4.7 Review

Phase separation in cancer at a glance

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Review Biochemistry & Molecular Biology

DEAD-box ATPases as regulators of biomolecular condensates and membrane-less organelles

Daan Overwijn et al.

Summary: RNA-dependent DEAD-box ATPases (DDXs) are key regulators of RNA-containing membrane-less organelles (MLOs), acting both 'in cis' by promoting condensate formation and 'in trans' by remodeling interactions underlying MLO assembly. This review discusses the role of DDXs in modulating MLOs and their contribution to the dynamic assembly and turnover of these organelles, enabling cells to regulate RNA sequestration and processing in a spatial and temporal manner.

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Review Oncology

Targeting p53 for the treatment of cancer

Michael J. Duffy et al.

Summary: Dysfunction of the TP53 gene is prevalent in human malignancies, making it an attractive target for new anticancer drugs. Two strategies, reactivating mutant p53 and inhibiting the interaction between wild-type p53 and MDM2/MDM4, are being explored in clinical trials. The development of compounds targeting these strategies has the potential to revolutionize cancer treatment.

SEMINARS IN CANCER BIOLOGY (2022)

Review Biochemistry & Molecular Biology

Melatonin: Regulation of Prion Protein Phase Separation in Cancer Multidrug Resistance

Doris Loh et al.

Summary: The ability of cancer cells to adapt and thrive in unfavorable tumor microenvironments makes them resistant to traditional chemotherapy and novel pharmaceuticals. This resistance is facilitated by metabolic alterations, cellular stress responses, and prion proteins. Melatonin has the potential to improve multidrug resistance by regulating the functions of prion proteins and modulating the tumor microenvironment.

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Article Multidisciplinary Sciences

53BP1 regulates heterochromatin through liquid phase separation

Lei Zhang et al.

Summary: The 53BP1 protein plays a key role in DNA repair and also contributes to the maintenance of heterochromatin integrity and genome stability through liquid-liquid phase separation (LLPS).

NATURE COMMUNICATIONS (2022)

Review Oncology

Hallmarks of Cancer: New Dimensions

Douglas Hanahan

Summary: The concept of the hallmarks of cancer is a tool for simplifying the complexity of cancer phenotypes and genotypes into basic principles. This article proposes phenotypic plasticity and disrupted differentiation as distinct hallmark capabilities, and discusses nonmutational epigenetic reprogramming and polymorphic microbiomes as enabling characteristics. Additionally, the importance of senescent cells in the tumor microenvironment is highlighted. The integrative concept of the hallmarks of cancer helps in understanding the mechanisms of cancer development and applying that knowledge to cancer medicine.

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Editorial: The Role of Protein Post-Translational Modifications in Protein-RNA Interactions and RNP Assemblies

Roberto Giambruno et al.

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A natural product targets BRD4 to inhibit phase separation and gene transcription

Cong Wang et al.

Summary: The BET-bromodomain protein BRD4 utilizes two bromodomains to target acetyl-histones and other domains, stimulating transcription of proto-oncogenes and key cell identity genes. Recent studies highlight the importance of BRD4's ability to form phase-separated condensates that cluster at the super-enhancer regions of target genes. Through the discovery of a natural product called PCG, derived from the Chinese medicinal herb polygonum cuspidatum Sieb. et Zucc., a BET inhibitor that selectively targets BRD4 and suppresses phase separation, a unique mechanism of action among known BET inhibitors, has been identified.

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Poly(ADP-ribosylation) of P-TEFb by PARP1 disrupts phase separation to inhibit global transcription after DNA damage

Huanyi Fu et al.

Summary: DNA damage leads to transcriptional stalling to prevent mutagenesis and initiate repair signaling. Poly(ADP-ribose) polymerase (PARP1) inhibits Pol II elongation by inactivating the transcription elongation factor P-TEFb, promoting DNA repair and cell survival.

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A two-component protein condensate of the EGFR cytoplasmic tail and Grb2 regulates Ras activation by SOS at the membrane

Chun-Wei Lin et al.

Summary: This study demonstrates the importance of a protein condensation phase transition between EGFR and Grb2 in regulating signal propagation from EGFR to the MAPK pathway. The condensation state of the EGFR tail controls the ability of SOS to activate Ras.

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Phase separation of p53 induced by its unstructured basic region and prevented by oncogenic mutations in tetramerization domain

Chen Chen et al.

