Titration of SF3B1 Activity Reveals Distinct Effects on the Transcriptome and Cell Physiology

SF3B1 is a core component of the U2 spliceosome that is frequently mutated in cancer. We have previously shown that titrating the activity of SF3B1, using the inhibitor pladienolide B (PB), affects distinct steps of the heat shock response (HSR). Here, we identify other genes that are sensitive to different levels of SF3B1 (5 vs. 100 nM PB) using RNA sequencing. Significant changes to mRNA splicing were identified at both low PB and high PB concentrations. Changes in expression were also identified in the absence of alternative splicing, suggesting that SF3B1 influences other gene expression pathways. Surprisingly, gene expression changes identified in low PB are not predictive of changes in high PB. Specific pathways were identified with differential sensitivity to PB concentration, including nonsense-mediated decay and protein-folding homeostasis, both of which were validated using independent reporter constructs. Strikingly, cells exposed to low PB displayed enhanced protein-folding capacity relative to untreated cells. These data reveal that the transcriptome is exquisitely sensitive to SF3B1 and suggests that the activity of SF3B1 is finely regulated to coordinate mRNA splicing, gene expression and cellular physiology.

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Faculty Opinions recommendation of Endogenous morphine/nitric oxide-coupled regulation of cellular physiology and gene expression: implications for cancer biology.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1165036.625915 ◽

2009 ◽

Author(s):

Marc De Kock ◽

Patrice Forget

Keyword(s):

Gene Expression ◽

Nitric Oxide ◽

Cancer Biology ◽

Cellular Physiology ◽

Endogenous Morphine

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Faculty Opinions recommendation of Research resource: interactome of human embryo implantation: identification of gene expression pathways, regulation, and integrated regulatory networks.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.13686956.15102056 ◽

2012 ◽

Author(s):

Lois Salamonsen

Keyword(s):

Gene Expression ◽

Human Embryo ◽

Regulatory Networks ◽

Embryo Implantation ◽

Expression Pathways

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Nanoparticle-plasma Membrane Interactions: Thermodynamics, Toxicity and Cellular Response

Current Medicinal Chemistry ◽

10.2174/0929867325666181112090648 ◽

2020 ◽

Vol 27 (20) ◽

pp. 3330-3345

Author(s):

Ana G. Rodríguez-Hernández ◽

Rafael Vazquez-Duhalt ◽

Alejandro Huerta-Saquero

Keyword(s):

Gene Expression ◽

Immune Responses ◽

Cellular Response ◽

Cellular Level ◽

Membrane Interactions ◽

Daily Lives ◽

Cellular Physiology ◽

Associated Proteins ◽

First Contact ◽

Insight Into

Nanomaterials have become part of our daily lives, particularly nanoparticles contained in food, water, cosmetics, additives and textiles. Nanoparticles interact with organisms at the cellular level. The cell membrane is the first protective barrier against the potential toxic effect of nanoparticles. This first contact, including the interaction between the cell membranes -and associated proteins- and the nanoparticles is critically reviewed here. Nanoparticles, depending on their toxicity, can cause cellular physiology alterations, such as a disruption in cell signaling or changes in gene expression and they can trigger immune responses and even apoptosis. Additionally, the fundamental thermodynamics behind the nanoparticle-membrane and nanoparticle-proteins-membrane interactions are discussed. The analysis is intended to increase our insight into the mechanisms involved in these interactions. Finally, consequences are reviewed and discussed.

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274 Tumoral and peripheral immunophenotype of refractory vs relapse to PD-(L)1 blockade in patients with advanced non-small cell lung cancer

Journal for ImmunoTherapy of Cancer ◽

10.1136/jitc-2020-sitc2020.0274 ◽

2020 ◽

Vol 8 (Suppl 3) ◽

pp. A299-A299

Author(s):

Maria Ascierto ◽

Matthew Hellmann ◽

Nathan Standifer ◽

Song Wu ◽

Han Si ◽

...

