bims-ectoca 2024-02-04 papers

bims-ectoca

Biomed News

on Epigenetic control of tolerance in cancer

Issue of 2024–02–04
twelve papers selected by
Ankita Daiya, Birla Institute of Technology and Science

Regulation of YAP Promotor Accessibility in Endothelial Mechanotransduction.
Epigenetic control of the vicious cycle.
Polycomb-mediated histone modifications and gene regulation.
HIRA vs. DAXX: the two axes shaping the histone H3.3 landscape.
LncRNA RPARP-AS1 promotes the progression of osteosarcoma cells through regulating lipid metabolism.
CRUX, a platform for visualising, exploring and analysing cancer genome cohort data.
Genetic and non-genetic drug resistance: Darwin or Lamarck?
EZH2/G9a interact to mediate drug resistance in non-small-cell lung cancer by regulating the SMAD4/ERK/c-Myc signaling axis.
Decoding the Ubiquitin Language: Orchestrating Transcription Initiation and Gene Expression Through Chromatin Remodelers and Histones.
SIRT7 promotes Hippo/YAP activation and cancer cell proliferation in hepatocellular carcinoma via suppressing MST1.
Specialized replication of heterochromatin domains ensures self-templated chromatin assembly and epigenetic inheritance.
Osteosarcoma neutrophil extracellular trap network-associated gene recurrence and metastasis model.

Arterioscler Thromb Vasc Biol. 2024 Feb 01.

Regulation of YAP Promotor Accessibility in Endothelial Mechanotransduction.

Aarren J Mannion, Honglei Zhao, Yuanyuan Zhang, Ylva von Wright, Otto Bergman, Joy Roy, Pipsa Saharinen, Lars Holmgren.

   BACKGROUND: Endothelial cells are constantly exposed to mechanical forces in the form of fluid shear stress, extracellular stiffness, and cyclic strain. The mechanoresponsive activity of YAP (Yes-associated protein) and its role in vascular development are well described; however, whether changes to transcription or epigenetic regulation of YAP are involved in these processes remains unanswered. Furthermore, how mechanical forces are transduced to the nucleus to drive transcriptional reprogramming in endothelial cells is poorly understood. The YAP target gene, AmotL2 (angiomotin-like 2), is a junctional mechanotransducer that connects cell-cell junctions to the nuclear membrane via the actin cytoskeleton.
METHODS: We applied mechanical manipulations including shear flow, stretching, and substrate stiffness to endothelial cells to investigate the role of mechanical forces in modulating YAP transcription. Using in vitro and in vivo endothelial depletion of AmotL2, we assess nuclear morphology, chromatin organization (using transposase-accessible chromatin sequencing), and whole-mount immunofluorescent staining of the aorta to determine the regulation and functionality of YAP. Finally, we use genetic and chemical inhibition to uncouple the nuclear-cytoskeletal connection to investigate the role of this pathway on YAP transcription.
RESULTS: Our results reveal that mechanical forces sensed at cell-cell junctions by the YAP target gene AmotL2 are directly involved in changes in global chromatin accessibility and activity of the histone methyltransferase EZH2, leading to modulation of YAP promotor activity. Functionally, shear stress-induced proliferation of endothelial cells in vivo was reliant on AmotL2 and YAP/TAZ expression. Mechanistically, uncoupling of the nuclear-cytoskeletal connection from junctions and focal adhesions led to altered nuclear morphology, chromatin accessibility, and YAP promotor activity.
CONCLUSIONS: Our findings reveal a role for AmotL2 and nuclear-cytoskeletal force transmission in modulating the epigenetic and transcriptional regulation of YAP to maintain a mechano-enforced positive feedback loop of vascular homeostasis. These findings may offer an explanation as to the proinflammatory phenotype that leads to aneurysm formation observed in AmotL2 endothelial deletion models.

Keywords:  aneurysm; aorta; homeostasis; phenotype; staining and labeling

DOI:  https://doi.org/10.1161/ATVBAHA.123.320300
J Bone Oncol. 2024 Feb;44 100524

Epigenetic control of the vicious cycle.

Madeline B Searcy, Rachelle W Johnson.

