Bento: a toolkit for subcellular analysis of spatial transcriptomics data.

The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell-cell interactions, and spatial expression patterns, they are limited to the multicellular scale. We present Bento, a Python toolkit that takes advantage of single-molecule information to enable spatial analysis at the subcellular scale. Bento ingests molecular coordinates and segmentation boundaries to perform three analyses: defining subcellular domains, annotating localization patterns, and quantifying gene-gene colocalization. We demonstrate MERFISH, seqFISH + , Molecular Cartography, and Xenium datasets. Bento is part of the open-source Scverse ecosystem, enabling integration with other single-cell analysis tools.

Computational cell-cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment.

Complex networks of cell-cell interactions (CCIs) within the tumor microenvironment (TME) play a crucial role in cancer persistence. These communication axes represent prime targets for therapeutic intervention, but our incomplete understanding of the cellular heterogeneity and interacting partners within the TME remains a stubborn barrier to complete drug responses. This review outlines recent advances in the study of CCIs that leverage single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) technologies that can clarify TME dynamics. We anticipate that these strategies will promote discovery of CCIs critical to the tumor-immune interface and will, by extension, expand the repertoire of druggable tumor biomarkers.

Chromatin landscapes reveal developmentally encoded transcriptional states that define human glioblastoma.

Glioblastoma is an incurable brain cancer characterized by high genetic and pathological heterogeneity. Here, we mapped active chromatin landscapes with gene expression, whole exomes, copy number profiles, and DNA methylomes across 44 patient-derived glioblastoma stem cells (GSCs), 50 primary tumors, and 10 neural stem cells (NSCs) to identify essential super-enhancer (SE)-associated genes and the core transcription factors that establish SEs and maintain GSC identity. GSCs segregate into two groups dominated by distinct enhancer profiles and unique developmental core transcription factor regulatory programs. Group-specific transcription factors enforce GSC identity; they exhibit higher activity in glioblastomas versus NSCs, are associated with poor clinical outcomes, and are required for glioblastoma growth in vivo. Although transcription factors are commonly considered undruggable, group-specific enhancer regulation of the MAPK/ERK pathway predicts sensitivity to MEK inhibition. These data demonstrate that transcriptional identity can be leveraged to identify novel dependencies and therapeutic approaches.

Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups.

There is a pressing need to identify therapeutic targets in tumors with low mutation rates such as the malignant pediatric brain tumor medulloblastoma. To address this challenge, we quantitatively profiled global proteomes and phospho-proteomes of 45 medulloblastoma samples. Integrated analyses revealed that tumors with similar RNA expression vary extensively at the post-transcriptional and post-translational levels. We identified distinct pathways associated with two subsets of SHH tumors, and found post-translational modifications of MYC that are associated with poor outcomes in group 3 tumors. We found kinases associated with subtypes and showed that inhibiting PRKDC sensitizes MYC-driven cells to radiation. Our study shows that proteomics enables a more comprehensive, functional readout, providing a foundation for future therapeutic strategies.

An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data.

Single-cell RNA sequencing (scRNA-seq) has emerged as a popular method to profile gene expression at the resolution of individual cells. While there have been methods and software specifically developed to analyze scRNA-seq data, they are most accessible to users who program. We have created a scRNA-seq clustering analysis GenePattern Notebook that provides an interactive, easy-to-use interface for data analysis and exploration of scRNA-Seq data, without the need to write or view any code. The notebook provides a standard scRNA-seq analysis workflow for pre-processing data, identification of sub-populations of cells by clustering, and exploration of biomarkers to characterize heterogeneous cell populations and delineate cell types.

An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays.

Illumina Infinium DNA methylation arrays are a cost-effective technology to measure DNA methylation at CpG sites genome-wide and across cohorts of normal and cancer samples. While copy number alterations are commonly inferred from array-CGH, SNP arrays, or whole-genome DNA sequencing, Illumina Infinium DNA methylation arrays have been shown to detect copy number alterations at comparable sensitivity. Here we present an accessible, interactive GenePattern notebook for the analysis of copy number variation using Illumina Infinium DNA methylation arrays. The notebook provides a graphical user interface to a workflow using the R/Bioconductor packages minfi and conumee. The environment allows analysis to be performed without the installation of the R software environment, the packages and dependencies, and without the need to write or manipulate code.

Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States.

The systematic sequencing of the cancer genome has led to the identification of numerous genetic alterations in cancer. However, a deeper understanding of the functional consequences of these alterations is necessary to guide appropriate therapeutic strategies. Here, we describe Onco-GPS (OncoGenic Positioning System), a data-driven analysis framework to organize individual tumor samples with shared oncogenic alterations onto a reference map defined by their underlying cellular states. We applied the methodology to the RAS pathway and identified nine distinct components that reflect transcriptional activities downstream of RAS and defined several functional states associated with patterns of transcriptional component activation that associates with genomic hallmarks and response to genetic and pharmacological perturbations. These results show that the Onco-GPS is an effective approach to explore the complex landscape of oncogenic cellular states across cancers, and an analytic framework to summarize knowledge, establish relationships, and generate more effective disease models for research or as part of individualized precision medicine paradigms.