Liquid-liquid phase separation in biology: mechanisms, physiological functions and human diseases

Natural product sennoside B disrupts liquid-liquid phase separation of SARS-CoV-2 nucleocapsid protein by inhibiting its RNA-binding activity

The nucleocapsid protein (NP) of SARS-CoV-2, an RNA-binding protein, is capable of undergoing liquid-liquid phase separation (LLPS) during viral infection, which plays a crucial role in virus assembly, replication, and immune regulation. In this study, we developed a homogeneous time-resolved fluorescence (HTRF) method for identifying inhibitors of the SARS-CoV-2 NP-RNA interaction. Using this HTRF-based approach, we identified two natural products, sennoside A and sennoside B, as effective blockers of this interaction. Bio-layer interferometry assays confirmed that both sennosides directly bind to the NP, with binding sites located within the C-terminal domain. Additionally, fluorescence recovery after photobleaching (FRAP) experiments revealed that sennoside B significantly inhibited RNA-induced LLPS of the NP, while sennoside A displayed comparatively weaker activity. Thus, the developed HTRF-based assay is a valuable tool for identifying novel compounds that disrupt the RNA-binding activity and LLPS of the SARS-CoV-2 NP. Our findings may facilitate the development of antiviral drugs targeting SARS-CoV-2 NP.

Coacervates meet the RNP-world: liquid-liquid phase separation and the emergence of biological compartmentalization

Understanding the emergence of biological compartmentalization in the context of the primordial soup is essential for unraveling the origin of life on Earth. This study revisits the classical coacervate theory, examining its historical development, supporting evidence, and major criticisms. Building upon Alexandr Oparin's foundational ideas, we propose an updated perspective in which the first biological compartments emerged through the formation of ribonucleoprotein (RNP) condensates-complexes of intrinsically disordered peptides and RNAs-via liquid-liquid phase separation (LLPS). Drawing on contemporary insights into how LLPS mediates intracellular organization, we argue that such membraneless RNP-based aggregates could have facilitated biochemical reactions in the aqueous environments of early Earth. By reinterpreting Oparin's coacervates through the lens of modern molecular biology, this study offers a renewed framework for understanding the origin of biological compartmentalization within the RNP-world hypothesis.

Phase separation in mitochondrial fate and mitochondrial diseases

Mitochondria are central metabolic organelles that control cell fate and the development of mitochondrial diseases. Traditionally, phase separation directly regulates cell functions by driving RNA, proteins, or other molecules to concentrate into lipid droplets. Recent studies show that phase separation regulates cell functions and diseases through the regulation of subcellular organelles, particularly mitochondria. In fact, phase separation is involved in various mitochondrial activities including nucleoid assembly, autophagy, and mitochondria-related inflammation. Here, we outline the key mechanisms through which phase separation influences mitochondrial activities and the development of mitochondrial diseases. Insights into how phase separation regulates mitochondrial activities and diseases will help us develop interventions for related diseases.

DDX10 Exacerbates Exosomal PD-L1-Dependent T Cell Exhaustion via Phase Separation of Rab27b in Oral Squamous Cell Carcinoma

DEAD-box ATPase 10 (DDX10), a prominent RNA-binding protein in the DDX family, has a critical function in cancer progression. Nevertheless, its well-defined mechanisms in oral squamous cell carcinoma (OSCC) are still not well understood. Here, we identify that DDX10 is substantially increased in OSCC, which is positively correlated with poor prognosis and malignant behavior. Mechanistically, we found that DDX10 had physical interaction with Rab27b by undergoing phase separation. Knockdown of DDX10 inhibited Rab27b-mediated exosome secretion and the expression of programmed cell death-ligand 1 (PD-L1) within its contents. Furthermore, knocking down DDX10 could restore the function and infiltration of T cells, hence inhibiting the progression of OSCC. These findings highlight that the oncogenic role of DDX10 in promoting exosomal PD-L1 secretion via phase separation with Rab27b has been preliminarily validated in T cell exhaustion in OSCC. A potential strategy for improving OSCC immunotherapy may involve the inhibition of DDX10.

Phase separation in DNA repair: orchestrating the cellular response to genomic stability

DNA repair is a hierarchically organized, spatially and temporally regulated process involving numerous repair factors that respond to various types of damage. Despite decades of research, the mechanisms by which these factors are recruited to and depart from repair sites have been a subject of intrigue. Recent advancements in the field have increasingly highlighted the role of phase separation as a critical facilitator of the efficiency of DNA repair. This review emphasizes how phase separation enhances the concentration and coordination of repair factors at damage sites, optimizing repair efficiency. Understanding how dysregulation of phase separation can impair DNA repair and alter nuclear organization, potentially leading to diseases such as cancer and neurodegenerative disorders, is crucial. This manuscript provides a comprehensive understanding of the pivotal role of phase separation in DNA repair, sheds light on the current research, and suggests potential future directions for research and therapeutic interventions.

Phase separation participates in the genetic regulation mechanism of hematopoietic stem cells: potential therapeutic methods

Hematopoietic stem cells (HSCs) are the primitive cells that give rise to common precursors for all blood cell lineages. Abnormalities in their number and/or function are important factors leading to the decline of immune function and the occurrence of various systemic diseases. Phase separation refers to a physicochemical mechanism in which intracellular liquid-liquid phase separation (LLPS) forms membrane-less organelles. It participates in various physiological activities and is related to the occurrence of diseases. Studies have shown that the functional activity of HSCs is regulated by complex mechanisms, and phase separation is closely related to these complex mechanisms such as genetic regulation, epigenetic regulation, microenvironment regulation, gene expression, autophagy degradation, and cell proliferation. With the deepening of research, the importance of phase separation in the pathogenesis and treatment of diseases such as leukemia and tumors has gradually emerged, but the deep mechanism of its regulation of HSCs genetic regulation still lacks exploration, and the direction of clinical targeted therapy is not yet clear. Here, we will summarize and elaborate the genetic regulation mechanism of HSCs, discuss the relationship between phase separation and the functional regulation of HSCs, and analyze the possibility of phase separation participating in the genetic regulation of HSCs to treat diseases, in order to provide help for the clinical implementation of targeted therapy for HSCs regulation.

Targeting redox-sensitive MBD2-NuRD condensate in cancer cells

Transcriptional silencing of hypermethylated tumour suppressor genes is a hallmark of tumorigenesis but the underlying mechanism remains enigmatic. Here we show that methyl-CpG-binding domain protein 2 (MBD2) forms nuclear condensate in diverse cancer cells, where it assembles and navigates the chromatin remodeller NuRD complex to these gene loci for transcriptional suppression, thus fuelling tumour growth. Disturbance of MBD2 condensate reduces the level of NuRD complex-specific proteins, destabilizes heterochromatin foci, facilitates chromatin relaxation and consequently impedes tumour progression. We demonstrate that MBD2 condensate is redox sensitive, mediated by C359. Pro-oxidative interventions disperse MBD2-NuRD condensate, thereby alleviating the transcriptional repression of tumour suppressor genes. Our findings illuminate a hitherto unappreciated function of MBD2 condensate in sustaining a repressive chromatin state essential for cancer cell proliferation and suggest an oxidative stress targeting approach for malignancies with excessive MBD2 condensate.

