Emerging Implications of Phase Separation in Cancer

Aqueous Two-Phase Submicron Droplets Catalyze DNA Nanostructure Assembly for Confined Fluorescent Biosensing

Membraneless organelles (MLOs) are fundamental to cellular organization, enabling biochemical processes by concentrating biomolecules and regulating reactions within confined environments. While micrometer-scale synthetic droplets are extensively studied as models of MLOs, submicron droplets remain largely unexplored despite their potential to uniquely regulate biomolecular processes. Here, submicron droplets are generated by a polyethylene glycol (PEG)/dextran aqueous two-phase system (ATPS) as a model to investigate their effect on DNA assembly in crowded environments. The findings reveal that submicron droplets exhibit distinct advantages over microdroplets by acting as submicron catalytic centers that concentrate DNA and accelerate assembly kinetics. This enhancement is driven by a cooperative mechanism wherein global crowding from PEG induces an excluded volume effect, while local crowding from dextran provides weak but nonspecific interactions with DNA. By exploiting both the confinement and phase properties of submicron droplets, a rapid and sensitive assay is developed for miRNA detection using confined fluorescent readouts. These findings highlight the unique ability of submicron droplets to amplify biomolecular assembly processes, provide new insights into the interplay between global and local crowding effects in cellular-like environments, and present a platform for biomarker detection and visualization.

Current perspectives in drug targeting intrinsically disordered proteins and biomolecular condensates

Intrinsically disordered proteins (IDPs) and biomolecular condensates are critical for cellular processes and physiological functions. Abnormal biomolecular condensates can cause diseases such as cancer and neurodegenerative disorders. IDPs, including intrinsically disordered regions (IDRs), were previously considered undruggable due to their lack of stable binding pockets. However, recent evidence indicates that targeting them can influence cellular processes. This review explores current strategies to target IDPs and biomolecular condensates, potential improvements, and the challenges and opportunities in this evolving field.

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.

Coacervates Composed of Low-Molecular-Weight Compounds- Molecular Design, Stimuli Responsiveness, Confined Reaction

The discovery of coacervation within living cells through liquid-liquid phase separation has inspired scientists to investigate its fundamental principles and significance. Indeed, coacervates composed of low-molecular-weight compounds based on supramolecular strategy can offer valuable models for biomolecular condensates and useful tools. This mini-review highlights recent findings and advances in coacervates (artificial condensates), primarily composed of low-molecular-weight compounds, with focuses on their molecular design, stimuli responsiveness, and controlled reactions within or leading to the coacervates.

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 in cell physiology and cancer biology: recent advances and therapeutic implications

Liquid-liquid phase separation (LLPS) is a pivotal biophysical phenomenon that plays a critical role in cellular organization and has garnered significant attention in the fields of molecular mechanism and pathophysiology of cancer. This dynamic process involves the spontaneous segregation of biomolecules, primarily proteins and nucleic acids, into condensed, liquid-like droplets under specific conditions. LLPS drives the formation of biomolecular condensates, which are crucial for various cellular functions. Increasing evidences link alterations in LLPS to the onset and progression of various diseases, particularly cancer. This review explores the diverse roles of LLPS in cancer, highlighting its underlying molecular mechanisms and far-reaching implications. We examine how dysregulated LLPS contributes to cancer development by influencing key processes such as genomic instability, metabolism, and immune evasion. Furthermore, we discuss emerging therapeutic strategies aimed at modulating LLPS, underscoring their potential to revolutionize cancer treatment.

Liquid-liquid phase separation in hepatocellular carcinoma

Liquid-liquid phase separation (LLPS) drives the formation of membraneless intracellular compartments within both cytoplasm and nucleus. These compartments can form distinct physicochemical environments, and in particular display different concentrations of proteins, RNA, and macromolecules compared to the surrounding cytosol. Recent studies have highlighted the significant role of aberrant LLPS in cancer development and progression, impacting many core processes such as oncogenic signalling pathways, transcriptional dysregulation, and genome instability. In hepatocellular carcinoma (HCC), aberrant formation of biomolecular condensates has been observed in a number of preclinical models, highlighting their significance as an emerging factor in understanding cancer biology and its molecular underpinnings. In this review, we summarize emerging evidence and recent advances in understanding the role of LLPS in HCC, with a particular focus on the regulation and dysregulation of cytoplasmic and nuclear condensates in cancer cells. We finally discuss how an emerging understanding of phase separation processes in HCC opens up new potential treatment avenues.

