bims-ectoca 2023-06-25 papers

Issue of 2023‒06‒25
six papers selected by
Ankita Daiya
BITS Pilani

Gene. 2023 Jun 21. pii: S0378-1119(23)00425-0. [Epub ahead of print] 147584

JARID2 and EZH2, The Eminent Epigenetic Drivers In Human Cancer.

Cancer has become a prominent cause of death, accounting for approximately 10 million death worldwide as per the World Health Organization reports 2020. Epigenetics deal with the alterations of heritable phenotypes, except for DNA alterations. Currently, we are trying to comprehend the role of utmost significant epigenetic genes involved in the burgeoning of human cancer. A sundry of studies reported the Enhancer of Zeste Homologue2 (EZH2) as a prime catalytic subunit of Polycomb Repressive Complex2, which is involved in several pivotal activities, including embryogenesis. In addition, EZH2 has detrimental effects leading to the onset and metastasis of several cancers. Jumonji AT Rich Interacting Domain2 (JARID2), an undebated crucial nuclear factor, has strong coordination with the PRC2 family. In this review, we discuss various epigenetic entities, primarily focusing on the possible role and mechanism of EZH2 and the significant contribution of JARID2 in human cancers.

Keywords: Cancer; EZH2; Epigenetics; JARID2; Polycomb repressive complex

DOI: https://doi.org/10.1016/j.gene.2023.147584

Cell Commun Signal. 2023 06 19. 21(1): 149

Lipid kinase PIP5Kα contributes to Hippo pathway activation via interaction with Merlin and by mediating plasma membrane targeting of LATS1.

Truc Phan Hoang Le, Nga Thi Thanh Nguyen, Duong Duy Thai Le, Muhammad Ayaz Anwar, Sang Yoon Lee.

BACKGROUND: The Hippo pathway plays a critical role in controlled cell proliferation. The tumor suppressor Merlin and large tumor suppressor kinase 1 (LATS1) mediate activation of Hippo pathway, consequently inhibiting the primary effectors, Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ). Phosphatidylinositol 4,5-bisphosphate (PIP2), a lipid present in the plasma membrane (PM), binds to and activates Merlin. Phosphatidylinositol 4-phosphate 5-kinase α (PIP5Kα) is an enzyme responsible for PIP2 production. However, the functional role of PIP5Kα in regulation of Merlin and LATS1 under Hippo signaling conditions remains unclear.METHODS: PIP5Kα, Merlin, or LATS1 knockout or knockdown cells and transfected cells with them were used. LATS1, YAP, and TAZ activities were measured using biochemical methods and PIP2 levels were evaluated using cell imaging. Low/high cell density and serum starvation/stimulation conditions were tested. Colocalization of PIP5Kα and PIP2 with Merlin and LATS1, and their protein interactions were examined using transfection, confocal imaging, immunoprecipitation, western blotting, and/or pull-down experiments. Colony formation and adipocyte differentiation assays were performed.
RESULTS: We found that PIP5Kα induced LATS1 activation and YAP/TAZ inhibition in a kinase activity-dependent manner. Consistent with these findings, PIP5Kα suppressed cell proliferation and enhanced adipocyte differentiation of mesenchymal stem cells. Moreover, PIP5Kα protein stability and PIP2 levels were elevated at high cell density compared with those at low cell density, and both PIP2 and YAP phosphorylation levels initially declined, then recovered upon serum stimulation. Under these conditions, YAP/TAZ activity was aberrantly regulated by PIP5Kα deficiency. Mechanistically, either Merlin deficiency or LATS1 deficiency abrogated PIP5Kα-mediated YAP/TAZ inactivation. Additionally, the catalytic domain of PIP5Kα directly interacted with the band 4.1/ezrin/radixin/moesin domain of Merlin, and this interaction reinforced interaction of Merlin with LATS1. In accordance with these findings, PIP5Kα and PIP2 colocalized with Merlin and LATS1 in the PM. In PIP5Kα-deficient cells, Merlin colocalization with PIP2 was reduced, and LATS1 solubility increased.
CONCLUSIONS: Collectively, our results support that PIP5Kα serves as an activator of the Hippo pathway through interaction and colocalization with Merlin, which promotes PIP2-dependent Merlin activation and induces local recruitment of LATS1 to the PIP2-rich PM and its activation, thereby negatively regulating YAP/TAZ activity. Video Abstract.

Keywords: Hippo pathway; LATS1; Merlin; PIP2; PIP5Kα; Plasma membrane; YAP/TAZ

DOI: https://doi.org/10.1186/s12964-023-01161-w

Aging Cell. 2023 Jun 20. e13913

Releasing YAP dysfunction-caused replicative toxicity rejuvenates mesenchymal stem cells.

Fanyuan Yu, Lin Yao, Feifei Li, Chenglin Wang, Ling Ye.

Hippo-independent YAP dysfunction has been demonstrated to cause chronological aging of stromal cells by impairing the integrity of nuclear envelope (NE). In parallel with this report, we uncover that YAP activity also controls another type of cellular senescence, the replicative senescence in in vitro expansion of mesenchymal stromal cells (MSCs), but this event is Hippo phosphorylation-dependent, and there exist another NE integrity-independent downstream mechanisms of YAP. Specifically, Hippo phosphorylation causes reduced nuclear/active YAP and then decreases the level of YAP protein in the proceeding of replicative senescence. YAP/TEAD governs RRM2 expression to release replicative toxicity (RT) via licensing G1/S transition. Besides, YAP controls the core transcriptomics of RT to delay the onset of genome instability and enhances DNA damage response/repair. Hippo-off mutations of YAP (YAPS127A/S381A ) satisfactorily release RT via maintaining cell cycle and reducing genome instability, finally rejuvenating MSCs and restoring their regenerative capabilities without risks of tumorigenesis.

