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

Stem Cell Research & Therapy volume 16, Article number: 214 (2025) Cite this article

Abstract

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.

Introduction

Hematopoietic stem cells (HSCs) are a type of stem cell with long-term self-renewal ability and multi-directional differentiation ability [1]. They are at the top of the hematopoietic hierarchy and play a crucial role in development, tissue repair and regeneration. The functional activity of HSCs is regulated by multiple complex mechanisms, including genetic regulation, epigenetic regulation, and microenvironment regulation. These heterogeneous and diverse HSCs abnormalities are related to the occurrence and development of multiple diseases [2].

As a new intracellular regulatory mechanism, phase separation has received extensive attention in recent years. Studies have shown that the liquid-liquid phase separation (LLPS) of biological macromolecules can form multiple membrane-less compartments in cells. The biomolecular condensates generated by phase separation in cells can participate in various biological activities and functional processes, such as gene expression, stem cell regulation, transcriptional dysregulation, signal transduction and stress response, providing a method to regulate cell function. There are many factors that affect phase separation, including molecular concentration, temperature, ionic strength (salt concentration), pH value, crowding effect, and the impact of nucleic acid molecules on protein phase separation. These factors, acting alone or in combination, affect the fusion and infiltration of biomolecules [3]. Abnormal phase separation is closely related to various diseases such as neurodegenerative diseases and cancer, and may play a role in disease treatment [4]. Phase separation also plays a key role in the regulation of stem cells. Existing studies have found that biomolecular condensates represented by phase separation will affect the epigenetic regulation of cancer stem cells. Understanding its principles and characteristics will help accurately curb the occurrence and development of diseases and find potential therapeutic targets, bringing new possibilities for tumor treatment [5].

At present, there are few studies on the genetic regulation mechanism of HSCs, regulated by phase separation, and the extent to which phase separation contributes to disease treatment remains unclear. In this review, we will summarize the genetic regulation mechanism of HSCs and the possibility of regulating the functional activity of HSCs through phase separation, aiming to explore the phase separation regulation mechanism in HSCs and provide new strategies for targeted therapy of diseases.

Genetic regulation mechanism of HSCs

During the process of HSCs producing mature blood cells, their differentiation potential gradually decreases, and their functional activity is regulated by multiple mechanisms. The intracellular and extracellular mechanisms involved in regulating HSCs include genetic regulation, epigenetic regulation and hematopoietic microenvironment regulation [6]. These regulatory mechanisms enable HSCs to flexibly and actively switch between resting and activated states, exert normal physiological functions, and be able to respond to various stress needs of the body [7]. We previously summarized the functional regulation and resting and activated states of HSCs, and analyzed their potential in disease treatment [8]. Genetic regulation of HSCs plays a crucial position in the study of blood diseases. Its mechanism is complex and diverse, including multiple aspects such as epigenetic regulation, transcription factor regulation, and gene editing. Cell cycle-related proteins, enzymes related to phosphorylation and ubiquitination, transcription factors, signal transduction factors and various signaling pathways work together to participate in the regulation of HSCs physiological functions and are related to cell cycle, cell proliferation and repair, and disease occurrence [9].

Epigenetic regulation

The maintenance of the multi-directional differentiation ability of HSCs depends on strict gene expression regulation. Epigenetic changes are related to the expression of cell differentiation-related genes. These genes may have specific epigenetic modifications [10, 11]. The epigenetic regulation of gene expression can prepare for the multi-lineage differentiation of HSCs [12]. Chromatin remodeling, histone modification, non coding RNA (ncRNA), epigenetic regulatory factor modification, etc. all belong to epigenetic modifications.

Chromatin is a dynamic structure composed of DNA and histones, with its basic unit being the core granules of nucleosomes. It is composed of histones H2A, H2B, H3, and H4 and exists in the form of heterochromatin or euchromatin [13]. Chromatin structure is involved in various aspects of RNA polymerase II mediated transcription, and its structural and functional changes can affect epigenetic regulation [14]. The organization of chromatin space within the nucleus can make certain genes, enhancers, and promoters more easily accessible to transcription factors [15].

Histone modification refers to the post-translational modification of N-terminal amino acids in histones, which participates in regulating chromatin structure and gene expression, and is related to developmental changes in the body, affecting the occurrence and prognosis of various tumors such as peripheral T-cell lymphoma [16]. On the other hand, ncRNA is involved in mRNA editing, splicing, and other processes of post transcriptional regulation, which is also a crucial part of epigenetic regulation [17]. Past studies have shown that abnormal epigenetic modifications can lead to changes in chromosome structure and post transcriptional regulation. ncRNA plays an important role in the process of post transcriptional regulation. It may be a signal to change the state of chromatin, related to various systemic diseases such as heart and liver, and has clinical treatment and diagnostic potential [18].