[Latest Findings on the Role of Liquid-Liquid Phase Separation in the Regulation of Immune Cell Activation and Key Signaling]

Liquid-liquid phase separation (LLPS) is a process in which certain proteins or protein-RNA complexes form phase-separated droplets with different components and properties through multivalent interactions within a cell. In recent years, the role of LLPS in immunomodulation has received extensive attention. Compared with phase separation-related studies in other fields, limited research has been done on LLPS and the immune system. In this review, we first introduced the basic characteristics of LLPS associated with the immune system, and then explored the functions of LLPS in innate immune-related signaling pathways and adaptive immune cells. LLPS plays a crucial role in immune signal transduction, immune cell activation, and antigen presentation. It is involved in facilitating the aggregation of signaling molecules, regulating the intensity and duration of signal transduction, and influencing the functional state of immune cells. The discovery of LLPS provides a new theoretical basis for elucidating the activation mechanism of the immune system and is expected to bring new perspectives for understanding the cellular defense mechanisms. In-depth investigation of the role of LLPS in the immune system not only helps us gain a more comprehensive understanding of the immune response process, but also provides potential targets and strategies for the development of new immunotherapies and the treatment of autoimmune diseases.

Membraneless organelles in health and disease: exploring the molecular basis, physiological roles and pathological implications

Once considered unconventional cellular structures, membraneless organelles (MLOs), cellular substructures involved in biological processes or pathways under physiological conditions, have emerged as central players in cellular dynamics and function. MLOs can be formed through liquid-liquid phase separation (LLPS), resulting in the creation of condensates. From neurodegenerative disorders, cardiovascular diseases, aging, and metabolism to cancer, the influence of MLOs on human health and disease extends widely. This review discusses the underlying mechanisms of LLPS, the biophysical properties that drive MLO formation, and their implications for cellular function. We highlight recent advances in understanding how the physicochemical environment, molecular interactions, and post-translational modifications regulate LLPS and MLO dynamics. This review offers an overview of the discovery and current understanding of MLOs and biomolecular condensate in physiological conditions and diseases. This article aims to deliver the latest insights on MLOs and LLPS by analyzing current research, highlighting their critical role in cellular organization. The discussion also covers the role of membrane-associated condensates in cell signaling, including those involving T-cell receptors, stress granules linked to lysosomes, and biomolecular condensates within the Golgi apparatus. Additionally, the potential of targeting LLPS in clinical settings is explored, highlighting promising avenues for future research and therapeutic interventions.

How to drug a cloud? Targeting intrinsically disordered proteins

Biologically active proteins/regions without stable structure (i.e., intrinsically disordered proteins and regions (IDPs and IDRs)) are commonly found in all proteomes. They have a unique functional repertoire that complements the functionalities of ordered proteins and domains. IDPs/IDRs are multifunctional promiscuous binders capable of folding at interaction with specific binding partners on a template- or context-dependent manner, many of which undergo liquid-liquid phase separation, leading to the formation of membrane-less organelles and biomolecular condensates. Many of them are frequently related to the pathogenesis of various human diseases. All this defines IDPs/IDRs as attractive targets for the development of novel drugs. However, their lack of unique structures, multifunctionality, binding promiscuity, and involvement in unusual modes of action preclude direct use of traditional structure-based drug design approaches for targeting IDPs/IDRs, and make disorder-based drug discovery for these "protein clouds" challenging. Despite all these complexities there is continuing progress in the design of small molecules affecting IDPs/IDRs. This article describes the major structural features of IDPs/IDRs and the peculiarities of the disorder-based functionality. It also discusses the roles of IDPs/IDRs in various pathologies, and shows why the approaches elaborated for finding drugs targeting ordered proteins cannot be directly used for the intrinsic disorder-based drug design, and introduces some novel methodologies suitable for these purposes. Finally, it emphasizes that regardless of their multifunctionality, binding promiscuity, lack of unique structures, and highly dynamic nature, "protein clouds" are principally druggable. Significance Statement Intrinsically disordered proteins and regions are highly abundant in nature, have multiple important biological functions, are commonly involved in the pathogenesis of a multitude of human diseases, and are therefore considered as very attractive drug targets. Although dealing with these unstructured multifunctional protein/regions is a challenging task, multiple innovative approaches have been designed to target them by small molecules.