Oligolysine Enhances and Inhibits DNA Condensate Formation

The formation of biomolecular condensates via phase separation relates to various cellular functions. Reconstituting these condensates with designed molecules facilitates the exploration of their mechanisms and potential applications. Sequence-designed DNA nanostructures enable the investigation of how structural design influences condensate formation and the construction of functional artificial condensates. Despite the high designability of DNA-based condensates, free nanostructures that do not assemble into condensates remain a challenge. Combining DNA nanostructures with other molecules, such as peptides, represents a promising approach to overcoming the limitations of DNA condensates and gaining a deeper understanding of molecular condensates. Herein, we report the effects of cationic oligolysines with several residues on DNA condensate formation assembled from Y-shaped DNA nanostructures. DNA condensate formation was enhanced by oligolysines at an appropriate L/P ratio, which refers to the ratio of positively charged amine groups in lysine (L) to negatively charged nucleic acid phosphate groups (P). Oligolysines with five residues enhanced condensate formation while maintaining the sequence-specific interaction of DNA. In contrast, oligolysines inhibited condensate formation depending on the L/P ratio and residue number. This was attributed to nanostructure deformation caused by oligolysines. These results suggest that the amount and length of cationic peptides significantly affect the self-assembly of branched DNA nanostructures. This study offers important insights into biomolecular condensates that can guide further development of DNA/peptide hybrid condensates to enhance the functions of artificial condensates for use in artificial cells and molecular robots.

CircDNA2-Educated YTHDF2 Phase Separation Promotes PM2.5-Induced Malignant Transformation Through the Blunting of GADD45A Expression

Substantial epidemiological evidence suggests a significant correlation between particulate matter 2.5 (PM2.5) and lung cancer. However, the mechanism underlying this association needs to be further elucidated. Circular RNAs (circRNAs) have emerged as an important topic in the field of epigenetics and are involved in various cancers. This study aimed to explore the molecular basis of PM2.5-induced lung cancer from an epigenetic perspective and identify potential biomarkers. Initially, the construction of a chronic PM2.5 exposure model confirmed that PM2.5 exposure promoted the malignant transformation of human bronchial epithelial (HBE) cells. Mechanistically, abnormally upregulated circDNA2 inhibited the tumor suppressor gene growth arrest and DNA damage 45 alpha (GADD45A) mRNA in an N6-methyladenosine (m6A)-dependent manner, mediated by YTH N6-Methyladenosine RNA Binding Protein F2 (YTHDF2) after PM2.5 exposure. Further analyses revealed that circDNA2 can specifically bind to the YTHDF2 LC domain to promote YTHDF2 protein liquid-liquid phase separation (LLPS), providing sufficient evidence linking LLPS and particulate pollutant-induced tumorigenesis. In conclusion, this study provides new insights into the role of circDNA2 in PM2.5-induced lung cancer and confirms its clinical value as a potential prognostic biomarker for lung cancer.

Liquid-liquid phase separation drives immune signaling transduction in cancer: a bibliometric and visualized study from 1992 to 2024

Background

Liquid-liquid phase separation (LLPS) is a novel concept that could explain how living cells precisely modulate internal spatial and temporal functions. However, a comprehensive bibliometric analysis on LLPS and immune signaling processes in cancer is still scarce. This study aims to perform a bibliometric assessment of research to explore the landscape of LLPS research in immune signaling pathways for cancer.

Methods

Utilizing the Web of Science Core Collection database and multiple analysis software, we performed quantitative and qualitative analyses of the study situation between LLPS and immune signaling in cancer from 1992 to 2024.

Results

The corresponding authors were primarily from China and the USA. The most relevant references were the "International Journal of Molecular Sciences", "Proteomics". The annual number of publications exhibited a fast upward tendency from 2020 to 2024. The most frequent key terms included expression, separation, activation, immunotherapy, and mechanisms. Qualitative evaluation emphasized the TCR, BCR, cGAS-STING, RIG-1, NF-κB signaling pathways associated with LLPS processes.

Conclusion

This research is the first to integratively map out the knowledge structure and forward direction in the area of immune transduction linked with LLPS over the past 30 years. In summary, although this research area is still in its infancy, illustrating the coordinated structures and communications between cancer and immune signaling with LLPS within a spatial framework will offer deeper insights into the molecular mechanisms of cancer development and further enhance the effectiveness of existing immunotherapies.

Establishment of liquid-liquid phase separation-related prognostic model in lung adenocarcinoma and systematic analysis of its clinical significance

PurposeTo detect the prognostic importance of liquid-liquid phase separation (LLPS) in lung adenocarcinoma.MethodsThe gene expression files, copy number variation data, and clinical data were downloaded from The Cancer Genome Atlas cohort. LLPS-related genes were acquired from the DrLLPS website. The prognostic model based on LLPS was constructed by the Cox regression and LASSO regression analyses after the identification of LLPS-related differentially expressed genes (DEGs). Gene Ontology functional and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed. The LLPS-related prognostic risk score was validated by GSE31210 and GSE72094. The overall survival of lung adenocarcinoma patients was predicted by plotting a nomogram. The biological features of the high-risk lung adenocarcinoma were evaluated by the CIBERSORT, ESTIMATE, Gene Set Variation Analysis, and Genomics of Drug Sensitivity in Cancer. Reverse transcription-quantitative polymerase chain reaction detected hub gene expression.ResultsA total of 91 DEGs were screened out in LLPS, among which 9 genes were discovered as prognostic biomarkers of lung adenocarcinoma. GRIA1, CRTAC1, MAGEA4, and MAPK4 were identified as hub genes by the LASSO Cox regression analysis. High-risk and low-risk groups were divided according to the risk index, with the high-risk group displaying a markedly worse outcome. CRTAC1 expression was significantly decreased, MAGEA4 and MAPK4 expressions were increased, while GRIA1 expression was altered in lung adenocarcinoma cells. Tumor microenvironment, signaling pathway enrichment, and drug sensitivity significantly differed between different risk groups.ConclusionsThis work proposed a prognostic tool based on the LLPS-related gene signature to offer prospective and effective biomarkers for lung adenocarcinoma prognosis.

Engineering microbial cell factories by multiplexed spatiotemporal control of cellular metabolism: Advances, challenges, and future perspectives

Generally, the metabolism in microbial organism is an intricate, spatiotemporal process that emerges from gene regulatory networks, which affects the efficiency of product biosynthesis. With the coming age of synthetic biology, spatiotemporal control systems have been explored as versatile strategies to promote product biosynthesis at both spatial and temporal levels. Meanwhile, the designer synthetic compartments provide new and promising approaches to engineerable spatiotemporal control systems to construct high-performance microbial cell factories. In this article, we comprehensively summarize recent developments in spatiotemporal control systems for tailoring advanced cell factories, and illustrate how to apply spatiotemporal control systems in different microbial species with desired applications. Future challenges of spatiotemporal control systems and perspectives are also discussed.

Regulation of alternative splicing by CBF-mediated protein condensation in plant response to cold stress

Cold acclimation is critical for the survival of plants in temperate regions under low temperatures, and C-REPEAT BINDING FACTORs (CBFs) are well established as key transcriptional factors that regulate this adaptive process by controlling the expression of cold-responsive genes. Here we demonstrate that CBFs are involved in modulating alternative splicing during cold acclimation through their interaction with subunits of the spliceosome complex. Under cold stress, CBF proteins accumulate and directly interact with SKI-INTERACTING PROTEIN (SKIP), a key component of the spliceosome, which positively regulates acquired freezing tolerance. This interaction facilitates the formation of SKIP nuclear condensates, which enhances the association between SKIP and specific cold-responsive transcripts, thereby increasing their splicing efficiency. Our findings uncover a regulatory role of CBFs in alternative splicing and highlight their pivotal involvement in the full development of cold acclimation, bridging transcriptional and post-transcriptional regulatory mechanisms.