Epigenetic regulation is a key part in maintaining the normal physiological role of HSCs and regulating the aging of HSCs [19]. Epigenetic regulators are crucial for the multi-lineage differentiation of HSCs. Among them, as an epigenetic regulator, long-term lack of PHF19 (a subunit of polycomb repressive complex 2) will lead to abnormal hematopoiesis. The deletion of the PHF19 gene will make the genomic region containing the genes related to the regulation of HSCs differentiation more compact, resulting in the inability of these genes to be expressed. HSCs are forced to be in a quiescent state and cannot undergo specific lineage differentiation. At the molecular level, the loss of PHF19 triggers the redistribution of the histone repressive mark H3K27me3, which accumulates significantly in PHF19-specific genes [20]. This shows that PHF19 is crucial for maintaining the normal differentiation function of HSCs. Defects in differentiation will further lead to the inability of blood cells to be produced normally, affecting hematopoiesis, and ultimately leading to the occurrence of diseases. These findings provide us with directions for studying its internal mechanisms and as therapeutic targets.

Transcription factor regulation

Transcription factors play an important role in the processes of HSCs resting and activation, self-renewal, multi-directional differentiation, cell proliferation and apoptosis [21]. Among them, RUNX1, as an important transcription factor related to hematopoiesis development, participates in about 40.9% of enhancer-promoter interactions. The enhancer-promoter interactions with temporarily or continuously increased interaction intensity are significantly related to hematopoiesis and immune processes and play a key role in the functional regulation of HSCs. The deletion of RUNX1 is related to abnormal hematopoiesis. It is important to note that RUNX1 also functions as a DNA-binding region. HSCs originate from a specialized region in the embryo called the aorta-gonad-mesonephros (AGM) region during embryonic development. The key process occurs in the wall of the dorsal aorta within the AGM, where HSCs first emerge [22]. Studies have demonstrated that knocking out genes expressing RUNX1 in vascular endothelial cadherin-positive endothelial cells significantly impacts the formation of arterial cell clusters. The results indicate that RUNX1 is essential for HSCs generation, as HSCs cannot develop in its absence [23]. In addition, many studies have shown that RUNX1 is one of the common mutant genes in various blood diseases. Somatic mutations and chromosomal rearrangements involving RUNX1 can be seen in various blood system diseases including myeloid and lymphoid leukemia [24]. In short, RUNX1 plays an important role in the functional regulation of HSCs and various blood diseases.

In addition, based on the promoter and enhancer regions of RUNX1 binding interaction, other transcription factors that synergistically regulate HSCs with RUNX1 are predicted, such as GFI1b, PU.1, IRF family proteins, SMAD family proteins, etc [25,26,27,28]. Studies have shown that RUNX1, PAX6, and SMAD3 proteins interact to form a core transcriptional regulatory loop specific to leukemia stem cells (LSCs). Josephine et al. conducted a comprehensive genomic study on the transcriptome and chromatin landscape of a cellular component (iLSC), and discovered a LSCs gene feature that can predict patient survival. They also revealed the dependence of LSC on RUNX1 transcription factor across acute myeloid leukemia (AML) genotypes, identifying RUNX1 as a therapeutic AML LSC dependency [29]. These transcription factors and RUNX1 jointly regulate the functional activity of HSCs, providing an important direction for in-depth understanding of the genetic regulation of HSCs (Fig. 1). These studies demonstrate that a range of epigenetic regulators and transcription factors play a pivotal role in the genetic regulation of HSCs, offering valuable insights for further investigating their involvement in disease development and their potential as therapeutic targets.

Fig. 1
figure 1

Genetic regulation of hematopoietic stem cells (The self-renewal and multi-directional differentiation process of hematopoietic stem cells is influenced by the genetic regulation, including epigenetic regulation and transcription factor regulation, enabling HSCs to flexibly and actively switch between resting and activated states, perform normal physiological functions, and respond to various stress demands of the body.)

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Phase separation participates in the genetic regulation of HSCs

Phase separation refers to the process in which biological macromolecules spontaneously aggregate through non-covalent interactions to form different liquid phases under certain conditions. As an emerging biological phenomenon, phase separation forms many membrane-less compartments in cells. These compartments are collectively referred to as biomolecular condensates, which participate in various cellular activities in a spatio-temporally defined manner, including gene expression, misfolding and autophagy degradation, providing concentrated and separated cellular components for various functional processes [30]. HSCs have the ability of self-renewal and multi-directional differentiation, and their fate determination is strictly regulated. In recent years, studies have shown that phase separation plays a key role in the transcriptional regulation and epigenetic regulation of HSCs [31].