Liquid-liquid phase separation in diseases

Liquid-liquid phase separation (LLPS), an emerging biophysical phenomenon, can sequester molecules to implement physiological and pathological functions. LLPS implements the assembly of numerous membraneless chambers, including stress granules and P-bodies, containing RNA and protein. RNA-RNA and RNA-protein interactions play a critical role in LLPS. Scaffolding proteins, through multivalent interactions and external factors, support protein-RNA interaction networks to form condensates involved in a variety of diseases, particularly neurodegenerative diseases and cancer. Modulating LLPS phenomenon in multiple pathogenic proteins for the treatment of neurodegenerative diseases and cancer could present a promising direction, though recent advances in this area are limited. Here, we summarize in detail the complexity of LLPS in constructing signaling pathways and highlight the role of LLPS in neurodegenerative diseases and cancers. We also explore RNA modifications on LLPS to alter diseases progression because these modifications can influence LLPS of certain proteins or the formation of stress granules, and discuss the possibility of proper manipulation of LLPS process to restore cellular homeostasis or develop therapeutic drugs for the eradication of diseases. This review attempts to discuss potential therapeutic opportunities by elaborating on the connection between LLPS, RNA modification, and their roles in diseases.

Phase separation-mediated biomolecular condensates and their relationship to tumor

Phase separation is a cellular phenomenon where macromolecules aggregate or segregate, giving rise to biomolecular condensates resembling "droplets" and forming distinct, membrane-free compartments. This process is pervasive in biological cells, contributing to various essential cellular functions. However, when phase separation goes awry, leading to abnormal molecular aggregation, it can become a driving factor in the development of diseases, including tumor. Recent investigations have unveiled the intricate connection between dysregulated phase separation and tumor pathogenesis, highlighting its potential as a novel therapeutic target. This article provides an overview of recent phase separation research, with a particular emphasis on its role in tumor, its therapeutic implications, and outlines avenues for further exploration in this intriguing field.

[Research Progress in the Role of Liquid-Liquid Phase Separation in Human Cancer]

Liquid-liquid phase separation (LLPS) is a reversible process, during which biological macromolecules, including proteins and nucleic acids, condense into liquid membraneless organelles under the influence of weak multivalent interactions. Currently, fluorescence recovery after photobleaching is the primary method used to detect the phase separation of biological macromolecules. Recent studies have revealed the link between abnormal LLPS and the pathogenesis and development of various human cancers. Through phase separation or abnormal phase separation, tumor-related biological macromolecules, such as mRNA, long noncoding RNAs (lncRNAs), and tumor-related proteins, can affect transcriptional translation and DNA damage repair, regulate the autophagy and ferroptosis functions of cells, and thus regulate the development of various tumors. In this review, we summarized the latest research findings on the mechanism of LLPS in the pathogenesis and progression of tumors and elaborated on the promotion or inhibition of autophagy, tumor immunity, DNA damage repair, and cell ferroptosis after abnormal phase separation of biomolecules, including mRNA, lncRNA, and proteins, which subsequently affects the pathogenesis and progression of tumors. According to published findings, many biological macromolecules can regulate transcriptional translation, expression, post-transcriptional modification, cell signal transduction, and other biological processes through phase separation. Therefore, further expansion of the research field of phase separation and in-depth investigation of its molecular mechanisms and regulatory processes hold extensive research potential.