  Epigenetic alterations, including DNA methylation and post translational modifications to histones, drive tumorigenesis and metastatic progression. In the context of bone metastasis, epigenetic modifications in tumor cells can modulate dissemination of cancer cells to the bone, tumor progression in the bone marrow, and may be associated with patient survival rates. Bone disseminated tumor cells may enter a dormant state or stimulate osteolysis through the "vicious cycle" of bone metastasis where bone disseminated tumor cells disrupt the bone microenvironment, which fuels tumor progression. Epigenetic alterations may either exacerbate or abrogate the vicious cycle by regulating tumor suppressors and oncogenes, which alter proliferation of bone-metastatic cancer cells. This review focuses on the specific epigenetic alterations that regulate bone metastasis, including DNA methylation, histone methylation, and histone acetylation. Here, we summarize key findings from researchers identifying epigenetic changes that drive tumor progression in the bone, along with pre-clinical and clinical studies investigating the utility of targeting aberrant epigenetic alterations to treat bone metastatic cancer.

Keywords:  Acetylation; Bone metastasis; Epigenetics; HDAC; Histone; Histone Deacetylase; Methylation

DOI:  https://doi.org/10.1016/j.jbo.2024.100524
Biochem Soc Trans. 2024 Jan 30. pii: BST20230336. [Epub ahead of print]

Polycomb-mediated histone modifications and gene regulation.

Shinsuke Ito, Takashi Umehara, Haruhiko Koseki.

  Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) are transcriptional repressor complexes that play a fundamental role in epigenomic regulation and the cell-fate decision; these complexes are widely conserved in multicellular organisms. PRC1 is an E3 ubiquitin (ub) ligase that generates histone H2A ubiquitinated at lysine (K) 119 (H2AK119ub1), whereas PRC2 is a histone methyltransferase that specifically catalyzes tri-methylation of histone H3K27 (H3K27me3). Genome-wide analyses have confirmed that these two key epigenetic marks highly overlap across the genome and contribute to gene repression. We are now beginning to understand the molecular mechanisms that enable PRC1 and PRC2 to identify their target sites in the genome and communicate through feedback mechanisms to create Polycomb chromatin domains. Recently, it has become apparent that PRC1-induced H2AK119ub1 not only serves as a docking site for PRC2 but also affects the dynamics of the H3 tail, both of which enhance PRC2 activity, suggesting that trans-tail communication between H2A and H3 facilitates the formation of the Polycomb chromatin domain. In this review, we discuss the emerging principles that define how PRC1 and PRC2 establish the Polycomb chromatin domain and regulate gene expression in mammals.

Keywords:  CpG island; H2AK119ub1; H3K27me3; PRC1; PRC2; transcriptional repression

DOI:  https://doi.org/10.1042/BST20230336
Exp Mol Med. 2024 Feb 01.

HIRA vs. DAXX: the two axes shaping the histone H3.3 landscape.

Jinmi Choi, Taewan Kim, Eun-Jung Cho.

H3.3, the most common replacement variant for histone H3, has emerged as an important player in chromatin dynamics for controlling gene expression and genome integrity. While replicative variants H3.1 and H3.2 are primarily incorporated into nucleosomes during DNA synthesis, H3.3 is under the control of H3.3-specific histone chaperones for spatiotemporal incorporation throughout the cell cycle. Over the years, there has been progress in understanding the mechanisms by which H3.3 affects domain structure and function. Furthermore, H3.3 distribution and relative abundance profoundly impact cellular identity and plasticity during normal development and pathogenesis. Recurrent mutations in H3.3 and its chaperones have been identified in neoplastic transformation and developmental disorders, providing new insights into chromatin biology and disease. Here, we review recent findings emphasizing how two distinct histone chaperones, HIRA and DAXX, take part in the spatial and temporal distribution of H3.3 in different chromatin domains and ultimately achieve dynamic control of chromatin organization and function. Elucidating the H3.3 deposition pathways from the available histone pool will open new avenues for understanding the mechanisms by which H3.3 epigenetically regulates gene expression and its impact on cellular integrity and pathogenesis.

DOI: https://doi.org/10.1038/s12276-023-01145-3
BMC Cancer. 2024 Feb 02. 24(1): 166

LncRNA RPARP-AS1 promotes the progression of osteosarcoma cells through regulating lipid metabolism.

Feng Cai, Luhua Liu, Yuan Bo, Wenjing Yan, Xuchang Tao, Yuanxiang Peng, Zhiping Zhang, Qi Liao, Yangyan Yi.