Keyword(s):

Gene Expression ◽

Informed Consent ◽

Checkpoint Inhibitors ◽

Patient Response ◽

Calcium Dependent ◽

Immune Exhaustion ◽

Previously Treated ◽

Expression Pathways ◽

Relapsed Disease ◽

Written Informed Consent

BackgroundDespite the encouraging successes of immune checkpoint inhibitors, many patients do not benefit and are either refractory or relapse. The mechanisms of refractory or relapsed disease following PD-(L)1 blockade are largely unknown. To identify characteristics associated with refractory or relapsed disease we explored the immune and genomic landscape of samples derived from NSCLC patients who previously received PD-(L)1 blockade and had blood and fresh tumor biopsies collected at the time of progression.MethodsPatient response categories were defined prospectively; ‘refractory’ defined as progression within 16 weeks of initiating PD-(L)1 and ‘relapse’ defined as initial clinical benefit (CR, PR, SD) followed by progression. RNAseq (n=52) and PD-L1 IHC (n=22) were performed on tumor tissue. Immune profiling of whole blood was assessed using flow cytometry or Biomark HD (Fluidigm) gene expression panel (n=54 and n=62, respectively). Differential gene expression was defined as unadjusted p<0.05 and fold-difference >1.5. Pathways analysis was conducted by David tool. Patient samples were collected during screening for clinical trial of second line immunotherapy. Written informed consent was obtained from the patients for publication of this abstract.ResultsIn patients with NSCLC previously treated with PD-(L)1 blockade, tumors of relapsed patients were characterized by increased expression of genes associated with interferon signaling (e.g. CXCL9, SPIC, IFNg), immune suppression (e.g. ARG1, TGFB), immune exhaustion (e.g. ADORA2A), and increased PD-L1 expression (by gene expression and IHC). Refractory disease was associated with increased cadherin signaling and calcium-dependent-cell-adhesion gene expression pathways. In the periphery, reduced quantities of B cells and activated (HLA-DR+ or CD38+) or proliferating (Ki67+) CD8+ T cells were observed in refractory patients.ConclusionsThe tumor and peripheral compartments of patients with NSCLC previously treated with PD-(L)1 blockade differ based on prior response. Relapsed patients tend to have signals of sturdy immune activation and chronic inflammation thus ultimately leading to immune exhaustion. These results may help inform rational therapeutic strategies to overcome resistance to PD-(L)1 blockade in NSCLC.Trial RegistrationNCT02000947Ethics ApprovalResearch on human samples here analyzed have been performed in accordance with the Declaration of Helsinki.ConsentWritten informed consent was obtained from the patient for publication of this abstract.

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Pericytes contribute to the islet basement membranes to promote beta-cell gene expression

Scientific Reports ◽

10.1038/s41598-021-81774-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Lina Sakhneny ◽

Alona Epshtein ◽

Limor Landsman

Keyword(s):

Gene Expression ◽

Cell Function ◽

Basement Membranes ◽

Cell Physiology ◽

Β Cells ◽

Β Cell ◽

Cell Clustering ◽

Β Cell Function ◽

Cell Gene Expression ◽

Glucose Stimulated Insulin Secretion

Abstractβ-Cells depend on the islet basement membrane (BM). While some islet BM components are produced by endothelial cells (ECs), the source of others remains unknown. Pancreatic pericytes directly support β-cells through mostly unidentified secreted factors. Thus, we hypothesized that pericytes regulate β-cells through the production of BM components. Here, we show that pericytes produce multiple components of the mouse pancreatic and islet interstitial and BM matrices. Several of the pericyte-produced ECM components were previously implicated in β-cell physiology, including collagen IV, laminins, proteoglycans, fibronectin, nidogen, and hyaluronan. Compared to ECs, pancreatic pericytes produce significantly higher levels of α2 and α4 laminin chains, which constitute the peri-islet and vascular BM. We further found that the pericytic laminin isoforms differentially regulate mouse β-cells. Whereas α2 laminins promoted islet cell clustering, they did not affect gene expression. In contrast, culturing on Laminin-421 induced the expression of β-cell genes, including Ins1, MafA, and Glut2, and significantly improved glucose-stimulated insulin secretion. Thus, alongside ECs, pericytes are a significant source of the islet BM, which is essential for proper β-cell function.