Phase separation and epigenetic regulation

Epigenetic modification is one of the important regulatory mechanisms that determine the fate of HSCs. Epigenetic regulation factors are key factors in controlling the role of HSCs and determining cell fate [32]. Strict gene expression regulation is extremely important for HSCs. Gene expression that controls cell differentiation involves various epigenetic changes. Phase separation is involved in regulating different epigenetic stages, including transcription, splicing and post-transcriptional modification. The membrane-less organelles formed by phase separation also participate in epigenetic regulation, and their defects are related to the occurrence and development of various diseases [33]. The ways of epigenetic regulation mechanisms include histone modification, DNA methylation and ubiquitination [12]. Among them, histone modification enzymes can regulate gene transcription by changing the modification state of histones. Studies have found that some histone modification enzymes can also form membrane-less organelles through phase separation to achieve the regulation of histone modification and gene transcription [34]. For example, the H3K27me3 methyltransferase EZH2 can form membrane-less organelles through phase separation, thereby promoting the methylation of H3K27me3 and the inhibition of gene transcription [35]. Polycomb-mediated H3K27me3 can mediate the silencing of DNA hypomethylated promoters and limit the accessibility of maternal alleles in DNA hypomethylated regions [36]. In addition, DNA methylation is a crucial epigenetic modification that regulates gene transcription by altering the methylation status of DNA. Studies have found that some DNA methyltransferases can also achieve the regulation of DNA methylation and gene transcription through phase separation [37]. For example, DNMT3A and DNMT3B can form membrane-less organelles through phase separation, which promotes DNA methylation and inhibits gene transcription [38]. This demonstrates that phase separation plays a crucial regulatory role in various epigenetic processes. Abnormal epigenetic regulation caused by abnormal phase separation will affect histone modification, DNA methylation and gene transcription, and participate in the occurrence and development of diseases.

Phase separation and transcriptional regulation

Transcription factors are also one of the key regulatory factors that determine the fate of HSCs. Multiple transcription factors such as p53, Fox protein family, Oct4, Nanog, etc. participate in the regulation of the resting and activated states of HSCs, and can participate in the regulation of processes such as self-renewal, differentiation or apoptosis [39]. In recent years, studies have shown that some transcription factors can form membrane-less organelles through phase separation to achieve the regulation of gene transcription. For example, transcription factors such as Oct4, Sox2 and Nanog form membrane-less organelles in cells, called transcription factor condensates. These condensates can enrich specific DNA sequences and promote the self-renewal and multi-directional differentiation of HSCs [40, 41]. Chromatin remodeling factors are another important class of transcriptional regulatory factors. They can regulate gene transcription by changing the structure and state of chromatin [42]. Studies have found that some chromatin remodeling factors can also form membrane-less organelles through phase separation to achieve the remodeling of chromatin and the regulation of gene transcription [43]. For example, BRD4 is a chromatin remodeling factor that can form membrane-less organelles through phase separation and promote the activation of gene transcription [44]. Transcriptional regulation is at the core of normal and abnormal physiology. The membrane-less organelles formed by phase separation can affect the regulation of transcription factors and regulate gene transcription, which is related to the pathogenesis of various diseases.

Phase separation and signal transduction

Signal transduction is one of the important mechanisms for HSCs to respond to external signals [45]. Studies have found that some signal molecules can form membrane-less organelles through phase separation to regulate the signal transduction process and further interfere with the function of HSCs [46]. For example, β-catenin in the Wnt signaling pathway can form membrane-less organelles through phase separation to promote the transduction of Wnt signals [47]. The scaffold protein Dishevelled 2 (Dvl2) of the signalosome undergoes LLPS. The assembly of the signalosome is initiated by recruiting Dvl2 to the cell membrane and then recruiting Axin1. Axin LLPS mediates the assembly of the β-catenin destruction complex, and Dvl2 can weaken the LLPS of Axin. Experimental results show that Dvl2 LLPS can control the assembly of Wnt receptor signalosomes and destroy phase-separated β-catenin destruction complexes. Making Wnt/β-catenin signal transduction an important way to affect HSCs homeostasis and tumorigenesis [48]. Signal transduction often requires multiple signal molecules to form complexes to work together. Studies have found that some signal transduction complexes can also form membrane-less organelles through phase separation to achieve the regulation of signal transduction. The loss of TGF-β growth inhibitory response is related to the occurrence of human cancer. The Smad complex in the TGF-β signaling pathway can form membrane-less organelles through phase separation to promote the transduction of TGF-β signals. SFPQ is an effective inhibitor of TGF-β signaling and is often up-regulated in cancer individuals. This splicing factor SFPQ can inhibit TGF-β by driving LLPS. Specifically, SFPQ excludes Smad4 from Smad complexes and chromatin occupancy, thereby inhibiting Smad-dependent transcriptional responses [49]. The signal transduction regulation achieved by signal molecules through phase separation is extremely important for HSCs to exert normal functions, and research on this mechanism is of far-reaching significance. (Fig. 2)

Fig. 2
figure 2

Phase Separation Involved in HSC Genetic Regulation (Phase separation participates in cellular activities such as autophagic degradation, transcriptional regulation, misfolding, epigenetic regulation, signal transduction, gene expression, etc. by forming membraneless compartments within cells, providing concentrated and separated cellular components for the replication and differentiation process of hematopoietic stem cells, and playing a key role in the functional regulation of hematopoietic stem cells.)

