- Melissa R. Perrino
- Marjolijn C.J. Jongmans
- Gail E. Tomlinson
- Mary-Louise C. Greer
- Sarah R. Scollon
- Sarah G. Mitchell
- Jordan R. Hansford
- Kris Ann P. Schultz
- Wendy K. Kohlmann
- Jennifer M. Kalish
- Suzanne P. MacFarland
- Anirban Das
- Kara N. Maxwell
- Stefan M. Pfister
- Rosanna Weksberg
- Orli Michaeli
- Uri Tabori
- Gina M. Ney
- Philip J. Lupo
- Jack J. Brzezinski
- Douglas R. Stewart
- Emma R. Woodward
- Christian P. Kratz
IScience: Dissection of tumoral niches using spatial transcriptomics and deep learning (Chen)
Structure: Structural insights into the assembly and regulation of 2′-O RNA methylation by SARS-CoV-2 nsp16/nsp10 (Gupta Lab)
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SARS-CoV-2 nsp16/nsp10 oligomerizes on capped mRNA for efficient 2′-O methylation
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An aromatic zipper in nsp16 modulate oligomerization and methylation
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N-terminus of nsp10 is required for efficient 2′-O methylation
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A nucleotide-binding pocket on the backside of nsp16 modulates the 2′-O methylation
Summary
2′-O-ribose methylation of viral RNA’s first transcribed base (adenine or A1 in SARS-CoV-2) mimics host RNAs and subverts the innate immune response. How nsp16, with partner nsp10, assembles on the 5′-end of SARS-CoV-2 mRNA to methylate A1 is not fully understood. We present a ∼2.4 Å crystal structure of the heterotetrameric complex formed by the cooperative assembly of two nsp16/nsp10 heterodimers with one 10-mer Cap-1 RNA (product) bound to each. An aromatic zipper-like motif in nsp16 and the N-terminal regions of nsp10 and nsp16 orchestrate oligomeric assembly for efficient methylation. The front catalytic pocket of nsp16 stabilizes the upstream portion of the RNA while downstream RNA remains unresolved, likely due to flexibility. An inverted nsp16 dimer extends the positively charged surface for longer RNA to influence catalysis. Additionally, a non-specific nucleotide-binding pocket on the backside of nsp16 plays a critical role in catalysis, contributing to enzymatic activity.
Neuro-Oncology: Dual Inhibition of MAPK and TORC1 Signaling Retards Development of Radiation Resistance in Pediatric BRAF V600E Glioma Models (Chen, Houghton, et al labs)
Abstract
Molecular Oncology: Hijacking the BAF complex: the mechanistic interplay of ARID1A and EWS::FLI1 in Ewing sarcoma (Libich Lab)
Abstract
Ewing sarcoma, an aggressive pediatric cancer, is driven by the EWS::FLI1 fusion protein, which disrupts gene expression by hijacking the BAF chromatin remodeling complex. Central to this mechanism is the formation of biomolecular condensates, mediated by the prion-like domains (PrLDs) of EWS and ARID1A, a core BAF subunit. ARID1A serves as a critical interface between EWS::FLI1 and the BAF complex, with its condensate-forming ability essential for the aberrant gene expression that drives tumor growth. The loss of condensate-competent ARID1A significantly impairs tumor progression, identifying it as a potential therapeutic target. However, targeting condensate formation is challenging due to the transient nature of the interactions involved, complicating the development of effective inhibitors. This work underscores the importance of further investigation into therapeutic strategies aimed at disrupting condensate formation in Ewing sarcoma and other related malignancies.
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Biomolecular NMR Assignments: The 1H, 15N and 13C backbone resonance assignments of the N-terminal (1-149) domain of Serpine mRNA Binding Protein 1 (SERBP1) (Libich Lab)
Abstract
Serpine mRNA-Binding Protein 1 (SERBP1) is an RNA-binding protein implicated in diverse cellular functions, including translational regulation, tumor progression, and stress response. It interacts with ribosomal subunits, RNA, and proteins involved in stress granules, contributing to processes such as phase separation and epigenetic regulation. Recent studies have shown SERBP1’s role in glioblastoma progression and its involvement in ribosomal regulation. Structurally, SERBP1 contains N- and C-terminal hyaluronan-binding domains, two RG/RGG motifs, and is predicted to be predominantly disordered. Here, we report the backbone resonance assignment and secondary structure propensities of SERBP1’s N-terminal residues (1-149). Using NMR spectroscopy, we identified a stable α-helix (residues 28-40) and transient structural elements. These findings provide insight into the structural features of SERBP1 that may mediate its interactions with ribosomal subunits, RNA, and other binding partners, laying a foundation for future structural studies of its functional mechanisms.
Keywords: Intrinsically disordered protein; NMR; SERBP1; mRNA binding.