Ca2+/calmodulin-dependent protein kinase II β decodes ER Ca2+ transients to trigger autophagosome formation

In multicellular organisms, very little is known about how Ca2+ transients on the ER outer surface elicited by autophagy stimuli are sustained and decoded to trigger autophagosome formation. Here, we show that Ca2+/calmodulin-dependent protein kinase II β (CaMKIIβ) integrates ER Ca2+ transients to trigger liquid-liquid phase separation (LLPS) of the autophagosome-initiating FIP200 complex. In response to ER Ca2+ transients, CaMKIIβ is recruited from actin filaments and forms condensates, which serve as sites for the emergence of or interaction with FIP200 puncta. CaMKIIβ phosphorylates FIP200 at Thr269, Thr1127, and Ser1484 to modulate LLPS and properties of the FIP200 complex, thereby controlling its function in autophagosome formation. CaMKIIβ also controls the amplitude, duration, and propagation of ER Ca2+ transients during autophagy induction. CaMKIIβ mutations identified in the neurodevelopmental disorder MRD54 affect the function of CaMKIIβ in autophagy. Our study reveals that CaMKIIβ is essential for sustaining and decoding ER Ca2+ transients to specify autophagosome formation in mammalian cells.

Liquid-liquid phase separation in viral infection: From the occurrence and function to treatment potentials

Liquid-liquid phase separation (LLPS) of biomacromolecules, as a widespread cellular functional mechanism, is closely related to life processes, and is also commonly present in the lifecycle of viruses. Viral infection often leads to the recombination and redistribution of intracellular components to form biomacromolecule condensates assembled from viral replication-related proteins and intracellular components, which plays an important role in the process of viral infection. In this review, the key and influencing factors of LLPS are generalized, which mainly depend on various molecular interactions and environmental conditions in solution. Meanwhile, some examples of viruses utilizing LLPS are summarized, which are conducive to further understanding the subtle and complex biological regulatory processes between phase condensation and viruses. Finally, some representative antiviral drugs targeting phase separation that have been discovered are also outlined. In conclusion, in-depth study of the role of LLPS in viral infection is helpful to understand the mechanisms of virus-related diseases from a new perspective, and also provide a new therapeutic strategy for future treatments.

Protein Condensates Unfold G-Quadruplex Resembling a Helicase Activity

Membrane-less organelles, formed by liquid-liquid phase separation, participate in many vital cellular processes and have received extensive attention recently. A notable form of noncanonical nucleic acid secondary structure, G-quadruplex (G4), interacts with the scaffolding proteins in these membrane-less organelles and becomes an integral part of this condensed phase. However, the structure and stability features of the integrated G4 remain poorly characterized. Herein, we employed NMR along with other biophysical methods to investigate the conformation of a G4 within condensates formed by a disordered protein known as DDX4N1. We discovered that the human telomeric sequence MHT24, which forms a G4 structure in a non-condensed phase solution of protein DDX4N1, unfolds when it is within DDX4N1 condensates due to phase separation. Our findings provide an instance of a protein acquiring new functionality through phase separation process, which deepen our understanding of how protein condensates regulate G4 structure and their functions.

"Intrinsic disorder-protein modification-LLPS-tumor" regulatory axis: From regulatory mechanisms to precision medicine

Liquid-Liquid Phase Separation (LLPS) is an important mechanism for the formation of functional droplets. Protein modification is an important pathway to regulate LLPS, in which series of modifying groups realize dynamic regulation by changing the charge and spatial resistance of the modified proteins. Meanwhile, uncontrolled protein modifications associated with LLPS dysregulation are highly correlated with tumorigenesis and development, suggesting the existence of a potential regulatory axis between the three. In this review, we pioneered "protein modification-LLPS-tumor" regulatory axis and summarized protein modifications that regulate LLPS in cancer cells (including phosphorylation, acetylation, methylation, ubiquitination, SUMOylation, lactate, ADP-ribosylation, O-glycosylation, and acylation) and their associated modification mechanisms. Finally, we outline advances in precision medicine based on this regulatory axis. The aim of this review is to expand the understanding of protein modifications regulating LLPS under normal or abnormal cellular conditions and to provide possible ideas for precision therapy.

Rbfox3 Promotes Transformation of MDSC-Like Tumor Cells to Shape Immunosuppressive Microenvironment

Myeloid-derived suppressor cells (MDSCs) within the tumor microenvironment (TME) contribute to the malignant progression of tumors by exerting immunosuppressive effects. Bacterial lipopolysaccharides (LPS) have been widely demonstrated in various types of solid tumors. LPS can promote the malignant progression of tumors, which mechanism has not yet been fully elucidated. In this study, a type of MDSC-like tumor cells (MLTCs) is found in tumor tissues induced by low-dose and long-term LPS stimulation. MLTCs can simultaneously express tumor cell and MDSCs markers. Similar to MDSCs, MLTCs can produce arginine, nitric oxide, and reactive oxygen species and inhibit the activity of NK and T cells to promote the formation of an immunosuppressive microenvironment. MLTCs can also promote tumor cell proliferation and vasculogenic mimicry formation. CRISPR-Cas9 activity screening studies identified RNA-binding Fox-1 homolog 3 (Rbfox3) as a critical protein for MLTCs formation after LPS treatment. Rbfox3 can transcriptionally regulate the expression of Ass1 in the form of phase-separated particles. Crocin can inhibit the generation of MLTCs by disrupting phase-separated particles of Rbfox3 and enhance the anti-tumor effects of immune checkpoint inhibitors (ICIs).

Recent advances in the synthesis and application of biomolecular condensates

Biomolecular condensates (BMCs) represent a group of organized and programmed systems that participate in gene transcription, chromosome organization, cell division, tumorigenesis, and aging. However, the understanding of BMCs in terms of internal organizations and external regulations remains at an early stage. Recently, novel approaches such as synthetic biology have been used for de novo synthesis of BMCs. These synthesized BMCs (SBMCs) driven by phase separation adeptly resemble the self-assembly and dynamics of natural BMCs, offering vast potentials in basic and applied research. This review introduces recent progresses in phase separation-induced SBMCs, attempting to elaborate on the intrinsic principles and regulatory methodologies used to construct SBMCs. Furthermore, the scientific applications of SBMCs are illustrated, as indicated by the studies of chromosome structure, pathogenesis, biomanufacturing, artificial cell design, and drug delivery. The controllable SBMCs offer a powerful tool for understanding metabolic regulations, cellular organizations, and disease-associated protein aggregations, raising both opportunities and challenges in the future of biomaterial, biotechnology, and biomedicine.

