Search bioRxiv⌕ Search

Biology subjects

Seath, C. P.

Publications and source records attributed to Seath, C. P..

8 recordsLinked to original sources

Mutant p53 binds RNA to drive mitochondrial dysfunction

Tumor suppressor protein 53 (p53) is a transcription factor that is deregulated in 50% of cancers. Often termed the guardian of the genome, p53 is responsible for maintenance of genomic stability, cell cycle arrest, DNA repair, senescence, and apoptosis. In cancer cells, deregulation of p53 often occurs through mutations in the DNA binding domain which lead to a loss of the transcriptional activity. While 100s of somatic mutations in the DNA binding domain are known, a small number of mutants are enriched in cancer, suggesting a gain-of-function role. Here we deploy an intein-based approach to localize {micro}Map photoproximity labeling to p53 to define novel interactions contributing to the loss and gain of function roles of 5 separate hotspot mutants. These data revealed that G245S and R273H binds to RNA through its C-terminal domain. We show through CLIP experiments that mutant p53 has an RNA binding motif that conserved across mutants and is enriched in 3UTRs, promoting ribosomal localization and labeling of proteins at the mitochondrial surface. We further demonstrate that the RNA binding ability of mutant p53 promotes altered miRNA processing and mitochondrial dysfunction providing mechanistic rationale for historically reported but poorly understood phenotypes.

molecular biology↗

FlAsH-ID: A short peptide tag for live cell photoproximity labeling

Methods to determine how biomolecules interact in a cellular context has led to significant advances in our understanding of biology. Of these, proximity labeling has emerged as a valuable tool for the interrogation protein-protein and protein-RNA interactions. Almost all proximity labeling methods are deployed via large fusion proteins, which while powerful in many contexts, can disrupt native biology or obscure important epitopes on the protein under study. This challenge is especially prominent for small transcriptionally active proteins where the protein cistrome is vital for correct localization and function. Here, we have developed a photoproximity labeling method that is localized to a short 6 amino acid peptide sequence that employs the combination of the Tsien tetracysteine tag with FlAsH dye for localized singlet oxygen generation that we term FlAsH-ID. We demonstrate this method is non toxic and can be employed to label several cellular compartments, and generate high quality interactomics data around H3.1. Furthermore, we show that FlAsH-ID can be used to probe dynamic chnages in protein movement in response to immune stimuli, identifying several RNA-binding protiens that are trafficked to the nucleus following poly(I:C) treatment. Finally we demonstrate FlAsH-ID can be used for proximity proteomics in primary CD8+ T cells by focusing on the transcription factor RUNX3. RUNX3-tetracysteine, but not RUNX3-TurboID, recaptiulated the function of wildtype RUNX3 and rescued the phenotype of Runx3-deficeint CD8+ T cells in response to viral infection in vivo. In primary CD8+ T cells, FlAsH-ID identified RUNX3 in proximity to the nucleosome remodeler ARID1A and we show that both factors act concertedly during initial naive CD8+ T cell activation to drive chromatin accessibility in cis-regulatory regions that induce differentiation of effector and long-lived memory CD8+ T cells. Our results suggest this technique will expand the field of proximity labeling to small, functionally sensitive proteins in primary cells without perturbing their function.

molecular biology↗

Photoproximity labeling of c-Myc reveals SLK as a cancer specific co-regulator

Transcription factors (TFs) have long been aspirational therapeutic targets for the treatment of diseases, as their dysregulation is a common mechanism for altered cell states. Despite this, many TFs implicated in disease have disordered structures and lack canonical binding pockets, rendering them non-trivial targets for small molecule-based therapies. Directly inhibiting TF function has proven difficult, but indirect inhibition by targeting the effector molecules that modulate TF function is a promising, yet underexplored, alternative approach. Here we report a strategy for capturing cancer-specific protein-protein interactions using context-dependent {micro}Map photoproximity labeling. Using an intein-based method for catalyst conjugation in biochemically intact nuclei, we demonstrate that we can capture unique protein interactomes of c-Myc in healthy and cancerous prostate cell lines, and that these unique interactors can be mined to identify druggable vulnerabilities. We find that a cancer specific Myc interactor, SLK, selectively promotes c-Myc stabilization at the protein level, drives epithelial morphology, and is essential for tumorigenesis, validating it as a viable therapeutic target. Importantly, this stabilization is driven by a change in SLK splicing rather than expression at the protein or RNA levels. Furthermore, analysis of cancer patient data shows a strong correlation between this splice isoform and expression of c-Myc targets, suggesting this novel regulatory axis is operative across human cancer.

cancer biology↗

RNase L regulates the antiviral proteome by accelerating mRNA1decay, inhibiting nuclear mRNA export, and repressing RNAPII-2mediated transcription

Ribonuclease L (RNase L) is an antiviral endoribonuclease that triggers widespread degradation of cellular mRNAs. Here, we show that the degradation of cellular mRNA by RNase L is a conserved response to flaviviruses, including Zika virus (ZIKV), dengue virus serotype 2 (DENV-2), and West Nile virus (WNV). Quantitative mass spectrometry in response to dsRNA or ZIKV infection shows that RNase L broadly downregulates the cellular proteome, reducing proteins with short half-lives involved in cell cycle progression, cellular metabolism, and protein synthesis. The mRNAs encoded by interferon-stimulated genes (ISGs) evade mRNA decay by RNase L, allowing for protein synthesis of ISG-encoding mRNAs. However, RNase L dampens ISG protein synthesis by triggering a block in nuclear mRNA export and repressing RNAPII-mediated transcription at later times during the antiviral response. These findings implicate reprograming of the cellular proteome as primary means by which RNase L combats viral infection, tumorigenesis, and immune dysregulation. HIGHLIGHTSO_LIRNase L initiates widespread decay of cellular mRNA in response to flaviviruses C_LIO_LIRNase L-mediated mRNA decay broadly downregulates the homoeostatic proteome C_LIO_LIAntiviral mRNAs are translated due to their ability to evade RNase L-mediated decay C_LIO_LIRNase L reduces antiviral proteins by inhibiting mRNA export and RNAPII-mediated transcription C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/665572v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@13c4940org.highwire.dtl.DTLVardef@ed1bd9org.highwire.dtl.DTLVardef@bf5057org.highwire.dtl.DTLVardef@33bca9_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