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Int’l Journal of Molecular Sciences: The Role of the Tumor Microenvironment (TME) in Advancing Cancer Therapies: Immune System Interactions, Tumor-Infiltrating Lymphocytes (TILs), and the Role of Exosomes and Inflammasomes (Aune Lab)
Abstract
Understanding how different contributors within the tumor microenvironment (TME) function and communicate is essential for effective cancer detection and treatment. The TME encompasses all the surroundings of a tumor, such as blood vessels, fibroblasts, immune cells, signaling molecules, exosomes, and the extracellular matrix (ECM). Subsequently, effective cancer therapy relies on addressing TME alterations, known drivers of tumor progression, immune evasion, and metastasis. Immune cells and other cell types act differently under cancerous conditions, either driving or hindering cancer progression. For instance, tumor-infiltrating lymphocytes (TILs) include lymphocytes of B and T cell types that can invade malignancies, bringing in and enhancing the ability of the immune system to recognize and destroy cancer cells. Therefore, TILs display a promising approach to tackling the TME alterations and have the capability to significantly hinder cancer progression. Similarly, exosomes and inflammasomes exhibit a dual effect, resulting in either tumor progression or inhibition depending on the origin of exosomes, the type of inflammasome, and the tumor. This review will explore how cells function in the presence of a tumor, the communication between cancer cells and immune cells, and the role of TILs, exosomes, and inflammasomes within the TME. The efforts in this review are aimed at garnering interest in safer and durable therapies for cancer, in addition to providing a promising avenue for advancing cancer therapy and consequently improving survival rates.
Progress in Neurobiology: Pathogenic Oligomeric Tau alters Neuronal RNA Processes through the Formation of Nuclear Heteromeric Amyloids with RNA-Binding Protein Musashi1 (Penalva)
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Abstract
Alzheimer’s disease (AD) is marked by cytoplasmic proteinopathies, primarily involving misfolded Tau protein. Pathogenic Tau species, such as soluble oligomers and fibrils, disrupt RNA metabolism, though the mechanisms are unclear. Recent research indicates that RNA has a crucial role in Tau aggregation. Our study builds on this by noting significant co-deposition of RNA-Binding Proteins (RBPs) with Tau in AD and Frontotemporal dementia (FTLD) brains. We use molecular and cellular techniques to investigate the interaction between RNA dynamics and Tau aggregation, focusing on the localization and aggregation of Tau and RBPs, particularly Musashi (MSI), within neuronal nuclei. Through cyto-fluorometric, biochemical, and cellular assays, we reveal the importance of Tau/RBP interplay in primary cortical neurons expressing wild-type and mutant Tau. Pathogenic Tau oligomers alter MSI protein localization and function, causing cytoplasmic and nuclear aggregation. Mass spectrometry of the MSI1 nuclear interactome in Tau models shows disrupted RNA metabolism pathways, including ribosomal biogenesis, RNA splicing, and protein folding. Moreover, the RNA immunoprecipitation assay revealed a remarkable impact of mutant P301L Tau on MSI1’s ability to bind RNA targets. These findings highlight potential targets for early neurodegenerative therapeutic interventions.
Keywords
Musashi
Tau
Aggregation
Nucleus
RNA processing
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Texas Public Radio: Science & Medicine: Sabotaging the molecular engines of some pediatric cancers (Gupta)
Ewing sarcoma and rhabdomyosarcoma are cancers that overwhelmingly impact children. They’re soft tissue cancers that are thankfully rare because treatment options are limited, according to pediatric cancer researcher Yogesh Gupta, PhD, an associate professor at Greehey Children’s Cancer Research Institute at UT Health San Antonio.
“The drug treatment regimen has not been changed in the last three decades,” Gupta said.
Kids with these types of cancers will typically endure chemotherapy and radiation, and the aggressive treatment regimen can leave them with lifelong heart issues, problems with bone growth and development, impaired fertility, cognitive challenges, and an increased risk of secondary cancers.
Listen to the complete interview.
ELife: SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis (Libich, Penalva, et al)
Abstract
RNA binding proteins (RBPs) containing intrinsically disordered regions (IDRs) are present in diverse molecular complexes where they function as dynamic regulators. Their characteristics promote liquid-liquid phase separation (LLPS) and the formation of membraneless organelles such as stress granules and nucleoli. IDR-RBPs are particularly relevant in the nervous system, and their dysfunction is associated with neurodegenerative diseases and brain tumor development. Serpine1 mRNA-binding protein 1 (SERBP1) is a unique member of this group, being mostly disordered and lacking canonical RNA-binding domains. We defined SERBP1’s interactome, uncovered novel roles in splicing, cell division, and ribosomal biogenesis, and showed its participation in pathological stress granules and Tau aggregates in Alzheimer’s brains. SERBP1 preferentially interacts with other G-quadruplex (G4) binders, implicated in different stages of gene expression, suggesting that G4 binding is a critical component of SERBP1 function in different settings. Similarly, we identified important associations between SERBP1 and PARP1/polyADP-ribosylation (PARylation). SERBP1 interacts with PARP1 and its associated factors and influences PARylation. Moreover, protein complexes in which SERBP1 participates contain mostly PARylated proteins and PAR binders. Based on these results, we propose a feedback regulatory model in which SERBP1 influences PARP1 function and PARylation, while PARylation modulates SERBP1 functions and participation in regulatory complexes.
Keywords: PARP1; RNA binding protein; SERBP1; Alzheimer’s; biochemistry; chemical biology; genetics; genomics; glioblastoma; human; proteomics.