines and healthy cells, Hetzel et. al. find that unlike most cancers, ALL has a highly methylated genome, which points to a distinct mode of epigenome regulation in this cancer type.

Welm and colleagues present a biobank of human-derived xenografts and organoids and demonstrate its value for high-throughput drug screening and applied precision medicine.

Zhang and colleagues analyzed patients with lung cancer treated with anti-PD-1 with single-cell methods, finding the presence of precursor exhausted T cells in responders that accumulated through local expansion and clonal revival from peripheral T cells.

Lehtiö and colleagues perform proteogenomic analysis of non-small cell lung cancer and identify molecular subtypes with distinct immune-evasion mechanisms and therapeutic targets and validate their classification method in separate clinical cohorts.

Robbins and colleagues develop and test a machine learning neoantigen ranking model using experimentally validated neoantigens from human tumors, providing a resource of targetable neoantigens for future immunotherapies.

Using single-cell RNA sequencing, CyTOF and multiplex immunohistochemistry, Steele et al. survey the immune landscape in pancreatic cancers, adjacent tissue and blood, observing heterogeneous immune checkpoint receptor expression within patients.

Ferrando and colleagues analyze matched diagnostic and relapsed acute lymphocytic leukemia by whole-genome sequencing, and perform in vitro genome-wide CRISPR screens, to examine alterations associated with chemotherapy resistance.

Ghorani et al. use a multiomics approach to characterize the effect of tumour mutational burden on the differentiation of CD4 and CD8 T cell subpopulations in non-small cell lung cancer.

Marra and colleagues describe POG570, a pan-cancer, whole-genome, transcriptome and clinical dataset stressing the molecular interactions in advanced and post-therapy cancer patients.

Simpson et al. present a living biobank of 38 small cell lung cancer circulating-tumor-cell-derived explants and use them to study tumor heterogeneity. These models can be used further to study SCLC biology, progression and therapy responses.

Golub and colleagues tested thousands of drugs not originally developed for oncology across 578 human cancer cell lines, revealing growth-inhibitory effects and providing a resource to identify drugs with the potential to be repurposed for cancer.