  Osteosarcoma (OS) is a highly malignant tumor, and its dysregulated lipid metabolism is associated with tumorigenesis and unfavorable prognosis. Interestingly, long noncoding RNAs (lncRNAs) have emerged as pivotal regulators of lipid metabolism, exerting notable impacts on tumor proliferation. Nevertheless, the involvement of RPARP-AS1, a novel lipid metabolism-associated lncRNA, remains unexplored in the context of OS. This study aims to identify functionally relevant lncRNAs impacting OS proliferation and lipid metabolism and seeks to shed light on the upstream regulatory mechanisms governing lipogenic enzyme activity. Based on comprehensive bioinformatic analysis and the establishment of a risk model, we identified seven lncRNAs significantly associated with clinical characteristics and lipid metabolism-related genes in patients with OS. Among these, RPARP-AS1 was selected for in-depth investigation regarding its roles in OS proliferation and lipid metabolism. Experimental techniques including RT-qPCR, Western blot, cell viability assay, assessment, and quantification of free fatty acids (FFAs) and triglycerides (TGs) were utilized to elucidate the functional significance of RPARP-AS1 in OS cells and validate its effects on lipid metabolism. Manipulation of RPARP-AS1 expression via ectopic expression or siRNA-mediated knockdown led to alterations in epithelial-mesenchymal transition (EMT) and expression of apoptosis-associated proteins, thereby influencing OS cell proliferation and apoptosis. Mechanistically, RPARP-AS1 was found to augment the expression of key lipogenic enzymes (FABP4, MAGL, and SCD1) and potentially modulate the Akt/mTOR pathway, thereby contributing to lipid metabolism (involving alterations in FFA and TG levels) in OS cells. Collectively, our findings establish RPARP-AS1 as a novel oncogene in OS cells and suggest its role in fostering tumor growth through the enhancement of lipid metabolism.

Keywords:  Akt/mTOR pathway; Gene set enrichment analysis; Lipid metabolism; LncRNA RPARP-AS1; Osteosarcoma

DOI:  https://doi.org/10.1186/s12885-024-11901-x
NAR Genom Bioinform. 2024 Mar;6(1): lqae003

CRUX, a platform for visualising, exploring and analysing cancer genome cohort data.

Sam El-Kamand, Julian M W Quinn, Heena Sareen, Therese M Becker, Marie Wong-Erasmus, Mark J Cowley.

To better understand how tumours develop, identify prognostic biomarkers and find new treatments, researchers have generated vast catalogues of cancer genome data. However, these datasets are complex, so interpreting their important features requires specialized computational skills and analytical tools, which presents a significant technical challenge. To address this, we developed CRUX, a platform for exploring genomic data from cancer cohorts. CRUX enables researchers to perform common analyses including cohort comparisons, biomarker discovery, survival analysis, and to create visualisations including oncoplots and lollipop charts. CRUX simplifies cancer genome analysis in several ways: (i) it has an easy-to-use graphical interface; (ii) it enables users to create custom cohorts, as well as analyse precompiled public and private user-created datasets; (iii) it allows analyses to be run locally to address data privacy concerns (though an online version is also available) and (iv) it makes it easy to use additional specialized tools by exporting data in the correct formats. We showcase CRUX's capabilities with case studies employing different types of cancer genome analysis, demonstrating how it can be used flexibly to generate valuable insights into cancer biology. CRUX is freely available at https://github.com/CCICB/CRUX and https://ccicb.shinyapps.io/crux (DOI: 10.5281/zenodo.8015714).

DOI: https://doi.org/10.1093/nargab/lqae003
Mol Oncol. 2024 Feb 02.

Genetic and non-genetic drug resistance: Darwin or Lamarck?

Mariangela Russo.

  Drug resistance represents a major limitation to the long-term efficacy of anti-cancer treatments. The commonly accepted view is that the selection of inheritable genetic mechanisms governs the development of secondary resistance. However, compelling evidence suggests an important role for adaptive cell plasticity and non-genetic mechanisms in the development of therapy resistance. The two phenomena are not mutually exclusive and the interplay between genetic and non-genetic mechanisms may affect tumor evolution during treatment. A broader characterization of the genetic and non-genetic mechanisms of drug resistance may pave the way for more precise and effective therapeutic strategies to overcome resistance.

Keywords:  drug resistance; epigenetic; genetic; tumor evolution

DOI:  https://doi.org/10.1002/1878-0261.13601
Cell Rep. 2024 Jan 31. pii: S2211-1247(24)00042-1. [Epub ahead of print]43(2): 113714

EZH2/G9a interact to mediate drug resistance in non-small-cell lung cancer by regulating the SMAD4/ERK/c-Myc signaling axis.

Qiuyue Zhang, Yajie Shi, Sen Liu, Weiming Yang, Huiping Chen, Ning Guo, Wanyu Sun, Yongshan Zhao, Yuxiang Ren, Yong Ren, Lina Jia, Jingyu Yang, Yi Yun, Guoliang Chen, Lihui Wang, Chunfu Wu.