Keywords: DNA damage; aging; mesenchymal stromal cell; rejuvenation; replicative stress

DOI: https://doi.org/10.1111/acel.13913

J Mol Biol. 2023 Apr 12. pii: S0022-2836(23)00075-X. [Epub ahead of print] 168019

The Force is Strong with This Epigenome: Chromatin Structure and Mechanobiology.

Chieh-Ren Hsia, Daniël P Melters, Yamini Dalal.

All life forms sense and respond to mechanical stimuli. Throughout evolution, organisms develop diverse mechanosensing and mechanotransduction pathways, leading to fast and sustained mechanoresponses. Memory and plasticity characteristics of mechanoresponses are thought to be stored in the form of epigenetic modifications, including chromatin structure alterations. These mechanoresponses in the chromatin context share conserved principles across species, such as lateral inhibition during organogenesis and development. However, it remains unclear how mechanotransduction mechanisms alter chromatin structure for specific cellular functions, and if altered chromatin structure can mechanically affect the environment. In this review, we discuss how chromatin structure is altered by environmental forces via an outside-in pathway for cellular functions, and the emerging concept of how chromatin structure alterations can mechanically affect nuclear, cellular, and extracellular environments. This bidirectional mechanical feedback between chromatin of the cell and the environment can potentially have important physiological implications, such as in centromeric chromatin regulation of mechanobiology in mitosis, or in tumor-stroma interactions. Finally, we highlight the current challenges and open questions in the field and provide perspectives for future research.

Keywords: Chromatin; Epigenetics; Mechanobiology; Mechanoresponse; Mechanosensing

DOI: https://doi.org/10.1016/j.jmb.2023.168019

Environ Toxicol. 2023 Jun 19.

Histone methyltransferase enzyme enhancer of zeste homolog 2 counteracts ischemic brain injury via H3K27me3-mediated regulation of PI3K/AKT/mTOR signaling pathway.

Miao Chen, Limin Fan, Guoping Wu, Hairong Wang, Shuo Gu.

BACKGROUND: Epigenetic histone methylation plays a crucial role in cerebral ischemic injury, particularly in the context of ischemic stroke. However, the complete understanding of regulators involved in histone methylation, such as Enhancer of Zeste Homolog 2 (EZH2), along with their functional effects and underlying mechanisms, remains incomplete.METHODS: Here, we employed a rat model of MCAO (Middle cerebral artery occlusion) and an OGD (Oxygen-Glucose Deprivation) model of primary cortical neurons to study the role of EZH2 and H3K27me3 in cerebral ischemia-reperfusion injury. The infarct volume was measured through TTC staining, while cell apoptosis was detected using TUNEL staining. The mRNA expression levels were quantified through quantitative real-time polymerase chain reaction (qPCR), whereas protein expressions were evaluated via western blotting and immunofluorescence experiments.
RESULTS: The expression levels of EZH2 and H3K27me3 were upregulated in OGD; these expression levels were further enhanced by GSK-J4 but reduced by EPZ-6438 and AKT inhibitor (LY294002) under OGD conditions. Similar trends were observed for mTOR, AKT, and PI3K while contrasting results were noted for UTX and JMJD3. The phosphorylation levels of mTOR, AKT, and PI3K were activated by OGD, further stimulated by GSK-J4, but inhibited by EPZ-6438 and AKT inhibitor. Inhibition of EZH2 or AKT effectively counteracted OGD-/MCAO-induced cell apoptosis. Additionally, inhibition of EZH2 or AKT mitigated MCAO-induced infarct size and neurological deficit in vivo.
CONCLUSIONS: Collectively, our results demonstrate that EZH2 inhibition exerts a protective effect against ischemic brain injury by modulating the H3K27me3/PI3K/AKT/mTOR signaling pathway. The results provide novel insights into potential therapeutic mechanisms for stroke treatment.

Keywords: AKT; EZH2; H3K27me3; MCAO; OGD/R; PI3K; cerebral ischemia-reperfusion injury; histone methylation; mTOR

DOI: https://doi.org/10.1002/tox.23863

Comput Biol Chem. 2023 Jun 16. pii: S1476-9271(23)00093-2. [Epub ahead of print]105 107902

Drug repurposing for Basal breast cancer subpopulations using modular network signatures.

Hiram Coria-Rodríguez, Soledad Ochoa, Guillermo de Anda-Jáuregui, Enrique Hernández-Lemus.

Breast cancer is characterized as being a heterogeneous pathology with a broad phenotype variability. Breast cancer subtypes have been developed in order to capture some of this heterogeneity. Each of these breast cancer subtypes, in turns retains varied characteristic features impacting diagnostic, prognostic and therapeutics. Basal breast tumors, in particular have been challenging in these regards. Basal breast cancer is often more aggressive, of rapid evolution and no tailor-made targeted therapies are available yet to treat it. Arguably, epigenetic variability is behind some of these intricacies. It is possible to further classify basal breast tumor in groups based on their non-coding transcriptome and methylome profiles. It is expected that these groups will have differences in survival as well as in sensitivity to certain classes of drugs. With this in mind, we implemented a computational learning approach to infer different subpopulations of basal breast cancer (from TCGA multi-omic data) based on their epigenetic signatures. Such epigenomic signatures were associated with different survival profiles; we then identified their associated gene co-expression network structure, extracted a signature based on modules within these networks, and use these signatures to find and prioritize drugs (in the LINCS dataset) that may be used to target these types of cancer. In this way we are introducing the analytical workflow for an epigenomic signature-based drug repurposing structure.

Keywords: Basal breast cancer; Drug repurposing; Modular network signatures; MultiOmic regulation; Perturbation assays

DOI: https://doi.org/10.1016/j.compbiolchem.2023.107902