Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells

Developmental fate decisions are dictated by master transcription factors (TFs) that interact with cis-regulatory elements to direct transcriptional programs. Certain malignant tumors may also depend on cellular hierarchies reminiscent of normal development but superimposed on underlying genetic aberrations. In glioblastoma (GBM), a subset of stem-like tumor-propagating cells (TPCs) appears to drive tumor progression and underlie therapeutic resistance, yet remain poorly understood. Here, we identify a core set of neurodevelopmental TFs (POU3F2, SOX2, SALL2, OLIG2) essential for GBM propagation. These TFs coordinately bind and activate TPC-specific regulatory elements, and are sufficient to fully reprogram differentiated GBM cells to ‘induced’ TPCs, recapitulating the epigenetic landscape and phenotype of native TPCs. We reconstruct a network model that highlights critical interactions and identifies novel therapeutic targets for eliminating TPCs. Our study establishes the epigenetic basis of a developmental hierarchy in GBM, provides detailed insight into underlying gene regulatory programs, and suggests attendant therapeutic strategies

Genetic and Epigenetic Fine-Mapping of Causal Autoimmune Disease Variants

Summary Genome-wide association studies have identified loci underlying human diseases, but the causal nucleotide changes and mechanisms remain largely unknown. Here we developed a fine-mapping algorithm to identify candidate causal variants for 21 autoimmune diseases from genotyping data. We integrated these predictions with transcription and cis-regulatory element annotations, derived by mapping RNA and chromatin in primary immune cells, including resting and stimulated CD4+ T-cell subsets, regulatory T-cells, CD8+ T-cells, B-cells, and monocytes. We find that ~90% of causal variants are noncoding, with ~60% mapping to immune-cell enhancers, many of which gain histone acetylation and transcribe enhancer-associated RNA upon immune stimulation. Causal variants tend to occur near binding sites for master regulators of immune differentiation and stimulus-dependent gene activation, but only 10–20% directly alter recognizable transcription factor binding motifs. Rather, most noncoding risk variants, including those that alter gene expression, affect non-canonical sequence determinants not well-explained by current gene regulatory models

ERK positive feedback regulates a widespread network of tyrosine phosphorylation sites across canonical T cell signaling and actin cytoskeletal proteins in Jurkat T cells.

Competing positive and negative signaling feedback pathways play a critical role in tuning the sensitivity of T cell receptor activation by creating an ultrasensitive, bistable switch to selectively enhance responses to foreign ligands while suppressing signals from self peptides. In response to T cell receptor agonist engagement, ERK is activated to positively regulate T cell receptor signaling through phosphorylation of Ser(59) Lck. To obtain a wide-scale view of the role of ERK in propagating T cell receptor signaling, a quantitative phosphoproteomic analysis of 322 tyrosine phosphorylation sites by mass spectrometry was performed on the human Jurkat T cell line in the presence of U0126, an inhibitor of ERK activation. Relative to controls, U0126-treated cells showed constitutive decreases in phosphorylation through a T cell receptor stimulation time course on tyrosine residues found on upstream signaling proteins (CD3 chains, Lck, ZAP-70), as well as downstream signaling proteins (VAV1, PLCγ1, Itk, NCK1). Additional constitutive decreases in phosphorylation were found on the majority of identified proteins implicated in the regulation of actin cytoskeleton pathway. Although the majority of identified sites on T cell receptor signaling proteins showed decreases in phosphorylation, Tyr(598) of ZAP-70 showed elevated phosphorylation in response to U0126 treatment, suggesting differential regulation of this site via ERK feedback. These findings shed new light on ERK's role in positive feedback in T cell receptor signaling and reveal novel signaling events that are regulated by this kinase, which may fine tune T cell receptor activation

Quantitative phosphoproteomic analysis of proteins associated with the KEGG TCR signaling pathway.