A Combined Approach to Extract Rotational Dynamics of Globular Proteins Undergoing Liquid-Liquid Phase Separation

The formation of protein condensates (droplets) via liquid-liquid phase separation (LLPS) is a commonly observed phenomenon in vitro. Changing the environmental properties with cosolutes, molecular crowders, protein partners, temperature, pressure, etc. has been shown to favor or disfavor the formation of protein droplets by fine-tuning the water-water, water-protein, and protein-protein interactions. Therefore, these environmental properties and their spatiotemporal fine-tuning are likely to be important also in a cellular context at the existing protein expression levels. One of the key physicochemical properties of biomolecules impacted by molecular crowding is diffusion, which determines the viscoelastic behavior of the condensates. Here, we investigate the change in the rotational diffusion of γD-crystallin, undergoing LLPS in vitro in aqueous solutions in the absence and presence of cosolutes. We studied its rotational dynamics using molecular dynamics simulations (MD), electron paramagnetic resonance (EPR) spectroscopy, and fluorescence spectroscopy. MD simulations performed under dilute and crowded conditions show that the rotational diffusion of crystallin in water is retarded by 1 to 2 orders of magnitude in the condensed phase. To obtain the rotational dynamics in the dilute phase, we used fluorescence anisotropy and to extract the retardation factor in the condensed phase, we used spin-labeled γD-crystallin proteins as EPR viscosity nanoprobes. Aided by a viscosity nanoruler calibrated with solutions at increasing sucrose concentrations, we validated the rotational diffusion retardation predicted by MD simulations. This study underlines the predictive power of MD simulations and showcases the use of a sensitive EPR nanoprobe to extract the viscosity of biomolecular condensates.

C1orf115 interacts with clathrin adaptors to undergo endocytosis and induces ABCA1 to promote enteric cholesterol efflux

C1orf115 has been identified in high-throughput screens as a regulator of multidrug resistance possibly mediated through an interaction with ATP-dependent membrane transporter ABCB1. Here we show that C1orf115 not only shares structural similarities with FACI/C11orf86 to interact with clathrin adaptors to undergo endocytosis, but also induces ABCA1 transcription to promote cholesterol efflux. C1orf115 consists of an N-terminal intrinsically disordered region and a C-terminal α-helix. Its α-helix binds to phosphoinositides, and mediates C1orf115 localization to the plasma membrane, nucleolus and nuclear speckles. An acidic dileucine-like motif "ExxxIL" within C1orf115 binds with the AP2 complex and mediates its localization to clathrin-coating pits. The positively charged amphipathic α-helix undergoes acetylation, which redistributes C1orf115 from the plasma membrane and nucleolus to nuclear speckles. C1orf115 is widely expressed and most abundant in the small intestine. The ability of C1orf115 in clathrin-mediated endocytosis is required for its regulation of drug resistance, which is modulated by acetylation. RNA-seq analysis reveals that C1orf115 induces intestinal transcription of another ATP-dependent transporter ABCA1 and consequently promotes ABCA1-mediated cholesterol efflux in enterocytes. Our study provides mechanistic insight into how C1orf115 modulates drug resistance and cholesterol efflux through clathrin-mediated endocytosis and ABCA1 expression.

Feedback-induced phase separation of hollow condensates to create biomimetic membraneless compartments

Intracellular macromolecules have the ability to form membraneless compartments, such as vacuoles and hollow condensates, through liquid-liquid phase separation (LLPS) in order to adapt to changes in their environment. The development of artificial non-homogeneous compartments, such as multiphase hollow or multicavity condensates, has gained significant attention due to their potential to uncover the mechanisms underlying the formation of artificial condensates and biomolecular condensates. However, the complexity of design and construction has hindered progress, particularly in creating dynamic non-homogeneous compartments. In this study, we present a dynamic membraneless compartment using peptide-oligonucleotide conjugates derived from short elastin-like polypeptides (sELP-ONs), which undergo pH-mediated phase transition. Below pH 8.8, the microcompartment exists as microdroplets that transform into non-homogeneous hollow condensates above pH 8.8. Notably, these hollow condensates retain liquid properties and high molecular ordering, and effectively sequester guest molecules with a hollow condensed layer. Furthermore, our sELP-ON microcompartments exhibit a feedback-induced phase transition in response to environmental pH fluctuations generated by complex enzymatic reactions mimicking cellular metabolism, providing a novel dynamic model for creating biomimetic membraneless compartments.

Utilizing liquid-liquid biopolymer regulators to predict the prognosis and drug sensitivity of hepatocellular carcinoma

BACKGROUND

Liquid-liquid phase separation (LLPS) is essential for the formation of membraneless organelles and significantly influences cellular compartmentalization, chromatin remodeling, and gene regulation. Previous research has highlighted the critical function of liquid-liquid biopolymers in the development of hepatocellular carcinoma (HCC).

METHODS

This study conducted a comprehensive review of 3,685 liquid-liquid biopolymer regulators, leading to the development of a LLPS related Prognostic Risk Score (LPRS) for HCC through bootstrap-based univariate Cox, Random Survival Forest (RSF), and LASSO analyses. A prognostic nomogram for HCC patients was developed using LPRS and other clinicopathological factors. We utilized SurvSHAP to identify key genes within the LPRS influencing HCC prognosis. To validate our findings, we collected 49 HCC cases along with adjacent tissue samples and confirmed the correlation between DCAF13 expression and HCC progression through qRT-PCR analysis and in vitro experiments.

RESULTS

LPRS was established with 8 LLPS-related genes (TXN, CBX2, DCAF13, SLC2A1, KPNA2, FTCD, MAPT, and SAC3D1). Further research indicated that a high LPRS is closely associated with vascular invasion, histological grade (G3-G4), and TNM stage (III-IV) in HCC, concurrently establishing LPRS as an independent risk factor for prognosis. A nomogram that integrates LPRS with TNM staging and patient age markedly improves the predictive accuracy of survival outcomes for HCC patients. Our findings suggest that increased DCAF13 expression in HCC plays a crucial role in cancer progression and angiogenesis. Navitoclax has emerged as a promising treatment for HCC patients with high LPRS levels, offering a novel therapeutic direction by targeting LLPS.

CONCLUSION

We have formulated a novel LPRS model that is capable of accurately predicting the clinical prognosis and drug sensitivity of HCC. DCAF13 might play a pivotal role in malignant progression mediated by LLPS.

Novel insights into RNA polymerase II transcription regulation: transcription factors, phase separation, and their roles in cardiovascular diseases

Transcription factors (TFs) are specialized proteins that bind DNA in a sequence-specific manner and modulate RNA polymerase II (Pol II) in multiple steps of the transcription process. Phase separation is a spontaneous or driven process that can form membrane-less organelles called condensates. By creating different liquid phases at active transcription sites, the formation of transcription condensates can reduce the water content of the condensate and lower the dielectric constant in biological systems, which in turn alters the structure and function of proteins and nucleic acids in the condensate. In RNA Pol II transcription, phase separation formation shortens the time at which TFs bind to target DNA sites and promotes transcriptional bursting. RNA Pol II transcription is engaged in developing several diseases, such as cardiovascular disease, by regulating different TFs and mediating the occurrence of phase separation. This review aims to summarize the advances in the molecular mechanisms of RNA Pol II transcriptional regulation, in particular the effect of TFs and phase separation. The role of RNA Pol II transcriptional regulation in cardiovascular disease will be elucidated, providing potential therapeutic targets for the management and treatment of cardiovascular disease.

