Resources

Zeng et al. analyzed cfDNA methylation and fragmentomic data from 1,294 patient plasma samples across 14 major cancer types to present a comprehensive landscape of pancancer and cancer-specific cell-free DNA methylation and fragmentomic features.

Pilcher et al. present a single-cell transcriptomics-based immune atlas of participants with newly diagnosed multiple myeloma, reporting on the association of cell types, gene expression and intercellular interactions with disease progression phenotypes.

Zhao et al. used single-cell and spatial multiomics data analysis of human and mouse lung adenocarcinoma tumors and cell lines to reveal TP53 mutation-associated changes in cancer cells and their microenvironment.

Han et al. present TabulaTIME, a multicancer scRNA-seq resource, and report enrichment of extracellular matrix-related CTHRC1⁺ cancer-associated fibroblasts in proximity to SLPI⁺ macrophages, creating a profibrotic ecotype associated with tumor immunity.

Tyler et al. introduce a curated collection of 124 multicancer, single-cell RNA-sequencing datasets with 2,836 samples and present recurrent cancer cell expression metaprograms, quantifying context-dependent expression and proliferation across cell and cancer types.

Bennett et al. conducted a population-based study in adolescents and young adults with gliomas, revealing the specific molecular alterations and identifying potential subclassifications and targets.

Sato and colleagues present a biobank of patient-derived SCLC organoids, conducting a comprehensive genome and transcriptome profiling that reveals the existence of NE and non-NE subtypes with distinct molecular dependencies.

Snyder and colleagues present a comprehensive multiomic atlas of normal mucosal, benign polyps and dysplastic polyps from six persons with familial adenomatous polyposis, comprising transcriptomic, proteomic, metabolomic and lipidomic datasets.

Ding and colleagues use bulk, single-cell and single-nucleus multi-omics together with spatial transcriptomics and multiplex imaging of clinical tumor samples to characterize gene expression and chromatin accessibility of breast cancer lineages.

Qui et al. perform co-detection by indexing profiling of 401 hepatocellular carcinoma patient samples and identify a role for vimentin^high macrophages in instructing an immune-suppressive microenvironment by enhancing the suppressive activity of regulatory T cells via interleukin-1β.

Dong et al. present an integrative proteogenomic analysis of high-risk prostate cancer samples from a cohort of Chinese patients and highlight potential therapeutic vulnerabilities and diagnostic markers.

Liang and colleagues establish a high-quality protein expression resource for 8,000 The Cancer Genome Atlas patient samples and 900 Cancer Cell Line Encyclopedia cell lines for approximately 450 proteins, which they use to identify synthetic lethality pairs and metastasis markers.

Krönke and colleagues present a multiomic resource of plasma cell malignancies, including multiple myeloma, that comprises phosphoproteomics, RNA and DNA sequencing and provides insights into cancer type biology and candidate therapeutic targets.

Shao and colleagues present a multiomic analysis of breast tumor samples from Chinese patients, consisting of genomic, transcriptomic, proteomic, metabolomic, radiomic and digital pathology data.

Ganesan and colleagues characterize T cell clonality and transcriptomes at the single-cell level in pediatric brain tumor samples, providing insights into existing tumor neoantigens and T cell responses and the potential for effective immunotherapy.

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.