Targeting Biomolecular Condensation and Protein Aggregation against Cancer

Biomolecular condensates, membrane-less entities arising from liquid-liquid phase separation, hold dichotomous roles in health and disease. Alongside their physiological functions, these condensates can transition to a solid phase, producing amyloid-like structures implicated in degenerative diseases and cancer. This review thoroughly examines the dual nature of biomolecular condensates, spotlighting their role in cancer, particularly concerning the p53 tumor suppressor. Given that over half of the malignant tumors possess mutations in the TP53 gene, this topic carries profound implications for future cancer treatment strategies. Notably, p53 not only misfolds but also forms biomolecular condensates and aggregates analogous to other protein-based amyloids, thus significantly influencing cancer progression through loss-of-function, negative dominance, and gain-of-function pathways. The exact molecular mechanisms underpinning the gain-of-function in mutant p53 remain elusive. However, cofactors like nucleic acids and glycosaminoglycans are known to be critical players in this intersection between diseases. Importantly, we reveal that molecules capable of inhibiting mutant p53 aggregation can curtail tumor proliferation and migration. Hence, targeting phase transitions to solid-like amorphous and amyloid-like states of mutant p53 offers a promising direction for innovative cancer diagnostics and therapeutics.

Biomolecule-Based Coacervates with Modulated Physiological Functions

Liquid-liquid phase separation (LLPS) exists widely in living systems, and understanding the working mechanisms of the formed condensed droplets is of great significance for the prevention and treatment of diseases as well as for the development of biomimetic materials. Herein, in this Perspective we try to focus on the in vitro reconstructions of biomolecule-based coacervates and outline the associations between the functional components and droplets as well as the physiological and pathological functions associated with coacervates. Coacervates are formed by functional components through weak, multivalent interactions. The interaction strengths that determine coacervate properties such as electability and phase state, which in turn influence the functional components to limit their fluidity, stability, or diffusion coefficients, are specially discussed. At the end of this Perspective, the current challenges are summarized; progress will require our great efforts to reveal the mechanisms of action at the molecular level and then develop biomolecule-based coacervate models with complexity, integration of methods, and intellectualization.

Liquid-liquid phase separation throws novel insights into treatment strategies for skin cutaneous melanoma

BACKGROUND

In recent years, there has been growing evidence indicating a relationship between liquid-liquid phase separation (LLPS) and cancer development. However, to date, the clinical significance of LLPS in skin cutaneous melanoma (SKCM, hereafter referred to as melanoma) remains to be elucidated. In the current study, the impact of LLPS-related genes on melanoma prognosis has been explored.

METHODS

LLPS-related genes were retrieved from the DrLLPS database. The prognostic feature for LLPS in melanoma was developed in The Cancer Genome Atlas (TCGA) dataset and verified in the GSE65904 cohort. Based on risk scores, melanoma patients were categorized into high- and low-risk groups. Thereafter, the differences in clinicopathological correlation, functional enrichment, immune landscape, tumor mutational burden, and impact of immunotherapy between the two groups were investigated. Finally, the role of key gene TROAP in melanoma was validated by in vitro and in vivo experiments.

RESULTS

The LLPS-related gene signature was developed based on MLKL, PARVA, PKP1, PSME1, RNF114, and TROAP. The risk score was a crucial independent prognostic factor for melanoma and patients with high-risk scores were related to a worse prognosis. Approximately, all immune-relevant characteristics, such as immune cell infiltration and immune scores, were extremely evident in patients with low-risk scores. The findings from the in vitro and in vivo experiments indicated that the viability, proliferation, and invasion ability of melanoma cells were drastically decreased after the knockdown of TROAP.

CONCLUSION

Our gene signature can independently predict the survival of melanoma patients. It provides a basis for the exploration of the relationship between LLPS and melanoma and can offer a fresh perspective on the clinical diagnosis and treatment of the disease.

Phase separation in cancer at a glance

Eukaryotic cells are segmented into multiple compartments or organelles within the cell that regulate distinct chemical and biological processes. Membrane-less organelles are membrane-less microscopic cellular compartments that contain protein and RNA molecules that perform a wide range of functions. Liquid-liquid phase separation (LLPS) can reveal how membrane-less organelles develop via dynamic biomolecule assembly. LLPS either segregates undesirable molecules from cells or aggregates desired ones in cells. Aberrant LLPS results in the production of abnormal biomolecular condensates (BMCs), which can cause cancer. Here, we explore the intricate mechanisms behind the formation of BMCs and its biophysical properties. Additionally, we discuss recent discoveries related to biological LLPS in tumorigenesis, including aberrant signaling and transduction, stress granule formation, evading growth arrest, and genomic instability. We also discuss the therapeutic implications of LLPS in cancer. Understanding the concept and mechanism of LLPS and its role in tumorigenesis is crucial for antitumor therapeutic strategies.