Advances in Aggrephagy: Mechanisms, Disease Implications, and Therapeutic Strategies

The accumulation of misfolded proteins within cells leads to the formation of protein aggregates that disrupt normal cellular functions and contribute to a range of human pathologies, notably neurodegenerative disorders. Consequently, the investigation into the mechanisms of aggregate formation and their subsequent clearance is of considerable importance for the development of therapeutic strategies. The clearance of protein aggregates is predominantly achieved via the autophagy-lysosomal pathway, a process known as aggrephagy. In this pathway, autophagosome biogenesis and lysosomal digestion provide necessary conditions for the clearance of protein aggregates, while autophagy receptors such as P62, NBR1, TAX1BP1, TOLLIP, and CCT2 facilitate the recognition of protein aggregates by the autophagy machinery, playing a pivotal role in their degradation. This review will introduce the mechanisms of aggregate formation, progression, and degradation, with particular emphasis on advances in aggrephagy, providing insights for aggregates-related diseases and the development of novel therapeutic strategies.

Nuclear Structure, Size Regulation, and Role in Cell Migration

The nucleus serves as a pivotal regulatory and control hub in the cell, governing numerous aspects of cellular functions, including DNA replication, transcription, and RNA processing. Therefore, any deviations in nuclear morphology, structure, or organization can strongly affect cellular activities. In this review, we provide an updated perspective on the structure and function of nuclear components, focusing on the linker of nucleoskeleton and cytoskeleton complex, the nuclear envelope, the nuclear lamina, and chromatin. Additionally, nuclear size should be considered a fundamental parameter for the cellular state. Its regulation is tightly linked to environmental changes, development, and various diseases, including cancer. Hence, we also provide a concise overview of different mechanisms by which nuclear size is determined, the emerging role of the nucleus as a mechanical sensor, and the implications of altered nuclear morphology on the physiology of diseased cells.

RNA-dependent RNA polymerase of predominant human norovirus forms liquid-liquid phase condensates as viral replication factories

Many viral proteins form biomolecular condensates via liquid-liquid phase separation (LLPS) to support viral replication and evade host antiviral responses, and thus, they are potential targets for designing antivirals. In the case of nonenveloped positive-sense RNA viruses, forming such condensates for viral replication is unclear and less understood. Human noroviruses (HuNoVs) are positive-sense RNA viruses that cause epidemic and sporadic gastroenteritis worldwide. Here, we show that the RNA-dependent RNA polymerase (RdRp) of pandemic GII.4 HuNoV forms distinct condensates that exhibit all the signature properties of LLPS with sustained polymerase activity and the capability of recruiting components essential for viral replication. We show that such condensates are formed in HuNoV-infected human intestinal enteroid cultures and are the sites for genome replication. Our studies demonstrate the formation of phase-separated condensates as replication factories in a positive-sense RNA virus, which plausibly is an effective mechanism to dynamically isolate RdRp replicating the genomic RNA from interfering with the ribosomal translation of the same RNA.

The nuclear condensates of ESE3/EHF induce cellular senescence without the associated inflammatory secretory phenotype in pancreatic ductal adenocarcinoma

Senescent cells are in a stable state of cell cycle arrest, leading to a natural barrier to tumorigenesis. Senescent cells secrete a pool of molecules, including cytokines, chemokines, proteases, and growth factors, termed the senescence-associated secretory phenotype (SASP), paradoxically contributing to pro-tumorigenic processes. However, the mechanism for regulating senescence and SASP in tumor cells remains unclear. Here, SPiDER senescence probe-based CRISPR/Cas9 library screening has identified ETS homologous factor (EHF) could effectively induce cellular senescence but without SASP, which could further significantly inhibit PDAC progression. Mechanically, tumoral EHF could form liquid-like condensates and further transcriptionally repress the expression of telomerase reverse transcriptase (TERT) and associated inflammatory factors, such as IL-6, CXCL12, etc. The reduction of TERT led to the telomere shortening and dysfunction of cancer cells, which further drove cellular senescence in PDAC. Moreover, EHF-mediated repression of inflammatory factors effectively declined the infiltration of immunosuppressive cells including MDSCs, Tregs, neutrophils, and promoted the accumulation of CD8+T cells and NK cells, which enhanced tumor immune surveillance. Furthermore, high throughput drug screening identified that Bilobetin could effectively promote the phase separation of EHF, which could further induce tumoral senescence but without SASP. In vivo, preclinical translational research uncovered that Bilobetin could ameliorate immunosuppressive tumor microenvironment (TME) and sensitize PDAC to anti-PD-1 therapy. Overall, our study revealed EHF as a potential candidate to overcome the paradoxical function of cellular senescence and elucidated the effects of its phase separation state on gene regulation, which provided new insights and strategies for PDAC treatment.

Comprehensive analysis of liquid-liquid phase separation propensities of HSV-1 proteins and their interaction with host factors

In recent years, it has been shown that the liquid-liquid phase separation (LLPS) of virus proteins plays a crucial role in their life cycle. It promotes the formation of viral replication organelles, concentrating viral components for efficient replication and facilitates the assembly of viral particles. LLPS has emerged as a crucial process in the replication and assembly of herpes simplex virus-1 (HSV-1). Recent studies have identified several HSV-1 proteins involved in LLPS, including the myristylated tegument protein UL11 and infected cell protein 4; however, a complete proteome-level understanding of the LLPS-prone HSV-1 proteins is not available. We provide a comprehensive analysis of the HSV-1 proteome and explore the potential of its proteins to undergo LLPS. By integrating sequence analysis, prediction algorithms and an array of tools and servers, we identified 10 HSV-1 proteins that exhibit high LLPS potential. By analysing the amino acid sequences of the LLPS-prone proteins, we identified specific sequence motifs and enriched amino acid residues commonly found in LLPS-prone regions. Our findings reveal a diverse range of LLPS-prone proteins within the HSV-1, which are involved in critical viral processes such as replication, transcriptional regulation and assembly of viral particles. This suggests that LLPS might play a crucial role in facilitating the formation of specialized viral replication compartments and the assembly of HSV-1 virion. The identification of LLPS-prone proteins in HSV-1 opens up new avenues for understanding the molecular mechanisms underlying viral pathogenesis. Our work provides valuable insights into the LLPS landscape of HSV-1, highlighting potential targets for further experimental validation and enhancing our understanding of viral replication and pathogenesis.

Molecular Mechanisms Underlying Initiation and Activation of Autophagy

Autophagy is an important catabolic process to maintain cellular homeostasis and antagonize cellular stresses. The initiation and activation are two of the most important aspects of the autophagic process. This review focuses on mechanisms underlying autophagy initiation and activation and signaling pathways regulating the activation of autophagy found in recent years. These findings include autophagy initiation by liquid-liquid phase separation (LLPS), autophagy initiation in the endoplasmic reticulum (ER) and Golgi apparatus, and the signaling pathways mediated by the ULK1 complex, the mTOR complex, the AMPK complex, and the PI3KC3 complex. Through the review, we attempt to present current research progress in autophagy regulation and forward our understanding of the regulatory mechanisms and signaling pathways of autophagy initiation and activation.