  Drug resistance is the leading problem in non-small-cell lung cancer (NSCLC) therapy. The contribution of histone methylation in mediating malignant phenotypes of NSCLC is well known. However, the role of histone methylation in NSCLC drug-resistance mechanisms remains unclear. Here, our data show that EZH2 and G9a, two histone methyltransferases, are involved in the drug resistance of NSCLC. Gene manipulation results indicate that the combination of EZH2 and G9a promotes tumor growth and mediates drug resistance in a complementary manner. Importantly, clinical study demonstrates that co-expression of both enzymes predicts a poor outcome in patients with NSCLC. Mechanistically, G9a and EZH2 interact and promote the silencing of the tumor-suppressor gene SMAD4, activating the ERK/c-Myc signaling pathway. Finally, SU08, a compound targeting both EZH2 and G9a, is demonstrated to sensitize resistant cells to therapeutic drugs by regulating the SMAD4/ERK/c-Myc signaling axis. These findings uncover the resistance mechanism and a strategy for reversing NSCLC drug resistance.

Keywords:  CP: Cancer

DOI:  https://doi.org/10.1016/j.celrep.2024.113714
Gene. 2024 Jan 31. pii: S0378-1119(24)00099-4. [Epub ahead of print] 148218

Decoding the Ubiquitin Language: Orchestrating Transcription Initiation and Gene Expression Through Chromatin Remodelers and Histones.

Kartik Mandal, Shiva Kumar Tomar, Manas Kumar Santra.

  Eukaryotic transcription is a finely orchestrated process and it is controlled by transcription factors as well as epigenetic regulators. Transcription factors and epigenetic regulators undergo different types of posttranslational modifications including ubiquitination to control transcription process. Ubiquitination, traditionally associated with protein degradation, has emerged as a crucial contributor to the regulation of chromatin structure through ubiquitination of histone and chromatin remodelers. Ubiquitination introduces new layers of intricacy to the regulation of transcription initiation through controlling the equilibrium between euchromatin and heterochromatin states. Nucleosome, the fundamental units of chromatin, spacing in euchromatin and heterochromatin states are regulated by histone modification and chromatin remodeling complexes. Chromatin remodeling complexes actively sculpt the chromatin architecture and thereby influence the transcriptional states of genes. Therefore, understanding the dynamic behavior of nucleosome spacing is critical as it impacts various cellular functions through controlling gene expression profiles. In this comprehensive review, we discussed the intricate interplay between ubiquitination and transcription initiation, and illuminated the underlying molecular mechanisms that occur in a variety of biological contexts. This exploration sheds light on the complex regulatory networks that govern eukaryotic transcription, providing important insights into the fine orchestration of gene expression and chromatin dynamics.

Keywords:  Chromatin remodelers; H2A; H2B; Histone monoubiquitination; Transcription initiation; Ubiquitination

DOI:  https://doi.org/10.1016/j.gene.2024.148218
Cancer Sci. 2024 Jan 30.

SIRT7 promotes Hippo/YAP activation and cancer cell proliferation in hepatocellular carcinoma via suppressing MST1.

Yiying Gu, Cong Ding, Tingzi Yu, Bohao Liu, Wenbin Tang, Zhiqiang Wang, Xiaohui Tang, Gaoshuang Liang, Jinying Peng, Xiangwen Zhang, Zhuan Li.

  Abnormal activation of the oncogene YAP in the Hippo pathway is a major feature in liver cancer and inactivation of MST1/2 has been shown to be responsible for the overactivation of YAP that led to tumorigenesis. However, mechanisms underlying MST1/2 dysregulation remain poorly understood. RNA-seq analysis and genome (KEGG) pathway enrichment analysis were used to identify genes and pathways that were regulated by SIRT7. qRT-PCR, ChIP, and luciferase assay were used to investigate transcriptional regulation. Mass spectrometry, co-immunoprecipitation and immunoprecipitation were used to exam protein-protein interaction and post-transcriptional modification. A xenograft mouse model was used to confirm the effect of SIRT7 and SIRT7 inhibitors on hepatocellular carcinoma (HCC) proliferation in vivo. We found that SIRT7 suppresses MST1 by both transcriptional regulation and post-transcriptional modification, which in turn promotes YAP nuclear localization and transcriptional activation in liver cancer. Mechanistically, we revealed that SIRT7 suppresses MST1 transcription by binding to the MST1 promoter and inducing H3K18 deacetylation in its promoter region. In addition, SIRT7 directly binds to and deacetylates MST1, which primes acetylation-dependent MST1 ubiquitination and protein degradation. In clinical samples, we confirmed a negative correlation between SIRT7 and MST1 protein levels, and high SIRT7 expression correlated with elevated YAP expression and nuclear localization. In addition, SIRT7 specific inhibitor 2800Z sufficiently inhibited HCC growth by disrupting the SIRT7/MST1/YAP axis. Our data thus revealed the previously undescribed function of SIRT7 in regulating the Hippo pathway in HCC and further proved that targeting SIRT7 might provide novel therapeutic options for the treatment of liver cancer.

