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Human tumors are intricate ecosystems composed of diverse genetic clones and malignant cell states that evolve in a complex tumor micro-environment. Single-cell RNA-sequencing (scRNA-seq) provides a compelling strategy to dissect this intricate biology and has enabled a revolution in our ability to understand tumor biology over the last ten years. Here we reflect on this first decade of scRNA-seq in human tumors and highlight some of the powerful insights gleaned from these studies. We first focus on computational approaches for robustly defining cancer cell states and their diversity and highlight some of the most common patterns of gene expression intra -tumor heterogeneity (eITH) observed across cancer types. We then discuss ambiguities in the field in defining and naming such eITH programs. Finally, we highlight critical developments that will facilitate future research and the broader implementation of these technologies in clinical settings. Over the last 10 years, numerous studies have profiled human tumors by single-cell RNA-seq. In this perspective, Tirosh and Suva describe the cell states most commonly observed in cancer, highlight insights into cancer biology, and discuss challenges and future directions in single-cell analysis. [ABSTRACT FROM AUTHOR]

Background: Multiple glioblastoma studies have described a mesenchymal (MES) state, with each study defining the MES program by distinct sets of genes and highlighting distinct functional associations, including both immune activation and suppression. These variable descriptions complicate our understanding of the MES state and its implications. Here, we hypothesize that there is a range of glioma MES states, possibly reflecting distinct prior states in which a MES program can be induced, and/or distinct mechanisms that induce the MES states in those cells. Methods: We integrated multiple published single-cell and bulk RNA sequencing datasets and MES signatures to define a core MES program that recurs across studies, as well as multiple function-specific MES signatures that vary across MES cells. We then examined the co-occurrence of these signatures and their associations with genetic and microenvironmental features. Results: Based on co-occurrence of MES signatures, we found three main variants of MES states: hypoxia-related (MES-Hyp), astrocyte-related (MES-Ast), and an intermediate state. Notably, the MES states are differentially associated with genetic and microenvironmental features. MES-Hyp is preferentially associated with NF1 deletion, overall macrophage abundance, a high macrophage/microglia ratio, and M2-related macrophages, consistent with previous studies that associated MES with immune suppression. In contrast, MES-Ast is associated with T cell abundance and cytotoxicity, consistent with immune activation through expression of MHC-I/II. Conclusions: Diverse MES states occur in glioblastoma. These states share a subset of core genes but differ primarily in their association with hypoxia vs. astrocytic expression programs, and with immune suppression vs. activation, respectively. [ABSTRACT FROM AUTHOR]

B Correction: Genome Med 14, 106 (2022) b B https://doi.org/10.1186/s13073-022-01109-8 b The original publication of this article [[1]] contained an incorrect version of Fig. 1 are shown in this correction article as figure 1 & 2 respectively, the original article has been updated. [Extracted from the article]

Development of effective targeted cancer therapies is fundamentally limited by our molecular understanding of disease pathogenesis. Diffuse intrinsic pontine glioma (DIPG) is a fatal malignancy of the childhood pons characterized by a unique substitution to methionine in histone H3 at lysine 27 (H3K27M) that results in globally altered epigenetic marks and oncogenic transcription. Through primary DIPG tumor characterization and isogenic oncohistone expression, we show that the same H3K27M mutation displays distinct modes of oncogenic reprogramming and establishes distinct enhancer architecture depending upon both the variant of histone H3 and the cell context in which the mutation occurs. Compared with non-malignant pediatric pontine tissue, we identify and functionally validate both shared and variant-specific pathophysiology. Altogether, we provide a powerful resource of epigenomic data in 25 primary DIPG samples and 5 rare normal pediatric pontine tissue samples, revealing clinically relevant functional distinctions previously unidentified in DIPG. • H3.3K27M and H3.1K27M DIPG tumors exhibit distinct active enhancer profiles • Extensive chromatin studies in primary H3K27M samples reveal oncogenic signaling • Disparate genomic locations of each H3K27M variant disrupt different PRC2 targets • H3K27M remodeling differs between NPCs and OPCs Diffuse intrinsic pontine glioma is a lethal pediatric brain cancer characterized by H3K27M histone mutation. Nagaraja et al. characterize a large cohort of rare primary tumors and normal pontine tissue to reveal active regulatory element heterogeneity dependent upon the histone variant and cell context in which the mutation occurs. [ABSTRACT FROM AUTHOR]

H3K27M mutations resulting in epigenetic dysfunction are frequently observed in diffuse intrinsic pontine glioma (DIPGs), an incurable pediatric cancer. We conduct a CRISPR screen revealing that knockout of KDM1A encoding lysine-specific demethylase 1 (LSD1) sensitizes DIPG cells to histone deacetylase (HDAC) inhibitors. Consistently, Corin, a bifunctional inhibitor of HDACs and LSD1, potently inhibits DIPG growth in vitro and in xenografts. Mechanistically, Corin increases H3K27me3 levels suppressed by H3K27M histones, and simultaneously increases HDAC-targeted H3K27ac and LSD1-targeted H3K4me1 at differentiation-associated genes. Corin treatment induces cell death, cell-cycle arrest, and a cellular differentiation phenotype and drives transcriptional changes correlating with increased survival time in DIPG patients. These data suggest a strategy for treating DIPG by simultaneously inhibiting LSD1 and HDACs. • A CRISPR screen for HDAC inhibitor sensitizers in DIPG identifies KDM1A (LSD1) • Corin, a dual inhibitor of LSD1 and HDACs, inhibits DIPG growth in vitro and in vivo • Corin alters histone modifications to promote differentiation and block cell cycle • A Corin-induced gene expression signature correlates with prolonged survival in DIPG Anastas et al. show that inhibition of LSD1 sensitizes diffuse intrinsic pontine glioma (DIPG) cells to HDAC inhibition and that Corin, which inhibits both LSD1 and HDACs, potently suppresses DIPG cell growth. A Corin-induced gene expression profile correlates with improved survival of DIPG patients. [ABSTRACT FROM AUTHOR]