<p>Depicted is a SILAC heatmap representation of temporal changes in tyrosine phosphorylation of proteins associated with the KEGG TCR signaling pathway. Heatmaps were calculated from the averages of four biological replicate experiments. SILAC ratios between U0126-treated and control DMSO-treated Jurkat T cells are represented for each phosphopeptide and time point. A white dot within the SILAC heatmaps indicate a statistically significant difference (q value <0.02) in the comparison between U0126-treated and control SILAC ratios for that time point. Abbreviations: GSK3 beta, Glycogen synthase kinase 3 beta; PI3K alpha, Phosphatidylinositol 3 kinase regulatory subunit, alpha; SHP-2, Protein tyrosine phosphatase, nonreceptor type 11.</p

Quantitative phosphoproteomic analysis of proteins implicated in integrin signaling.

<p>Heatmaps were calculated from the averages of four biological replicate experiments. White dots within the SILAC heatmaps indicate a statistically significant difference (q value <0.02) in the comparison between U0126-treated and DMSO-treated control Jurkat T cell SILAC ratios for that time point.</p

Phosphorylation of Ser⁵⁹ Lck across a time course of TCR stimulation.

<p>(A) Cell lysates from a time course of TCR stimulation in the presence of 0.1% DMSO or 20 µM U0126 were separated by SDS-PAGE and immunodetected with phospho-Ser⁵⁹ Lck and Lck specific antibodies. (B) Densitometric analysis of phospho-Ser⁵⁹ Lck levels normalized to Lck levels was performed. Shown is the mean ± S.D. from 4 biological replicate experiments. Statistically significant differences in relative phospho-Ser⁵⁹ levels between U0126-treated and DMSO-treated cells for each time point are indicated with an asterisk (*-p value <0.007, **-p value <0.015).</p

Tyrosine phosphorylation in U0126-treated and DMSO-treated Jurkat T cells across a time course of TCR stimulation.

<p>Cell lysates from one replicate of a time course of TCR stimulation in the presence of 0.1% DMSO or 20 µM U0126 were separated by SDS-PAGE and immunodetected with a monoclonal 4G10 antibody that recognizes phosphotyrosines. The immunoblot is representative of data from 4 biological replicate experiments.</p

Quantitative phosphoproteomic analysis of proteins associated with the KEGG regulation of actin cytoskeleton category.

<p>Heatmaps were calculated from the averages of four biological replicate experiments. White dots within the SILAC heatmaps indicate a statistically significant difference (q value <0.02) in the comparison between U0126-treated and DMSO-treated control Jurkat T cell SILAC ratios for that time point. Abbreviations: A_Raf: A-Raf proto-oncogene; CYFIP1, Cytoplasmic FMR1 interacting protein 1; GIT1, G protein-coupled receptor kinase-interactor 1; IQGAP1, IQ motif containing GTPase activating protein 1.</p

Phosphorylation of the activation site of ZAP-70 across a time course of TCR stimulation.

<p>(A) Cell lysates from one replicate of a time course of TCR stimulation in the presence of 0.1% DMSO or 20 µM U0126 were separated by SDS-PAGE and immunodetected with phospho-ZAP-70 (Tyr⁴⁹³) and ZAP-70 specific antibodies. (B) Densitometric analysis of phospho-ZAP-70 levels normalized to ZAP-70 levels was performed. Shown is the mean ± S.D. from 4 biological replicate experiments. Statistically significant differences in relative phospho-ZAP-70 levels between U0126-treated and DMSO-treated cells for each time point are indicated with an asterisk (*-p value <0.003).</p

Effects of U0126 on the canonical TCR signaling pathway.

<p>Depicted is a model of ERK positive feedback with quantitative U0126-treated to DMSO-treated SILAC ratio heatmaps beside individual proteins, corresponding to the changes in phosphorylation between the two conditions across the four time points of TCR stimulation. Heatmaps were calculated from the averages of four biological replicate experiments. Green represents elevated phosphorylation in response to U0126 treatment relative to DMSO-treated controls, whereas red represents a decrease in phosphorylation relative to DMSO-treated controls. Blanks in the heatmap indicate that a clearly defined SIC peak was not observed for that phosphopeptide in that time point. Black represents no change. White dots within the heatmap indicate a statistically significant difference (q value <0.02) in the comparison between U0126-treated and control DMSO-treated SILAC ratios for that time point. Below each heatmap square is a color bar representing the percent CV for that time point. Orange represents a high degree of variation, while black represents a low degree of variation amongst the replicate analyses. Blanks indicate a lack of replicate data required to accurately determine the CV.</p