KCTD10 p.C124W variant contributes to schizophrenia by attenuating LLPS-mediated synapse formation

KCTD10, a member of the potassium channel tetramerization domain (KCTD) family, is implicated in neuropsychiatric disorders and functions as a substrate recognition component within the RING-type ubiquitin ligase complex. A rare de novo variant of KCTD10, p.C124W, was identified in schizophrenia cases, yet its underlying pathogenesis remains unexplored. Here, we demonstrate that heterozygous KCTD10 C124W mice display pronounced synaptic abnormalities and exhibit schizophrenia-like behaviors. Mechanistically, we reveal that KCTD10 undergoes liquid-liquid phase separation (LLPS), a process orchestrated by its intrinsically disordered region (IDR). p.C124W mutation disrupts this LLPS capability, leading to diminished degradation of RHOB and subsequent excessive accumulation in the postsynaptic density fractions. Notably, neither IDR deletion nor p.C124W mutation in KCTD10 mitigates the synaptic abnormalities caused by Kctd10 deficiency. Thus, our findings implicate that LLPS may be associated with the pathogenesis of KCTD10-associated brain disorders and highlight the potential of targeting RHOB as a therapeutic strategy for diseases linked to mutations in KCTD10 or RHOB.

HSD17B13 liquid-liquid phase separation promotes leukocyte adhesion in chronic liver inflammation

The rs72613567:TA polymorphism in 17-beta hydroxysteroid dehydrogenase 13 (HSD17B13) has been found to reduce the progression from steatosis to metabolic dysfunction-associated steatohepatitis (MASH). In this study, we sought to define the pathogenic role of HSD17B13 in triggering liver inflammation. Here, we demonstrate that HSD17B13 forms liquid-liquid phase separation (LLPS) around lipid droplets in the livers of MASH patients. The dimerization of HSD17B13 supports the LLPS formation and promotes its enzymatic function. HSD17B13 LLPS increases the biosynthesis of platelet activating factor (PAF), which in turn promotes fibrinogen synthesis and leukocyte adhesion. Blockade of the PAF receptor or STAT3 pathway inhibits the fibrinogen synthesis and leukocyte adhesion. Importantly, adeno-associated viral-mediated xeno-expression of human HSD17B13 exacerbates western diet/carbon tetrachloride-induced liver inflammation in Hsd17b13-/- mice. In conclusion, our results suggest that HSD17B13 LLPS triggers liver inflammation by promoting PAF-mediated leukocyte adhesion, and targeting HSD17B13 phase transition could be a promising therapeutic approach for treating hepatic inflammation in chronic liver disease.

Implications of liquid-liquid phase separation and ferroptosis in Alzheimer's disease

Neuronal cell demise represents a prevalent occurrence throughout the advancement of Alzheimer's disease (AD). However, the mechanism of triggering the death of neuronal cells remains unclear. Its potential mechanisms include aggregation of soluble amyloid-beta (Aβ) to form insoluble amyloid plaques, abnormal phosphorylation of tau protein and formation of intracellular neurofibrillary tangles (NFTs), neuroinflammation, ferroptosis, oxidative stress, liquid-liquid phase separation (LLPS) and metal ion disorders. Among them, ferroptosis is an iron-dependent lipid peroxidation-driven cell death and emerging evidences have demonstrated the involvement of ferroptosis in the pathological process of AD. The sensitivity to ferroptosis is tightly linked to numerous biological processes. Moreover, emerging evidences indicate that LLPS has great impacts on regulating human health and diseases, especially AD. Soluble Aβ can undergo LLPS to form liquid-like droplets, which can lead to the formation of insoluble amyloid plaques. Meanwhile, tau has a high propensity to condensate via the mechanism of LLPS, which can lead to the formation of NFTs. In this review, we summarize the most recent advancements pertaining to LLPS and ferroptosis in AD. Our primary focus is on expounding the influence of Aβ, tau protein, iron ions, and lipid oxidation on the intricate mechanisms underlying ferroptosis and LLPS within the domain of AD pathology. Additionally, we delve into the intricate cross-interactions that occur between LLPS and ferroptosis in the context of AD. Our findings are expected to serve as a theoretical and experimental foundation for clinical research and targeted therapy for AD.

DAZAP1 Phase Separation Regulates Mitochondrial Metabolism to Facilitate Invasion and Metastasis of Oral Squamous Cell Carcinoma

Tumor invasion and metastasis are the underlying causes of high mortality rate due to oral squamous cell carcinoma (OSCC). Energy metabolism reprogramming has been identified as a crucial process mediating tumor metastasis, thus indicating an urgent need for an in-depth investigation of the specific mechanisms of tumor energy metabolism. Here, we identified an RNA-binding protein, DAZ-associated protein 1 (DAZAP1), as a tumor-promoting factor with an important role in OSCC progression. DAZAP1 was significantly upregulated in OSCC, which enhanced the migration and invasion of OSCC cells and induced the epithelial-mesenchymal transition (EMT). RNA sequencing analysis and experimental validation demonstrated that DAZAP1 regulates mitochondrial energy metabolism in OSCC. Mechanistically, DAZAP1 underwent liquid-liquid phase separation to accumulate in the nucleus where it enhanced cytochrome c oxidase 16 (COX16) expression by regulating pre-mRNA alternative splicing, thereby promoting OSCC invasion and mitochondrial respiration. In mouse OSCC models, loss of DAZAP1 suppressed EMT, downregulated COX16, and reduced tumor growth and metastasis. In samples from patients with OSCC, expression of DAZAP1 positively correlated with COX16 and a high expression of both proteins was associated with poor patient prognosis. Together, these findings revealed a mechanism by which DAZAP1 supports mitochondrial metabolism and tumor development of OSCC, suggesting the potential of therapeutic strategies targeting DAZAP1 to block OSCC invasion and metastasis. Significance: The RNA-binding protein DAZAP1 undergoes phase separation to enhance COX16 expression and mediate metabolic reprogramming that enables tumor metastasis, highlighting DAZAP1 as a potential metabolic target for cancer therapy.

The role of liquid-liquid phase separation in the disease pathogenesis and drug development

Misfolding and aggregation of specific proteins are associated with liquid-liquid phase separation (LLPS), and these protein aggregates can interfere with normal cellular functions and even lead to cell death, possibly affecting gene expression regulation and cell proliferation. Therefore, understanding the role of LLPS in disease may help to identify new mechanisms or therapeutic targets and provide new strategies for disease treatment. There are several ways to disrupt LLPS, including screening small molecules or small molecule drugs to target the upstream signaling pathways that regulate the LLPS process, selectively dissolve and destroy RNA droplets or protein aggregates, regulate the conformation of mutant protein, activate the protein degradation pathway to remove harmful protein aggregates. Furthermore, harnessing the mechanism of LLPS can improve drug development, including preparing different kinds of drug delivery carriers (microneedles, nanodrugs, imprints), regulating drug internalization and penetration behaviors, screening more drugs to overcome drug resistance and enhance receptor signaling. This review initially explores the correlation between aberrant LLPS and disease, highlighting the pivotal role of LLPS in preparing drug development. Ultimately, a comprehensive investigation into drug-mediated regulation of LLPS processes holds significant scientific promise for disease management.

mInsc coordinates Par3 and NuMA condensates for assembly of the spindle orientation machinery in asymmetric cell division

As a fundamental process governing the self-renewal and differentiation of stem cells, asymmetric cell division is controlled by several conserved regulators, including the polarity protein Par3 and the microtubule-associated protein NuMA, which orchestrate the assembly and interplay of the Par3/Par6/mInsc/LGN complex at the apical cortex and the LGN/Gαi/NuMA/Dynein complex at the mitotic spindle to ensure asymmetric segregation of cell fate determinants. However, this model, which is well-supported by genetic studies, has been challenged by evidence of competitive interaction between NuMA and mInsc for LGN. Here, the solved crystal structure of the Par3/mInsc complex reveals that mInsc competes with Par6β for Par3, raising questions about how proteins assemble overlapping targets into functional macromolecular complexes. Unanticipatedly, we discover that Par3 can recruit both Par6β and mInsc by forming a dynamic condensate through phase separation. Similarly, the phase-separated NuMA condensate enables the coexistence of competitive NuMA and mInsc with LGN in the same compartment. Bridge by mInsc, Par3/Par6β and LGN/NuMA condensates coacervate, robustly enriching all five proteins both in vitro and within cells. These findings highlight the pivotal role of protein condensates in assembling multi-component signalosomes that incorporate competitive protein-protein interaction pairs, effectively overcoming stoichiometric constraints encountered in conventional protein complexes.