Summary: Liquid-liquid phase separation is closely related to cellular biological activities and cancer. Recent research has found that the tumor suppressor protein p53 undergoes phase separation, and mutations in p53 disrupt this process, promoting cancer progression.

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Dishevelled phase separation promotes Wnt signalosome assembly and destruction complex disassembly

Kexin Kang et al.

Summary: Kang et al. demonstrate that Dvl2 undergoes phase separation and rapidly accumulates to the plasma membrane upon Wnt stimulation. Dvl2 phase separation plays a crucial role in the assembly of the Wnt receptor signalosome and disruption of the beta-catenin destruction complex.

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Letting go: Dishevelled phase separation recruits Axin to stabilize β-catenin

Rachel L. Babcock et al.

Summary: This study reveals the mechanism of action of Dishevelled in cell fate by demonstrating its role in stabilizing beta-catenin through liquid-liquid phase separation.

JOURNAL OF CELL BIOLOGY (2022)

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Biomolecular Condensation of the Human Papillomavirus E2 Master Regulator with p53: Implications in Viral Replication

Silvia Susana Borkosky et al.

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A brief guideline for studies of phase-separated biomolecular condensates

Yifei Gao et al.

Summary: The article presents principles and guidelines for phase separation studies in biology, including experimental procedures, mechanisms of molecular driving forces, methods to correlate in vivo and in vitro observations, and strategies to relate phase separation phenomena to biological functions.

NATURE CHEMICAL BIOLOGY (2022)

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Modulating biomolecular condensates: a novel approach to drug discovery

Diana M. Mitrea et al.

Summary: Biomolecular condensates, membraneless assemblies that compartmentalize specific biomolecules, play important roles in cellular functions. They often form through phase separation and studying their functions and formation mechanisms can provide insights into human diseases and potential therapies.

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Regulation of Cellular Ribonucleoprotein Granules: From Assembly to Degradation via Post-translational Modification

Pureum Jeon et al.

Summary: This review summarizes current studies on the physiological or pathological roles of post-translational modifications of various cellular RNP granules and discusses the therapeutic methods in curing diseases related to abnormal RNP granules by autophagy.
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Emerging Implications of Phase Separation in Cancer

Jiang Ren et al.

Summary: In eukaryotic cells, membrane-bound organelles and membrane-less organelles (MLOs) play important roles in biological activities. MLOs are formed through a process called liquid-liquid phase separation (LLPS), which is initiated by multivalent molecules. Accumulating evidence suggests that LLPS helps concentrate and organize molecules in cells, with aberrant LLPS implicated in cancer hallmarks. Understanding the molecular mechanisms of LLPS provides insights for cancer therapeutics.

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Review Biochemistry & Molecular Biology

Post-translational modifications in liquid-liquid phase separation: a comprehensive review

Jingxian Li et al.

Summary: Liquid-liquid phase separation (LLPS) is a phenomenon that has attracted significant attention in biological studies. However, the comprehensive understanding of its physical mechanism is limited. The characteristics of side chains of amino acids and the interaction tendency of proteins play important roles in regulating LLPS and should receive more attention. This review introduces the driving forces and protein secondary structures involved in LLPS, summarizes existing reports on post-translational modifications (PTMs) related to LLPS, and analyzes the underlying basic principles to find potential connections between LLPS and PTM.

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Protein conformation and biomolecular condensates

Diego S. Vazquez et al.

Summary: Protein conformation and cell compartmentalization are fundamental concepts in scientific research. Recent studies have shown that biomolecular condensates play a central role in membraneless subcellular compartmentalization, enabling the organization and regulation of simultaneous biochemical reactions and macromolecular interactions. This review summarizes the latest research on the assembly, composition, conformation, and functions of biomolecular condensates, and provides an overview of the potential of studying the conformational dynamics of condensed proteins in cellular process regulation.

CURRENT RESEARCH IN STRUCTURAL BIOLOGY (2022)

Review Biochemistry & Molecular Biology

Phase separation in Cancer: From the Impacts and Mechanisms to Treatment potentials

Qiu Peng et al.

Summary: Cancer is a major cause of death worldwide, with its precise mechanisms still unclear. Liquid-liquid phase separation is a common strategy for cells to achieve various functions, and abnormal phase separations have been found to be related to cancer progression. Regulating signaling pathways through phase separation and targeting phase separation for cancer treatment are potential strategies.

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Liquid-liquid phase separation in tumor biology

Xuhui Tong et al.