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Phase separation and bone marrow microenvironment

The bone marrow microenvironment is composed of multiple cell types, soluble factors, and extracellular matrix, providing assistance for the self-renewal and differentiation of HSCs. It participates in regulating the self-renewal, proliferation, and differentiation functions of HSCs and is an indispensable part of maintaining HSC stemness and normal hematopoietic function [50]. HSCs undergo continuous changes during differentiation, and their functional activity is regulated by extracellular signals from the bone marrow hematopoietic microenvironment. The LLPS process may also be influenced by such cytokines, growth factors, and other extracellular signals. This dynamic and dependent LLPS behavior further affects cellular function, leading to the appearance of abnormal phenotypes and disease occurrence. Kuchma et al. found that there are artificial hematopoietic progenitor cells (HPCs) at different stages of differentiation in full-term placental tissue (FTPT), and they have multiple cell subpopulations at different stages of differentiation. They also found that the primitiveness of progenitor cells is closely related to the intensity of CD34 expression, and cells with high levels of CD34 expression from different sources include primitive hematopoietic cells. FTPT and HPCs derived from umbilical cord blood have similar potential for multilineage differentiation and a similar proportion of myeloid and erythroid progenitor cells in vitro. However, compared with umbilical cord blood, FTPT has higher phenotypic heterogeneity, indicating that HSCs constantly change during differentiation into various types of blood cells, and dynamically dependent hematopoiesis is closely related to the bone marrow microenvironment. As an intracellular regulatory mechanism, LLPS behavior is closely related to the regulation of HSCs’ bone marrow microenvironment [51]. Research on phase separation and the complex network of bone marrow hematopoietic microenvironment is currently underway, which is expected to bring new discoveries and provide new targets for clinical stem cell therapy (Fig. 3).

Fig. 3
figure 3

The mechanism of phase separation regulation of HSC function (Phase separation can generate multiple membraneless compartments within cells, forming biomacromolecule condensates that participate in genetic regulation, epigenetic regulation, signal transduction, and microenvironment regulation of HSCs, regulating their self-renewal, replication, and multipotent differentiation functions, which is of great significance for the diagnosis and treatment of diseases.)

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Application prospects of phase separation-regulated HSCs in treating diseases

The multi-directional differentiation of HSCs is the key to maintaining the normal physiological function of the body. Abnormal differentiation will affect the normal physiological needs of the body and lead to the occurrence of diseases. By regulating phase separation, precise regulation of the fate determination of HSCs can be achieved and the directional differentiation of HSCs can be promoted. Studies have shown that m6A dysregulation is related to the occurrence of leukemia. YTHDC1 can undergo LLPS and form nuclear YTHDC1-m6A condensates (nYACs), and this process requires the participation of m6A [52]. Compared with normal HSCs, the number of nYACs in leukemia cells increases. These nYACs are used to maintain cell survival and undifferentiated state [53]. In addition, nYACs enable YTHDC1 to protect m6A mRNAs from exosome-related RNA degradation. In short, m6A is necessary for the formation of nuclear bodies mediated by phase separation. These nuclear bodies maintain mRNA stability and control the survival and differentiation of cancer cells [54]. By regulating the phase separation of transcription factors, HSCs can be promoted to differentiate into specific cell types, providing new therapeutic strategies for tissue repair and regeneration.

In addition, phase separation can also participate in the maintenance of HSCs stemness. Layilin (LAYN) is an integrin membrane hyaluronic acid receptor related to cell aging. Wang et al. conducted research by constructing the stemness landscape of LAYN. The results found that LAYN participates in the methylation modification process and can affect the proliferation and metastasis of tumor cells by regulating cell stemness. Its transcript may be an RNA related to LLPS and is particularly important in the infiltration of immune cells in malignant tumors and has high value for tumor prognosis [55]. New evidence shows that TAZ can enhance the functional activity of cancer stem cells (CSCs) through the phase separation of Nanog. The phase separation of TAZ-Nanog can promote the transcription of SOX2 and OCT4. Targeting Nanog or TAZ can regulate CSCs activity and enhance the body’s chemosensitivity to achieve the purpose of treatment. This shows that there is a close relationship between the phase separation of transcription factors and the function of CSCs [56]. Abnormal phase separation is closely related to the occurrence and development of various diseases. By regulating phase separation, the stemness of HSCs can be maintained, and normal self-renewal ability and multi-directional differentiation potential can be exerted, providing a more stable cell source for HSCs treatment. In cancer treatment, the proliferation and metastasis of tumor cells can be inhibited by inhibiting abnormal phase separation. Correcting abnormal phase separation in a disease state is expected to provide new ideas and methods for disease treatment.

LLPS can be classified into functional and pathological types. Functional LLPS, as a beneficial intracellular regulatory mechanism, is an important part of supporting the functional regulation of HSCs; Abnormal phase separation and the formation of pathological aggregates are often believed to be associated with various diseases. For example, Pijush et al.‘s research suggests that neurodegenerative diseases are associated with the pathological deposition of many different intrinsic disordered proteins or proteins with intrinsic disordered regions, which can undergo LLPS. The resulting biomolecule aggregates may undergo liquid-solid phase changes, leading to the pathology of various neurodegenerative diseases [57]. Similarly, Mariana et al. found that abnormal phase separation is associated with protein lesions, and the in vitro phase separation of prion protein (PrP) is regulated by nucleic acid aptamers. The interaction between PrP and different ligands (such as proteins and nucleic acids) can play a role in the pathogenesis of prion diseases. The process of pathological phase separation has been proven to be a valuable novel therapeutic strategy that may address protein misfolding disorders such as prion diseases [58]. Distinguishing the beneficial LLPS and pathological condensed matter formation in HSCs may bring new hope for targeted therapy of diseases.