Stability and structure of the aqueous LiTFSI-LiCl interface

It has recently been demonstrated that aqueous lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) and lithium chloride (LiCl) solutions can form stable liquid-liquid biphasic systems when both electrolyte phases have sufficiently high concentrations. In this work, we combine molecular dynamics simulations and experimental analysis to investigate what drives the formation of the interface and how the interfacial molecular structure correlates with its thermodynamic stability. We observe that at the liquid-vapour interface, TFSI- anions exhibit surfactant-like properties, leading to a reduction in surface tension and an increase in interfacial thickness. In contrast, the interfacial stability of the LiTFSI-LiCl biphasic systems increases with the concentration of both salts, as evidenced by the increasing surface tension and decreasing interfacial thickness. The opposing effects that the ionic concentration has on the thermodynamic stability of the different interfaces are linked to the anions' interfacial adsorption/desorption, which in turn affects the number and strength of water-water hydrogen bonds, the interfacial molecular structure and the diffusion of cations across the interface. Finally, calculations and experiments indicate that the liquid-liquid separation is driven primarily by the concentration of LiCl, and is the result of a 'salting out' effect.

Exogenous Pregnane X Receptor Does Not Undergo Liquid-Liquid Phase Separation in Nucleus under Cell-Based In Vitro Conditions

Pregnane X receptor (PXR) belongs to the nuclear receptor superfamily that plays a crucial role in hepatic physiologic and pathologic conditions. Phase separation is a process in which biomacromolecules aggregate and condense into a dense phase as liquid condensates and coexist with a dilute phase, contributing to various cellular and biologic functions. Until now, whether PXR could undergo phase separation remains unclear. This study aimed to investigate whether PXR undergoes phase separation. Analysis of the intrinsically disordered regions (IDRs) using algorithm tools indicated a low propensity of PXR to undergo phase separation. Experimental assays such as hyperosmotic stress, agonist treatment, and optoDroplets assay demonstrated the absence of phase separation for PXR. OptoDroplets assay revealed the inability of the fusion protein of Cry2 with PXR to form condensates upon blue light stimulation. Moreover, phase separation of PXR did not occur even though the mRNA and protein expression levels of PXR target, cytochrome P450 3A4, changed after sorbitol treatment. In conclusion, for the first time, these findings suggested that exogenous PXR does not undergo phase separation following activation or under hyperosmotic stress in nucleus of cells. SIGNIFICANCE STATEMENT: PXR plays a critical role in hepatic physiological and pathological processes. The present study clearly demonstrated that exogenous PXR does not undergo phase separation after activation by agonist or under hyperosmotic stress in nucleus. These findings may help understand PXR biology.

Liquid-liquid phase separation of microtubule-binding proteins in the regulation of spindle assembly

Cell division is a highly regulated process essential for the accurate segregation of chromosomes. Central to this process is the assembly of a bipolar mitotic spindle, a highly dynamic microtubule (MT)-based structure responsible for chromosome movement. The nucleation and dynamics of MTs are intricately regulated by MT-binding proteins. Over the recent years, various MT-binding proteins have been reported to undergo liquid-liquid phase separation, forming either single- or multi-component condensates on MTs. Herein, we provide a comprehensive summary of the phase separation characteristics of these proteins. We underscore their critical roles in MT nucleation, spindle assembly and kinetochore-MT attachment during the cell division process. Furthermore, we discuss the current challenges and various remaining unsolved problems, highlights the ongoing research efforts aimed at a deeper understanding of the role of the phase separation process during spindle assembly and orientation. Our review aims to contribute to the collective knowledge in this area and stimulate further investigations that will enhance our comprehension of the intricate mechanisms governing cell division.

Unveiling the veil of RNA binding protein phase separation in cancer biology and therapy

RNA-binding protein (RBP) phase separation in oncology reveals a complex interplay crucial for understanding tumor biology and developing novel therapeutic strategies. Aberrant phase separation of RBPs significantly influences gene regulation, signal transduction, and metabolic reprogramming, contributing to tumorigenesis and drug resistance. Our review highlights the integral roles of RBP phase separation in stress granule dynamics, mRNA stabilization, and the modulation of transcriptional and translational processes. Furthermore, interactions between RBPs and non-coding RNAs add a layer of complexity, providing new insights into their collaborative roles in cancer progression. The intricate relationship between RBPs and phase separation poses significant challenges but also opens up novel opportunities for targeted therapeutic interventions. Advancing our understanding of the molecular mechanisms and regulatory networks governing RBP phase separation could lead to breakthroughs in cancer treatment strategies.

Advances in the understanding of androgen receptor structure and function and in the development of next-generation AR-targeted therapeutics

Androgen receptor (AR) and its ligand androgens are important for development and physiology of various tissues. AR and its ligands also play critical role in the development of various diseases, making it a valuable therapeutic target. AR ligands, both agonists and antagonists, are being widely used to treat pathological conditions, including prostate cancer and hypogonadism. Despite AR being studied widely over the last five decades, the last decade has seen striking advances in the knowledge on AR and discoveries that have the potential to translate to the clinic. This review provides an overview of the advances in AR biology, AR molecular mechanisms of action, and next generation molecules that are currently in development. Several of the areas described in the review are just unraveling and the next decade will bring more clarity on these developments that will put AR at the forefront of both basic biology and drug development.

Role of liquid-liquid phase separation in cancer: Mechanisms and therapeutic implications

Liquid-liquid phase separation (LLPS) has emerged as a pivotal biological phenomenon involved in various cellular processes, including the formation of membrane-less organelles and the regulation of biomolecular condensates through precise spatiotemporal coordination of signaling pathways in cells. Dysregulation of LLPSs results in aberrant biomolecular condensates, which are widely implicated in tumorigenesis and cancer progression. Here, we comprehensively summarize the multifaceted roles of LLPS in tumor biology from the perspective of cancer hallmarks, including genomic stability, metabolic reprogramming progression, ferroptosis, and metastasis, to unveil the intricate mechanisms by which LLPS occurs in tumorigenesis. We discuss current discoveries related to therapeutic involvement and potential clinical applications of LLPS in cancer treatment, highlighting the potential of targeting LLPS-driven processes as novel therapeutic strategies. Additionally, we discuss the challenges associated with new approaches for cancer treatment based on LLPS. This in-depth discussion of the impact of LLPS on fundamental aspects of tumor biology provides new insights into overcoming cancer.