DeSciDe: A tool for unbiased literature searching and gene list cu-ration unveils a new role for the acidic patch mutation H2A E92K

Omics analysis has become an indispensable tool for researchers in the life sciences, enabling the study of DNA, RNA, and proteins and how they respond to cellular stimulus. Many methods of data analysis exist for the generation and characterization of gene lists, however, selection of genes for further investigation is still heavily influenced by prior knowledge, with practitioners often studying well characterized genes, reinforcing bias in the literature. Here, we have developed an open-source, R package for impartial ranking of gene lists derived from omics analysis that we term Deciphering Scientific Discoveries (DeSciDe). We applied a pipeline that sorts a gene list first by precedence, which we define as co-occurrence of the gene with pre-defined search terms in publications. We then rank gene lists by connectivity, an underutilized metric for how related a gene is to other enriched genes. The combination of these rankings by scatterplot provides a method for gene selection by simple visual analysis. We apply this analysis methods to published Omics datasets, identifying novel avenues for investigation. Further, using this method we have been able to assign a novel loss of function role for the histone mutation H2A E92K.

bioinformatics↗

Mesoscale proximity labeling to study macro changes to chromatin occupancy

Proximity labeling traditionally identifies interactomes of a single protein or RNA, though this approach limits mechanistic understanding of biomolecules functioning within complex systems. Here, we demonstrate a strategy for deciphering ligand-induced changes to global biomolecular interactions by enabling proximity labelling at the mesoscale, across an entire cellular system. By inserting nanoscale proximity labelling catalysts throughout chromatin, this system, MesoMap, provided new insights into how HDAC inhibitors regulate gene expression. Furthermore, it revealed that the orphaned drug candidate, SR-1815, regulates disease-linked Syngap1 gene expression through direct inhibition of kinases implicated in both neurological disorders and cancer. Through precise mapping of global chromatin mobility, MesoMap promotes insights into how drug-like chemical probes induce transcriptional dynamics within healthy and disease-associated cellular states.

molecular biology↗

Tracking chromatin state changes using μMap photo-proximity labeling

Interactions between biomolecules, particularly proteins, underlie all cellular processes, and ultimately control cell fate. Perturbation of native interactions through mutation, changes in expression levels, or external stimuli leads to altered cellular physiology and can result in either disease or therapeutic effects.1,2 Mapping these interactions and determining how they respond to stimulus is the genesis of many drug development efforts, leading to new therapeutic targets and improvements in human health.1 However, in the complex environment of the nucleus it is challenging to determine protein-protein interactions due to low abundance, transient or multi-valent binding, and a lack of technologies that are able to interrogate these interactions without disrupting the protein binding surface under study.3 Chromatin remodelers, modifying enzymes, interactors, and transcription factors can all be redirected by subtle changes to the microenvironment, causing global changes in protein expression levels and subsequent physiology. Here, we describe the Chroma-Map method for the traceless incorporation of Ir-photosensitizers into the nuclear microenvironment using engineered split inteins. These Ir-catalysts can activate diazirine warheads to form reactive carbenes within a ~10 nm radius, cross-linking with proteins within the immediate microenvironment for analysis via quantitative chemoproteomics.4 We demonstrate this concept on nine different nuclear proteins with varied function and in each case, elucidating their microenvironments. Additionally, we show that this short-range proximity labeling method can reveal the critical changes in interactomes in the presence of cancer-associated mutations, as well as treatment with small-molecule inhibitors. Chroma-Map improves our fundamental understanding of nuclear protein-protein interactions, as well as the effects that small molecule therapeutics have on the local chromatin environment, and in doing so is expected to have a significant impact on the field of epigenetic drug discovery in both academia and industry.

cancer biology↗

Small molecule photocatalysis enables drug target identification via energy transfer

The identification of cellular targets that can be exploited for therapeutic benefit, broadly known as target ID, remains a fundamental goal in drug discovery. In recent years, the application of new chemical and biological technologies that accelerate target ID has become commonplace within drug discovery programs, as a complete understanding of how molecules react in a cellular environment can lead to increased binding selectivity, improved safety profiles, and clinical efficacy. Established approaches using photoaffinity labelling (PAL) are often costly and time-consuming due to poor signal-to-noise coupled with extensive probe optimization. Such challenges are exacerbated when dealing with low abundance membrane proteins or multiple protein target engagement, typically rendering target ID unfeasible. Herein, we describe a general platform for photocatalytic small molecule target ID, which hinges upon the generation of high-energy carbene intermediates via visible light-mediated Dexter energy transfer. By decoupling the reactive warhead from the drug, catalytic signal amplification results in multiple labelling events per drug, leading to unprecedented levels of target enrichment. Through the development of cell permeable photo-catalyst conjugates, this method has enabled the quantitative target and off target identification of several drugs including (+)-JQ1, paclitaxel, and dasatinib. Moreover, this methodology has led to the target ID of two GPCRs - ADORA2A and GPR40 - a class of drug target seldom successfully uncovered in small molecule PAL campaigns.

molecular biology↗