Summary: Liquid-liquid phase separation (LLPS) is a novel principle that explains the precise regulation of spatial and temporal organization in living cells. It plays a crucial role in various cellular processes and its dysregulation has been linked to cancer development. This review comprehensively summarizes the mechanisms of biomolecular condensate formation and function, and discusses recent advances in understanding the role of aberrant LLPS in cancer pathology. Furthermore, the therapeutic potential of targeting LLPS in cancer research and development of drug candidates is also discussed.

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A two-component protein condensate of the EGFR cytoplasmic tail and Grb2 regulates Ras activation by SOS at the membrane

Chun-Wei Lin et al.

Summary: This study demonstrates that the protein condensation phase transition of EGFR:Grb2 acts as a regulator of signal propagation from EGFR to the MAPK pathway.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

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Rich Phase Separation Behavior of Biomolecules

Yongdae Shin

Summary: Phase separation is a thermodynamic process that plays an important role in the formation of intracellular condensates. These condensates exhibit diverse phase behaviors, and the network of intermolecular interactions is crucial for their biophysical features. The regular solution models provide theoretical frameworks to explain the assembly, composition, and miscibility of biomolecular phases, shedding light on the thermodynamic principles of multicomponent intracellular phase separation.

MOLECULES AND CELLS (2022)

Review Oncology

Liquid-liquid phase separation drives cellular function and dysfunction in cancer

Sohum Mehta et al.

Summary: Cancer is a disease characterized by uncontrolled cell reproduction, and the formation and regulation of biomolecular condensates through liquid-liquid phase separation (LLPS) plays a significant role in the biochemical processes of cancer cells.

NATURE REVIEWS CANCER (2022)

Article Immunology

Phase separation in immune signalling

Qian Xiao et al.

Summary: Phase separation is a new biophysical principle in organizing biomolecules into fluidic clusters, with potential implications for immune signaling pathways. The formation of signaling condensates through liquid-liquid phase separation is crucial for understanding how immune responses are regulated in cells. Despite the challenges in fully understanding the mechanisms and functional consequences of these signaling clusters, studies in immunology are expected to provide new perspectives on immune responses.

NATURE REVIEWS IMMUNOLOGY (2022)

Review Biochemistry & Molecular Biology

Molecular mechanisms of stress granule assembly and disassembly

Sarah Hofmann et al.

Summary: Stress granules are membrane-less ribonucleoprotein-based cellular compartments that form in the cytoplasm in response to environmental stressors. Their function is not fully understood, but aberrant formation and impaired disassembly contribute to various pathological conditions. Recent studies suggest a novel mechanism for stress granule assembly involving a network of mRNAs and proteins.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH (2021)

Article Oncology

Biomolecular Condensates and Cancer

Ann Boija et al.

Summary: Biomolecular condensates, membraneless bodies formed by liquid-liquid phase separation, compartmentalize specific proteins and RNA molecules. Recent studies have revealed their potential roles in oncogenesis and influence on cancer therapeutics.

CANCER CELL (2021)

Article Biochemistry & Molecular Biology

Glycogen accumulation and phase separation drives liver tumor initiation

Qingxu Liu et al.

Summary: Glucose consumption is increased in tumor cells to support tumor growth, while glycogen accumulation plays a crucial role in liver malignant transformation. Glycogen accumulation blocks Hippo signaling and enhances tumor incidence in cancer-initiating cells.
Article Biochemistry & Molecular Biology

Phase-separated foci of EML4-ALK facilitate signalling and depend upon an active kinase conformation

Josephina Sampson et al.

Summary: Variants of the oncogenic EML4-ALK fusion protein form cytoplasmic foci containing components of various signaling pathways, which can be influenced by ALK inhibitors and rely on the conformational state of the ALK kinase domain for assembly.

EMBO REPORTS (2021)

Review Biochemistry & Molecular Biology

Phase Separation of Intrinsically Disordered Nucleolar Proteins Relate to Localization and Function

Francisco Guillen-Chable et al.

Summary: Phase separation process allows cells to establish and form subcompartmentalized structures, enabling simultaneous processes with precise organization and low energy requirements. Chemical modifications of proteins, RNA, and lipids alter the molecular environment, facilitating enzymatic reactions at higher concentrations in specific regions of the cell. The nucleolus serves as an example of a membraneless organelle with a high level of organization in terms of establishment, dynamics, and maintenance.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Microbiology

Phase separation and DAXX redistribution contribute to LANA nuclear body and KSHV genome dynamics during latency and reactivation

Olga Vladimirova et al.