Conclusion

As an emerging intracellular regulatory mechanism, phase separation plays a key role in the transcriptional regulation, epigenetic regulation and signal transduction of HSCs. Abnormal phase separation and transitions caused by mutations in phase separation proteins are related to the pathogenesis of various diseases. Deeply understanding the relationship between phase separation and HSCs regulation and identifying molecules that can regulate phase separation and transitions will provide new ideas and strategies for the development of stem cell biology and regenerative medicine. Currently, most research on phase separation focuses on biomolecular mechanisms. In clinical treatment, the potential of phase separation in treating diseases such as cancer, kidney disease and leukemia has also emerged. Future research needs to further reveal the specific mechanism of phase separation in HSCs regulation and the role of phase separation in the occurrence and development of stem cell damage-related diseases, providing a theoretical basis for the development of new stem cell therapies and disease treatment strategies.

Data availability

Not applicable.

Abbreviations

HSCs:

Hematopoietic stem cells

LLPS:

Liquid-liquid phase separation

AGM:

Aorta-gonad-mesonephros

LSCs:

Leukemia stem cells

AML:

Acute myeloid leukemia

Dvl2:

Dishevelled 2

FTPT:

Full-term placental tissue

HPCs:

Hematopoietic progenitor cells

nYACs:

Nuclear YTHDC1-m6A condensates

CSCs:

Cancer stem cells

LAYN:

Layilin

References

  1. Arai F, Suda T. Maintenance of quiescent hematopoietic stem cells in the osteoblastic niche. Ann N Y Acad Sci. 2007;1106:41–53.

    Article  CAS  PubMed  Google Scholar 

  2. Gajbhiye SS, Karwa AR, Dhok A, Jadhav SS. Clinical and etiological profiles of patients with pancytopenia in a tertiary care hospital. Cureus. 2022;14(10):e30449.

    PubMed  PubMed Central  Google Scholar 

  3. Ismail H, Liu X, Yang F, Li J, Zahid A, Dou Z, Liu X, Yao X. Mechanisms and regulation underlying membraneless organelle plasticity control. J Mol Cell Biol. 2021;13(4):239–58.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Parra AS, Johnston CA. Phase separation as a driver of stem cell organization and function during development. J Dev Biol. 2023;11(4):45.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Boija A, Klein IA, Sabari BR, Dall’Agnese A, Coffey EL, Zamudio AV, Li CH, Shrinivas K, Manteiga JC, Hannett NM, Abraham BJ, Afeyan LK, Guo YE, Rimel JK, Fant CB, Schuijers J, Lee TI, Taatjes DJ, Young RA. Transcription factors activate genes through the Phase-Separation capacity of their activation domains. Cell. 2018;175(7):1842–e185516.

    Article  CAS  PubMed  Google Scholar 

  6. Notta F, Doulatov S, Laurenti E, Poeppl A, Jurisica I, Dick JE. Isolation of single human hematopoietic stem cells capable of long-term multilineage engraftment. Science. 2011;333(6039):218–21.

    Article  CAS  PubMed  Google Scholar 

  7. Seita J, Weissman IL. Hematopoietic stem cell:self-renewal versus differentiation. Wiley Interdiscip Rev Syst Biol Med. 2010;2(6):640–53.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Tang X, Wang Z, Wang J, Cui S, Xu R, Wang Y. Functions and regulatory mechanisms of resting hematopoietic stem cells: a promising targeted therapeutic strategy. Stem Cell Res Ther. 2023;14(1):73.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Kasbekar M, Mitchell CA, Proven MA, Passegué E. Hematopoietic stem cells through the ages: A lifetime of adaptation to organismal demands. Cell Stem Cell. 2023;30(11):1403–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. de Haan G, Gerrits A, Bystrykh L. Modern genome-wide genetic approaches to reveal intrinsic properties of stem cells. Curr Opin Hematol. 2006;13(4):249–53.

    Article  PubMed  Google Scholar 

  11. Månsson R, Hultquist A, Luc S, Yang L, Anderson K, Kharazi S, et al. Molecular evidence for hierarchical transcriptional lineage priming in fetal and adult stem cells and multipotent progenitors. Immunity. 2007;26(4):407–19.

    Article  PubMed  Google Scholar 

  12. Kouzarides T. Chromatin modifications and their function. Cell. 2007;128(4):693–705.

    Article  CAS  PubMed  Google Scholar 

  13. Wang K, Liu H, Hu Q, Wang L, Liu J, Zheng Z, Zhang W, Ren J, Zhu F, Liu GH. Epigenetic regulation of aging: implications for interventions of aging and diseases. Signal Transduct Target Ther. 2022;7(1):374.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Li B, Carey M, Workman JL. The role of chromatin during transcription. Cell. 2007;128(4):707–19.

    Article  CAS  PubMed  Google Scholar 

  15. Lin Y, Li Y, Zhu X, Huang Y, Li Y, Li M. Genetic contexts characterize dynamic histone modification patterns among cell types. Interdiscip Sci. 2019;11(4):698–710.

