Molly T. Soper-Hopper

A Derivatization-Free Parallel Reaction Monitoring-Based Proteomics Workflow for Quantitative, Site-Specific Analysis of Histone Post-Translational Modifications

Hyoungjoo Lee, Ashley K. Wiseman, Bailey M. Tibben, Ibukunoluwa Sodiya et autres

Histone post-translational modifications (PTMs) are key regulators of chromatin architecture and gene expression. Although mass spectrometry (MS)-based data-independent acquisition (DIA) pipelines for histone PTM quantification are available, multiplexed targeted assays remain underdeveloped. Here, we present a derivatization-free parallel reaction monitoring (PRM) workflow …

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SATB2 dysregulation generates a novel circular RNA and drives KRAS-like transcriptional reprogramming and transformation-associated phenotypes

Rebekah Eleazer, Smitha George, Luke Shoemaker, Wesley N. Saintilnord et autres

BACKGROUND: Even though epigenetic factors contribute to oncogenesis, most human cancer models still assume that disease originates from driver DNA mutations. Thus, it is still unclear if non-genetic mechanisms are sufficient to trigger malignant transformation. Special AT-rich binding protein 2 (SATB2) is …

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Additional file 1 of SATB2 dysregulation generates a novel circular RNA and drives KRAS-like transcriptional reprogramming and transformation-associated phenotypes

Rebekah Eleazer, Smitha George, Luke Shoemaker, Wesley N. Saintilnord et autres

Supplementary Material 1: Table S1. siRNA sequences for knocking down SATB2 and circ3915 RNAs. Table S2. shRNA sequences for stable SATB2 RNA knockdown. Table S3. RT-qPCR primers for SATB2 and circ3915. Table S4. NanoString codesets for verifying differentially expressed circular and linear …

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Additional file 3 of SATB2 dysregulation generates a novel circular RNA and drives KRAS-like transcriptional reprogramming and transformation-associated phenotypes

Rebekah Eleazer, Smitha George, Luke Shoemaker, Wesley N. Saintilnord et autres

Supplementary Material 3.

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Additional file 3 of SATB2 dysregulation generates a novel circular RNA and drives KRAS-like transcriptional reprogramming and transformation-associated phenotypes

Rebekah Eleazer, Smitha George, Luke Shoemaker, Wesley N. Saintilnord et autres

Supplementary Material 3.

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Additional file 1 of SATB2 dysregulation generates a novel circular RNA and drives KRAS-like transcriptional reprogramming and transformation-associated phenotypes

Rebekah Eleazer, Smitha George, Luke Shoemaker, Wesley N. Saintilnord et autres

Supplementary Material 1: Table S1. siRNA sequences for knocking down SATB2 and circ3915 RNAs. Table S2. shRNA sequences for stable SATB2 RNA knockdown. Table S3. RT-qPCR primers for SATB2 and circ3915. Table S4. NanoString codesets for verifying differentially expressed circular and linear …

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Additional file 2 of SATB2 dysregulation generates a novel circular RNA and drives KRAS-like transcriptional reprogramming and transformation-associated phenotypes

Rebekah Eleazer, Smitha George, Luke Shoemaker, Wesley N. Saintilnord et autres

Supplementary Material 2: Fig S1. General experimental methods. A, General location of ON-TARGETplus small interfering (si) RNAs for transiently knocking down SATB2 mRNA or circ3915. Numbers correspond to SATB2 exons. C+L = probe for circular and linear RNA. B, General location of …

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Additional file 2 of SATB2 dysregulation generates a novel circular RNA and drives KRAS-like transcriptional reprogramming and transformation-associated phenotypes

Rebekah Eleazer, Smitha George, Luke Shoemaker, Wesley N. Saintilnord et autres

Supplementary Material 2: Fig S1. General experimental methods. A, General location of ON-TARGETplus small interfering (si) RNAs for transiently knocking down SATB2 mRNA or circ3915. Numbers correspond to SATB2 exons. C+L = probe for circular and linear RNA. B, General location of …

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Improved chromatographic separation of modified deoxycytidine nucleosides enhances LC-MS sensitivity

Christine Isaguirre, Molly T. Soper-Hopper, Stacey L. Thomas, Rachel Shereda et autres

Cytosine methylation is an epigenetic modification that regulates transcription. DNA demethylation occurs through oxidation of methylcytosine to hydroxymethylcytosine, making hydroxymethylation an important and translationally relevant marker of DNA methylation dynamics. These epigenetic modifications can be measured in their deoxynucleoside forms from enzymatically …

Dietary restriction reprograms CD8+ T cell fate to enhance anti-tumour immunity and immunotherapy responses

Brandon M. Oswald, Lisa M. DeCamp, Joseph Longo, Michael S. Dahabieh et autres

Abstract Reducing calorie intake through dietary restriction (DR) slows tumour growth in mammals, yet the underlying mechanisms are poorly defined. Here, we show that DR enhances anti-tumour immunity by optimizing CD8 + T cell function within the tumour microenvironment (TME). Using syngeneic …

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Dietary Restriction Enhances CD8⁺ T Cell Ketolysis to Limit Exhaustion and Boost Anti-Tumor Immunity

Brandon M. Oswald, Lisa M. DeCamp, Joseph Longo, Michael S. Dahabieh et autres

Abstract Reducing calorie intake without malnutrition limits tumor progression but the underlying mechanisms are poorly understood. Here we show that dietary restriction (DR) suppresses tumor growth by enhancing CD8 + T cell-mediated anti-tumor immunity. DR reshapes CD8 + T cell differentiation within …

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A diverse proteome is present and enzymatically active in metabolite extracts

Rachel J. House, Molly T. Soper-Hopper, Michael P. Vincent, Abigail E. Ellis et autres

Metabolite extraction is the critical first-step in metabolomics experiments, where it is generally regarded to inactivate and remove proteins. Here, arising from efforts to improve extraction conditions for polar metabolomics, we discover a proteomic landscape of over 1000 proteins within metabolite extracts. …

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