Heterochromatin formation and remodeling by IRTKS condensates counteract cellular senescence

Heterochromatin, a key component of the eukaryotic nucleus, is fundamental to the regulation of genome stability, gene expression and cellular functions. However, the factors and mechanisms involved in heterochromatin formation and maintenance still remain largely unknown. Here, we show that insulin receptor tyrosine kinase substrate (IRTKS), an I-BAR domain protein, is indispensable for constitutive heterochromatin formation via liquid‒liquid phase separation (LLPS). In particular, IRTKS droplets can infiltrate heterochromatin condensates composed of HP1α and diverse DNA-bound nucleosomes. IRTKS can stabilize HP1α by recruiting the E2 ligase Ubc9 to SUMOylate HP1α, which enables it to form larger phase-separated droplets than unmodified HP1α. Furthermore, IRTKS deficiency leads to loss of heterochromatin, resulting in genome-wide changes in chromatin accessibility and aberrant transcription of repetitive DNA elements. This leads to activation of cGAS-STING pathway and type-I interferon (IFN-I) signaling, as well as to the induction of cellular senescence and senescence-associated secretory phenotype (SASP) responses. Collectively, our findings establish a mechanism by which IRTKS condensates consolidate constitutive heterochromatin, revealing an unexpected role of IRTKS as an epigenetic mediator of cellular senescence.

CEP112 coordinates translational regulation of essential fertility genes during spermiogenesis through phase separation in humans and mice

Spermiogenesis, the complex transformation of haploid spermatids into mature spermatozoa, relies on precise spatiotemporal regulation of gene expression at the post-transcriptional level. The mechanisms underlying this critical process remain incompletely understood. Here, we identify centrosomal protein 112 (CEP112) as an essential regulator of mRNA translation during this critical developmental process. Mutations in CEP112 are discovered in oligoasthenoteratospermic patients, and Cep112-deficient male mice recapitulate key phenotypes of human asthenoteratozoospermia. CEP112 localizes to the neck and atypical centrioles of mature sperm and forms RNA granules during spermiogenesis, enriching target mRNAs such as Fsip2, Cfap61, and Cfap74. Through multi-omics analyses and the TRICK reporter assay, we demonstrate that CEP112 orchestrates the translation of target mRNAs. Co-immunoprecipitation and mass spectrometry identify CEP112's interactions with translation-related proteins, including hnRNPA2B1, EEF1A1, and EIF4A1. In vitro, CEP112 undergoes liquid-liquid phase separation, forming condensates that recruit essential proteins and mRNAs. Moreover, variants in patient-derived CEP112 disrupt phase separation and impair translation efficiency. Our results suggest that CEP112 mediates the assembly of RNA granules through liquid-liquid phase separation to control the post-transcriptional expression of fertility-related genes. This study not only clarifies CEP112's role in spermatogenesis but also highlights the role of phase separation in translational regulation, providing insights into male infertility and suggesting potential therapeutic targets.

Liquid-liquid phase separation: a new perspective on respiratory diseases

Liquid-liquid phase separation (LLPS) is integral to various biological processes, facilitating signal transduction by creating a condensed, membrane-less environment that plays crucial roles in diverse physiological and pathological processes. Recent evidence has underscored the significance of LLPS in human health and disease. However, its implications in respiratory diseases remain poorly understood. This review explores current insights into the mechanisms and biological roles of LLPS, focusing particularly on its relevance to respiratory diseases, aiming to deepen our understanding and propose a new paradigm for studying phase separation in this context.

Navigating through the complexities of synucleinopathies: Insights into pathogenesis, heterogeneity, and future perspectives

The aggregation of alpha-synuclein (aSyn) represents a neuropathological hallmark observed in a group of neurodegenerative disorders collectively known as synucleinopathies. Despite their shared characteristics, these disorders manifest diverse clinical and pathological phenotypes. The mechanism underlying this heterogeneity is thought to be due to the diversity in the aSyn strains present across the diseases. In this perspective, we will explore recent findings on aSyn strains and discuss recent discoveries about Lewy bodies' composition. We further discuss the current hypothesis for aSyn spreading and emphasize the emerging biomarker field demonstrating promising results. A comprehension of these mechanisms holds substantial promise for future clinical applications. This understanding can pave the way for the development of personalized medicine strategies, specifically targeting the unique underlying causes of each synucleinopathy. Such advancements can revolutionize therapeutic approaches and significantly contribute to more effective interventions in the intricate landscape of neurodegenerative disorders.

Prion-like Proteins in Plants: Key Regulators of Development and Environmental Adaptation via Phase Separation

Prion-like domains (PrLDs), a unique type of low-complexity domain (LCD) or intrinsically disordered region (IDR), have been shown to mediate protein liquid-liquid phase separation (LLPS). Recent research has increasingly focused on how prion-like proteins (PrLPs) regulate plant growth, development, and stress responses. This review provides a comprehensive overview of plant PrLPs. We analyze the structural features of PrLPs and the mechanisms by which PrLPs undergo LLPS. Through gene ontology (GO) analysis, we highlight the diverse molecular functions of PrLPs and explore how PrLPs influence plant development and stress responses via phase separation. Finally, we address unresolved questions about PrLP regulatory mechanisms, offering prospects for future research.

A two-task predictor for discovering phase separation proteins and their undergoing mechanism

Liquid-liquid phase separation (LLPS) is one of the mechanisms mediating the compartmentalization of macromolecules (proteins and nucleic acids) in cells, forming biomolecular condensates or membraneless organelles. Consequently, the systematic identification of potential LLPS proteins is crucial for understanding the phase separation process and its biological mechanisms. A two-task predictor, Opt_PredLLPS, was developed to discover potential phase separation proteins and further evaluate their mechanism. The first task model of Opt_PredLLPS combines a convolutional neural network (CNN) and bidirectional long short-term memory (BiLSTM) through a fully connected layer, where the CNN utilizes evolutionary information features as input, and BiLSTM utilizes multimodal features as input. If a protein is predicted to be an LLPS protein, it is input into the second task model to predict whether this protein needs to interact with its partners to undergo LLPS. The second task model employs the XGBoost classification algorithm and 37 physicochemical properties following a three-step feature selection. The effectiveness of the model was validated on multiple benchmark datasets, and in silico saturation mutagenesis was used to identify regions that play a key role in phase separation. These findings may assist future research on the LLPS mechanism and the discovery of potential phase separation proteins.

Fusion Dynamics and Size-Dependence of Droplet Microstructure in ssDNA-Mediated Protein Phase Separation

Biomolecular condensation involving proteins and nucleic acids has been recognized to play crucial roles in genome organization and transcriptional regulation. However, the biophysical mechanisms underlying the droplet fusion dynamics and microstructure evolution during the early stage of liquid-liquid phase separation (LLPS) remain elusive. In this work, we study the phase separation of linker histone H1, which is among the most abundant chromatin proteins, in the presence of single-stranded DNA (ssDNA) capable of forming a G-quadruplex by using molecular simulations and experimental characterization. We found that droplet fusion is a rather stochastic and kinetically controlled process. Productive fusion events are triggered by the formation of ssDNA-mediated electrostatic bridges within the droplet contacting zone. The droplet microstructure is size-dependent and evolves driven by maximizing the number of electrostatic contacts. We also showed that the folding of ssDNA to the G-quadruplex promotes LLPS by increasing the multivalency and strength of protein-DNA interactions. These findings provide deep mechanistic insights into the growth dynamics of biomolecular droplets and highlight the key role of kinetic control during the early stage of ssDNA-protein condensation.