Summary: KSHV genomes associate with LANA to form stable nuclear bodies during latent infection. LANA-NB formation and KSHV genome conformation involves liquid-liquid phase separation. Disruption of LLPS alters the LANA-dependent KSHV chromosome conformation but does not induce lytic reactivation, indicating dynamic super-molecular nuclear structures of LANA-NBs during different modes of viral replication.

PLOS PATHOGENS (2021)

Article Cell Biology

TGF-β-induced DACT1 biomolecular condensates repress Wnt signalling to promote bone metastasis

Mark Esposito et al.

Summary: Intracellular signaling involves a diverse array of molecular players and spatial segregation mechanisms, with liquid-liquid phase separation identified as a distinct mechanism. DACT1 induced by TGF-beta forms protein condensates in the cytoplasm to repress Wnt signaling, impacting breast and prostate cancer bone metastasis through its role in sequestering CK2.

NATURE CELL BIOLOGY (2021)

Article Oncology

BRD4 PROTAC degrader ARV-825 inhibits T-cell acute lymphoblastic leukemia by targeting 'Undruggable' Myc-pathway genes

Shuiyan Wu et al.

Summary: BRD4 expression is elevated in pediatric T-ALL samples, indicating a poor prognosis. ARV-825 effectively suppresses T-ALL cell proliferation by arresting the cell cycle and inducing apoptosis, reducing BRD4, BRD3, and BRD2 proteins, and perturbing the H3K27Ac-Myc pathway. In addition, ARV-825 inhibits tumor growth in a T-ALL xenograft model by depleting BET and c-Myc proteins.

CANCER CELL INTERNATIONAL (2021)

Review Cell Biology

Biomolecular condensates in membrane receptor signaling

Khuloud Jaqaman et al.

Summary: Clustering of receptors at the plasma membrane is a prominent feature and is influenced by liquid-liquid phase separation of proteins. Proteins involved in LLPS can act as core components or be enriched at the condensates. Formation of condensates regulates signaling by increasing protein binding avidity and modulating the local biochemical environment. Further research is needed to explore the interplay between protein LLPS, receptor clustering, and their signaling and functional consequences at the plasma membrane of living cells.

CURRENT OPINION IN CELL BIOLOGY (2021)

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The STING phase-separator suppresses innate immune signalling

Xiaoyu Yu et al.

Summary: Yu et al. discovered that STING biomolecular condensates can form in virus-infected cells, leading to the restriction of TBK1 activation and innate immunity responses. The study revealed the presence of a unique STING phase-separator in the ER membrane, which plays a crucial role in regulating innate immune signaling pathways.

NATURE CELL BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Induced phase separation of mutant NF2 imprisons the cGAS-STING machinery to abrogate antitumor immunity

Fansen Meng et al.

Summary: Mutations in the tumor suppressor NF2 can affect tumor formation by impacting anti-tumor immune mechanisms, revealing a novel pathogenic mechanism for NF2-related tumors.

MOLECULAR CELL (2021)

Review Cell Biology

Emerging Roles of Liquid-Liquid Phase Separation in Cancer: From Protein Aggregation to Immune-Associated Signaling

Jiahua Lu et al.

Summary: Liquid-liquid phase separation (LLPS) of proteins and nucleic acids is a new paradigm in the study of cellular activities, driving the formation of membrane-less condensates in living cells. The biophysical and biochemical principles underlying LLPS determine the molecular properties and composition of liquid condensates, while their function in cellular activities, especially in a pathological context, remains unclear. Current research is focused on uncovering the roles of LLPS in cancer, including signaling pathways, transcription regulation, and genome stability maintenance.

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Regulation of liquid-liquid phase separation with focus on post-translational modifications

Yun-Yi Luo et al.

Summary: Liquid-liquid phase separation (LLPS) is a unique means of forming biomolecular condensates in organisms, playing significant roles in various biological processes. Post-translational modifications (PTMs), including phosphorylation, methylation, citrullination, acetylation, ubiquitination and poly(ADP-ribosyl)ation, are important regulators of LLPS, affecting protein properties and phase transition behavior. Understanding the regulatory mechanisms of LLPS, especially the roles of PTMs, RNA and molecular chaperones, is essential for potential therapeutic interventions in diseases related to abnormal phase transitions.

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Phase separation of p53 precedes aggregation and is affected by oncogenic mutations and ligands

Elaine C. Petronilho et al.

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Wei Wang et al.

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