Keywords:  epigenetics; histone deacetylase; liver cancer; oncogenes; post-transcriptional modification

DOI:  https://doi.org/10.1111/cas.16091
Proc Natl Acad Sci U S A. 2024 Feb 06. 121(6): e2315596121

Specialized replication of heterochromatin domains ensures self-templated chromatin assembly and epigenetic inheritance.

Patroula Nathanailidou, Jothy Dhakshnamoorthy, Hua Xiao, Martin Zofall, Sahana Holla, Maura O'Neill, Thorkell Andresson, David Wheeler, Shiv I S Grewal.

  Heterochromatin, defined by histone H3 lysine 9 methylation (H3K9me), spreads across large domains and can be epigenetically inherited in a self-propagating manner. Heterochromatin propagation depends upon a read-write mechanism, where the Clr4/Suv39h methyltransferase binds to preexisting trimethylated H3K9 (H3K9me3) and further deposits H3K9me. How the parental methylated histone template is preserved during DNA replication is not well understood. Here, we demonstrate using Schizosaccharomyces pombe that heterochromatic regions are specialized replication domains demarcated by their surrounding boundary elements. DNA replication throughout these domains is distinguished by an abundance of replisome components and is coordinated by Swi6/HP1. Although mutations in the replicative helicase subunit Mcm2 that affect histone binding impede the maintenance of a heterochromatin domain at an artificially targeted ectopic site, they have only a modest impact on heterochromatin propagation via the read-write mechanism at an endogenous site. Instead, our findings suggest a crucial role for the replication factor Mcl1 in retaining parental histones and promoting heterochromatin propagation via a mechanism involving the histone chaperone FACT. Engagement of FACT with heterochromatin requires boundary elements, which position the heterochromatic domain at the nuclear peripheral subdomain enriched for heterochromatin factors. Our findings highlight the importance of replisome components and boundary elements in creating a specialized environment for the retention of parental methylated histones, which facilitates epigenetic inheritance of heterochromatin.

Keywords:  epigenetic; gene silencing; heterochromatin; histone methylation

DOI:  https://doi.org/10.1073/pnas.2315596121
J Cancer Res Clin Oncol. 2024 Jan 29. 150(2): 48

Osteosarcoma neutrophil extracellular trap network-associated gene recurrence and metastasis model.

Hao Tang, Jiang Xie, Yu-Xuan Du, Ze-Jiu Tan, Zhuo-Tao Liang.

  Osteosarcoma (OS) is the most common malignancy in children and adolescents and has a high probability of recurrence and metastasis. A growing number of studies have shown that neutrophil extracellular traps (NETs) are strongly associated with cancer metastasis, but in osteosarcoma, genes associated with NETs that promote osteosarcoma recurrence and metastasis remain to be explored. We systematically investigated the gene expression patterns of NETs in OS samples from the GEO database. NETs molecular typing was evaluated based on NETs expression profiles, and the association between NETs molecular subtypes and immune microenvironment and metastatic features were explored. Ultimately, we constructed a signature model and column line graph associated with metastasis prediction and screened possible potential drugs for metastatic osteosarcoma. We established two different molecular subtypes of NETs, which showed significant differences in metastatic status, metastasis time, tumor immune microenvironment, and biological effects. We also constructed a NETs-related gene metastasis signature(NRGMS) to assess the expression pattern of NETs in patients to predict metastatic recurrence in osteosarcoma patients. We screened for TOMM40 and FH associated with metastatic recurrence in osteosarcoma patients. Overall, this study constructs a predictive model for osteosarcoma metastasis of NETs-related genes, which is expected to provide new insights into the metastasis of osteosarcoma.

Keywords:  FH; Immunity; Metastasis model; NETs; Osteosarcoma; TOMM40

DOI:  https://doi.org/10.1007/s00432-023-05577-2