    Article  CAS  PubMed  Google Scholar 

  16. Bachy E, Camus V, Thieblemont C, Sibon D, Casasnovas RO, Ysebaert L, Damaj G, Guidez S, Pica GM, Kim WS, Lim ST, Andre M, Garcia-Sancho AM, Penarrubia MJ, Staber PB, Trotman J, Huttmann A, Stefoni V, Re A, Gaulard P, Delfau-Larue MH, de Leval L, Meignan M, Li J, Morschhauser F, Delarue R. Romidepsin plus CHOP versus CHOP in patients with previously untreated peripheral T-Cell lymphoma: results of the Ro-CHOP phase III study (conducted by LYSA). J Clin Oncol. 2022;40:242–51.

    Article  CAS  PubMed  Google Scholar 

  17. Zhou S, Liu J, Wan A, Zhang Y, Qi X. Epigenetic regulation of diverse cell death modalities in cancer: a focus on pyroptosis, ferroptosis, cuproptosis, and disulfidptosis. J Hematol Oncol., Dong Y, Xu S, Liu J, Ponnusamy M, Zhao Y, Zhang Y, Wang Q, Li P, Wang K. Non-coding RNA-linked epigenetic regulation in cardiac hypertrophy. Int J Biol Sci. 2018;14(9):1133–1141.

  18. Yang JJ, Tao H, Deng ZY, Lu C, Li J. Non-coding RNA-mediated epigenetic regulation of liver fibrosis. Metabolism. 2015;64(11):1386–94.

    Article  CAS  PubMed  Google Scholar 

  19. Buenrostro JD, Corces MR, Lareau CA, Wu B, Schep AN, Aryee MJ, Majeti R, Chang HY, Greenleaf WJ. Integrated Single-Cell analysis maps the continuous regulatory landscape of human hematopoietic differentiation. Cell. 2018;173(6):1535–e154816.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Vizán P, Gutiérrez A, Espejo I, García-Montolio M, Lange M, Carretero A, Lafzi A, de Andrés-Aguayo L, Blanco E, Thambyrajah R, Graf T, Heyn H, Bigas A, Di Croce L. The Polycomb-associated factor PHF19 controls hematopoietic stem cell state and differentiation. Sci Adv. 2020;6(32):eabb2745.

    Article  PubMed  PubMed Central  Google Scholar 

  21. Matsumoto A, Takeishi S, Kanie T, Susaki E, Onoyama I, Tateishi Y, et al. p57 is required for quiescence and maintenance of adult hematopoietic stem cells. Cell Stem Cell. 2011;9(3):262–71.

    Article  CAS  PubMed  Google Scholar 

  22. Gonzalez Galofre ZN, Kilpatrick AM, Marques M, Sá da Bandeira D, Ventura T, Gomez Salazar M, Bouilleau L, Marc Y, Barbosa AB, Rossi F, Beltran M, van de Werken HJG, van IJcken WFJ, Henderson NC, Forbes SJ, Crisan M. Runx1 + vascular smooth muscle cells are essential for hematopoietic stem and progenitor cell development in vivo. Nat Commun. 2024;15(1):1653.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Chen MJ, Yokomizo T, Zeigler BM, Dzierzak E, Speck NA. Runx1 is required for the endothelial to Haematopoietic cell transition but not thereafter. Nature. 2009;457(7231):887–91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Sood R, Kamikubo Y, Liu P. Role of RUNX1 in hematological malignancies. Blood. 2017;129(15):2070–82.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Van Bergen MGJM, Marneth AE, Hoogendijk AJ, Van Alphen FPJ, Van den Akker E, Laros-Van Gorkom BAP, Hoeks M, Simons A, De Munnik SA, Janssen JJWM, Martens JHA, Jansen JH, Meijer AB, Van der Reijden BA. Specific proteome changes in platelets from individuals with GATA1-, GFI1B-, and RUNX1-linked bleeding disorders. Blood. 2021;138(1):86–90.

    Article  PubMed  Google Scholar 

  26. Gamble N, Bradu A, Caldwell JA, McKeever J, Bolonduro O, Ermis E, Kaiser C, Kim Y, Parks B, Klemm S, Greenleaf WJ, Crabtree GR, Koh AS. PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape. Nat Immunol. 2024;25(5):860–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Saunthararajah Y, Boccuni P, Nucifora G. Combinatorial action of RUNX1 and PU.1 in the regulation of hematopoiesis. Crit Rev Eukaryot Gene Expr. 2006;16(2):183–92.

    Article  CAS  PubMed  Google Scholar 

  28. Nagamura-Inoue T, Tamura T, Ozato K. Transcription factors that regulate growth and differentiation of myeloid cells. Int Rev Immunol. 2001;20(1):83–105.

    Article  CAS  PubMed  Google Scholar 

  29. Wesely J, Kotini AG, Izzo F, Luo H, Yuan H, Sun J, Georgomanoli M, Zviran A, Deslauriers AG, Dusaj N, Nimer SD, Leslie C, Landau DA, Kharas MG, Papapetrou EP. Acute myeloid leukemia iPSCs reveal a role for RUNX1 in the maintenance of human leukemia stem cells. Cell Rep. 2020;31(9):107688.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Zhang H, Ji X, Li P, Liu C, Lou J, Wang Z, Wen W, Xiao Y, Zhang M, Zhu X. Liquid-liquid phase separation in biology: mechanisms, physiological functions and human diseases. Sci China Life Sci. 2020;63(7):953–85.