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Predicting tumor response to drugs based on gene-expression biomarkers of sensitivity learned from cancer cell lines

BMC Genomics ◽

10.1186/s12864-021-07581-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yuanyuan Li ◽

David M. Umbach ◽

Juno M. Krahn ◽

Igor Shats ◽

Xiaoling Li ◽

...

Keyword(s):

Gene Expression ◽

Cell Lines ◽

Cancer Cell ◽

Predictive Models ◽

Drug Sensitivity ◽

Human Cancer ◽

Cancer Cell Lines ◽

The Cancer Genome Atlas ◽

Differential Sensitivity ◽

Tumor Type

Abstract Background Human cancer cell line profiling and drug sensitivity studies provide valuable information about the therapeutic potential of drugs and their possible mechanisms of action. The goal of those studies is to translate the findings from in vitro studies of cancer cell lines into in vivo therapeutic relevance and, eventually, patients’ care. Tremendous progress has been made. Results In this work, we built predictive models for 453 drugs using data on gene expression and drug sensitivity (IC50) from cancer cell lines. We identified many known drug-gene interactions and uncovered several potentially novel drug-gene associations. Importantly, we further applied these predictive models to ~ 17,000 bulk RNA-seq samples from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) database to predict drug sensitivity for both normal and tumor tissues. We created a web site for users to visualize and download our predicted data (https://manticore.niehs.nih.gov/cancerRxTissue). Using trametinib as an example, we showed that our approach can faithfully recapitulate the known tumor specificity of the drug. Conclusions We demonstrated that our approach can predict drugs that 1) are tumor-type specific; 2) elicit higher sensitivity from tumor compared to corresponding normal tissue; 3) elicit differential sensitivity across breast cancer subtypes. If validated, our prediction could have relevance for preclinical drug testing and in phase I clinical design.

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H2O2 Induces Major Phosphorylation Changes in Critical Regulators of Signal Transduction, Gene Expression, Metabolism and Developmental Networks in Aspergillus nidulans

Journal of Fungi ◽

10.3390/jof7080624 ◽

2021 ◽

Vol 7 (8) ◽

pp. 624

Author(s):

Ulises Carrasco-Navarro ◽

Jesús Aguirre

Keyword(s):

Gene Expression ◽

Protein Phosphorylation ◽

Aspergillus Nidulans ◽

Regulation Of Gene Expression ◽

Antioxidant Response ◽

Eukaryotic Cell ◽

Cell Physiology ◽

Tor Signaling ◽

Developmental Networks ◽

General Metabolism

Reactive oxygen species (ROS) regulate several aspects of cell physiology in filamentous fungi including the antioxidant response and development. However, little is known about the signaling pathways involved in these processes. Here, we report Aspergillus nidulans global phosphoproteome during mycelial growth and show that under these conditions, H2O2 induces major changes in protein phosphorylation. Among the 1964 phosphoproteins we identified, H2O2 induced the phosphorylation of 131 proteins at one or more sites as well as the dephosphorylation of a larger set of proteins. A detailed analysis of these phosphoproteins shows that H2O2 affected the phosphorylation of critical regulatory nodes of phosphoinositide, MAPK, and TOR signaling as well as the phosphorylation of multiple proteins involved in the regulation of gene expression, primary and secondary metabolism, and development. Our results provide a novel and extensive protein phosphorylation landscape in A. nidulans, indicating that H2O2 induces a shift in general metabolism from anabolic to catabolic, and the activation of multiple stress survival pathways. Our results expand the significance of H2O2 in eukaryotic cell signaling.

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