SRRM2 phase separation drives assembly of nuclear speckle subcompartments

Non-coding RNAs in the pathogenesis of Alzheimer's disease: β-amyloid aggregation, Tau phosphorylation and neuroinflammation

Alzheimer's disease is a progressive neurodegenerative disorder primarily affecting individuals aged 65 and older, characterized by cognitive decline and diminished quality of life. The molecular hallmarks of AD include extracellular β-amyloid plaques, intracellular neurofibrillary tangles composed of hyperphosphorylated tau protein, and chronic neuroinflammation. Non-coding RNAs (ncRNAs), including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), have emerged as potential therapeutic targets due to their regulatory roles in AD pathogenesis. For example, miR-124 has been shown to modulate Aβ levels, while lncRNAs such as BACE1-AS regulate the expression of BACE1, a crucial enzyme in Aβ production. Transcriptomic studies of AD patients have revealed dysregulation of ncRNA expression, further supporting their involvement in disease progression. This review examines the regulatory functions of ncRNAs in AD, focusing on their impact on Aβ, tau hyperphosphorylation, and neuroinflammation. Additionally, we discuss the emerging role of ncRNAs in liquid-liquid phase separation and the formation of protein aggregates, key processes contributing to AD pathology.

Phosphorylation of a nuclear condensate regulates cohesion and mRNA retention

Nuclear speckles are membraneless organelles that associate with active transcription sites and participate in post-transcriptional mRNA processing. During the cell cycle, nuclear speckles dissolve following phosphorylation of their protein components. Here, we identify the PP1 family as the phosphatases that counteract kinase-mediated dissolution. PP1 overexpression increases speckle cohesion and leads to retention of mRNA within speckles and the nucleus. Using APEX2 proximity labeling combined with RNA-sequencing, we characterize the recruitment of specific RNAs. We find that many transcripts are preferentially enriched within nuclear speckles compared to the nucleoplasm, particularly chromatin- and nucleus-associated transcripts. While total polyadenylated RNA retention increases with nuclear speckle cohesion, the ratios of most mRNA species to each other are constant, indicating non-selective retention. We further find that cellular responses to heat shock, oxidative stress, and hypoxia include changes to the phosphorylation and cohesion of nuclear speckles and to mRNA retention. Our results demonstrate that tuning the material properties of nuclear speckles provides a mechanism for the acute control of mRNA localization.

μMap-Interface: Temporal Photoproximity Labeling Identifies F11R as a Functional Member of the Transient Phagocytic Surfaceome

Phagocytosis is usually carried out by professional phagocytic cells in the context of pathogen response or wound healing. The transient surface proteins that regulate phagocytosis pose a challenging proteomics target; knowledge thereof could lead to new therapeutic insights. Herein, we describe a novel photocatalytic proximity labeling method: "μMap-Interface", allowing for spatiotemporal mapping of phagocytosis. Utilizing photocatalyst-conjugated IGG-opsonized beads and initiating phagocytosis in a synchronized manner, we capture phagocytic interactome "snapshots" at the interface of the phagocyte and its target. This allows profiling of the dynamic surface proteome of human macrophages during the engulfment process. We reveal previously known phagocytic mediators as well as potential novel interactors and validate their presence with super-resolution microscopy. This includes F11R, an important cancer target yet to be investigated in the context of phagocytosis. Further, we demonstrate that knocking down F11R leads to an increased degree of phagocytosis; this insight could contribute to explaining its oncogenic activity. Lastly, we show capture of orthogonal phagocytic surfaceomes across different cells, using a neutrophil-like model. We believe this method will enable new insights into phagocytic processes in a variety of contexts.

Metabolic regulation of mRNA splicing

Alternative mRNA splicing enables the diversification of the proteome from a static genome and confers plasticity and adaptiveness on cells. Although this is often explored in development, where hard-wired programs drive the differentiation and specialization, alternative mRNA splicing also offers a way for cells to react to sudden changes in outside stimuli such as small-molecule metabolites. Fluctuations in metabolite levels and availability in particular convey crucial information to which cells react and adapt. We summarize and highlight findings surrounding the metabolic regulation of mRNA splicing. We discuss the principles underlying the biochemistry and biophysical properties of mRNA splicing, and propose how these could intersect with metabolite levels. Further, we present examples in which metabolites directly influence RNA-binding proteins and splicing factors. We also discuss the interplay between alternative mRNA splicing and metabolite-responsive signaling pathways. We hope to inspire future research to obtain a holistic picture of alternative mRNA splicing in response to metabolic cues.