    Article  PubMed  Google Scholar 

  31. Zhao YG, Zhang H. Phase separation in membrane biology: the interplay between membrane-Bound organelles and membraneless condensates. Dev Cell. 2020;55(1):30–44.

    Article  CAS  PubMed  Google Scholar 

  32. Miyamoto T, Iwasaki H, Reizis B, Ye M, Graf T, Weissman IL, et al. Myeloid or lymphoid promiscuity as a critical step in hematopoietic lineage commitment. Dev Cell. 2002;3(1):137–47.

    Article  CAS  PubMed  Google Scholar 

  33. Nsengimana B, Khan FA, Awan UA, Wang D, Fang N, Wei W, Zhang W, Ji S. Pseudogenes and liquid phase separation in epigenetic expression. Front Oncol. 2022;12:912282.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Yau TY, Sander W, Eidson C, Courey AJ. SUMO interacting motifs: structure and function. Cells. 2021;10(11):2825.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Verma A, Singh A, Singh MP, Nengroo MA, Saini KK, Satrusal SR, Khan MA, Chaturvedi P, Sinha A, Meena S, Singh AK, Datta D. EZH2-H3K27me3 mediated KRT14 upregulation promotes TNBC peritoneal metastasis. Nat Commun. 2022;13(1):7344.

    Article  PubMed  PubMed Central  Google Scholar 

  36. Deaton AM, Bird A. CpG Islands and the regulation of transcription. Genes Dev. 2011;25(10):1010–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Kurihara M, Kato K, Sanbo C, Shigenobu S, Ohkawa Y, Fuchigami T, Miyanari Y. Genomic profiling by ALaP-Seq reveals transcriptional regulation by PML bodies through DNMT3A exclusion. Mol Cell. 2020;78(3):493–e5058.

    Article  CAS  PubMed  Google Scholar 

  38. Zhang ZM, Lu R, Wang P, Yu Y, Chen D, Gao L, Liu S, Ji D, Rothbart SB, Wang Y, Wang GG, Song J. Structural basis for DNMT3A-mediated de Novo DNA methylation. Nature. 2018;554(7692):387–91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Friman ET, Deluz C, Meireles-Filho AC, Govindan S, Gardeux V, Deplancke B, et al. Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle. Elife. 2019;8:e50087.

    Article  PubMed  PubMed Central  Google Scholar 

  40. He J, Huo X, Pei G, Jia Z, Yan Y, Yu J, Qu H, Xie Y, Yuan J, Zheng Y, Hu Y, Shi M, You K, Li T, Ma T, Zhang MQ, Ding S, Li P, Li Y. Dual-role transcription factors stabilize intermediate expression levels. Cell. 2024;187(11):2746–e276625.

    Article  CAS  PubMed  Google Scholar 

  41. Sharp PA, Chakraborty AK, Henninger JE, Young RA. RNA in formation and regulation of transcriptional condensates. RNA. 2022;28(1):52–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Varga J, Kube M, Luck K, Schick S. The BAF chromatin remodeling complexes: structure, function, and synthetic lethalities. Biochem Soc Trans. 2021;49(4):1489–503.

    Article  CAS  PubMed  Google Scholar 

  43. Kim YR, Joo J, Lee HJ, Kim C, Park JC, Yu YS, Kim CR, Lee DH, Cha J, Kwon H, Hanssen KM, Grünewald TGP, Choi M, Han I, Bae S, Jung I, Shin Y, Baek SH. Prion-like domain mediated phase separation of ARID1A promotes oncogenic potential of Ewing’s sarcoma. Nat Commun. 2024;15(1):6569.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Sabari BR, Dall’Agnese A, Boija A, Klein IA, Coffey EL, Shrinivas K, Abraham BJ, Hannett NM, Zamudio AV, Manteiga JC, Li CH, Guo YE, Day DS, Schuijers J, Vasile E, Malik S, Hnisz D, Lee TI, Cisse II, Roeder RG, Sharp PA, Chakraborty AK, Young RA. Coactivator condensation at super-enhancers links phase separation and gene control. Science. 2018;361(6400):eaar3958.

    Article  PubMed  PubMed Central  Google Scholar 

  45. Cheng CW, Adams GB, Perin L, Wei M, Zhou X, Lam BS, Da Sacco S, Mirisola M, Quinn DI, Dorff TB, Kopchick JJ, Longo VD. Prolonged fasting reduces IGF-1/PKA to promote hematopoietic-stem-cell-based regeneration and reverse immunosuppression. Cell Stem Cell. 2014;14(6):810–23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Banani SF, Lee HO, Hyman AA, Rosen MK. Biomolecular condensates: organizers of cellular biochemistry. Nat Rev Mol Cell Biol. 2017;18(5):285–98.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Tripathi S, Miyake T, Kelebeev J, McDermott JC. TAZ exhibits phase separation properties and interacts with Smad7 and β-catenin to repress skeletal myogenesis. J Cell Sci. 2022;135(1):jcs259097.

    Article  CAS  PubMed  Google Scholar 

  48. Kang K, Shi Q, Wang X, Chen YG. Dishevelled phase separation promotes Wnt signalosome assembly and destruction complex disassembly. J Cell Biol. 2022;221(12):e202205069.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Xiao M, Wang F, Chen N, Zhang H, Cao J, Yu Y, Zhao B, Ji J, Xu P, Li L, Shen L, Lin X, Feng XH. Smad4 sequestered in SFPQ condensates prevents TGF-β tumor-suppressive signaling. Dev Cell. 2024;59(1):48–e638.

    Article  CAS  PubMed  Google Scholar 

  50. Babu Chandraprabha P, Thangavel S. Endocytosis as a critical regulator of hematopoietic stem cell fate -implications for hematopoietic stem cell and gene therapy. Stem Cell Res Ther. 2024;15(1):319.

    Article  PubMed  PubMed Central  Google Scholar 

  51. Kuchma MD, Kyryk VM, Svitina HM, Shablii YM, Lukash LL, Lobyntseva GS, Shablii VA. Comparative analysis of the hematopoietic progenitor cells from placenta, cord blood, and fetal liver, based on their immunophenotype. Biomed Res Int. 2015;2015:418752.

    Article  PubMed  PubMed Central  Google Scholar 

  52. Chang G, Shi L, Ye Y, Shi H, Zeng L, Tiwary S, Huse JT, Huo L, Ma L, Ma Y, et al. YTHDF3 induces the translation of m(6)A-Enriched gene transcripts to promote breast Cancer brain metastasis. Cancer Cell. 2020;38:857–e871857.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Paris J, Morgan M, Campos J, Spencer GJ, Shmakova A, Ivanova I, Mapperley C, Lawson H, Wotherspoon DA, Sepulveda C, et al. Targeting the RNA m(6)A reader YTHDF2 selectively compromises Cancer stem cells in acute myeloid leukemia. Cell Stem Cell. 2019;25:137–e148136.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Cheng Y, Xie W, Pickering BF, Chu KL, Savino AM, Yang X, Luo H, Nguyen DT, Mo S, Barin E, Velleca A, Rohwetter TM, Patel DJ, Jaffrey SR, Kharas MG. N6-Methyladenosine on mRNA facilitates a phase-separated nuclear body that suppresses myeloid leukemic differentiation. Cancer Cell. 2021;39(7):958–e9728.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Jiawen W, Jinfu W, Jianyong L, Yaoguang Z, Jianye W. Comprehensive landscape of the miRNA-regulated prognostic marker LAYN with immune infiltration and stemness in pan-cancer. J Cancer Res Clin Oncol. 2023;149(13):10989–1011.

    Article  PubMed  Google Scholar 

  56. Liu X, Ye Y, Zhu L, Xiao X, Zhou B, Gu Y, Si H, Liang H, Liu M, Li J, Jiang Q, Li J, Yu S, Ma R, Su S, Liao JY, Zhao Q. Niche stiffness sustains cancer stemness via TAZ and NANOG phase separation. Nat Commun. 2023;14(1):238.

    Article  PubMed  PubMed Central  Google Scholar 

  57. Chakraborty P, Zweckstetter M. Role of aberrant phase separation in pathological protein aggregation. Curr Opin Struct Biol. 2023;82:102678.

    Article  CAS  PubMed  Google Scholar 

  58. do Amaral MJ, Freire MHO, Almeida MS, Pinheiro AS, Cordeiro Y. Phase separation of the mammalian prion protein: physiological and pathological perspectives. J Neurochem. 2023;166(1):58–75.

    Article  PubMed  Google Scholar 

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Acknowledgements

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Funding

This study was supported by the National Natural Science Foundation of China (Grant Nos. 82174181; 82374237), Jointly built project by the Science and Technology Department of the State Administration of Traditional Chinese Medicine (Grant No. GZY-KJS-SD-2023-040) and the “Taishan Scholar” Project Special Fund (tsqn202211351).

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Authors and Affiliations

  1. Doctoral student of Grade 2024, First Clinical Medical College of, Shandong University of Traditional Chinese Medicine, Jinan, China

    XinYu Tang

  2. Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China

    Yan Wang & RuiRong Xu

  3. Institute of Hematology, Shandong University of Traditional Chinese Medicine, Jinan, China

    Yan Wang & RuiRong Xu

  4. Shandong Provincial Health Commission Key Laboratory of Hematology of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China

    Yan Wang & RuiRong Xu

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  1. XinYu Tang
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  2. Yan Wang
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XT wrote manuscripts, searched literature, and prepared charts, and was a major contributor in writing the manuscript. YW and RX provided ideas for the article, conducted literature research and revised the manuscript.

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Correspondence to Yan Wang or RuiRong Xu.

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Tang, X., Wang, Y. & Xu, R. Phase separation participates in the genetic regulation mechanism of hematopoietic stem cells: potential therapeutic methods. Stem Cell Res Ther 16, 214 (2025). https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s13287-025-04350-1

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  • DOI: https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s13287-025-04350-1

Keywords

Stem Cell Research & Therapy

ISSN: 1757-6512