bims-ectoca Biomed News
on Epigenetic control of tolerance in cancer
Issue of 2021–08–01
thirteen papers selected by
Ankita Daiya, Birla Institute of Technology and Science
  1. Live-Cell Imaging Probes to Track Chromatin Modification Dynamics.
  2. Recent advance in single-cell epigenomics.
  3. Spatial epi-proteomics enabled by histone post-translational modification analysis from low-abundance clinical samples.
  4. Single-cell transcriptomics reveals heterogeneous progression and EGFR activation in pancreatic adenosquamous carcinoma.
  5. LncGSEA: a versatile tool to infer lncRNA associated pathways from large-scale cancer transcriptome sequencing data.
  6. Pan-cancer analysis of non-coding recurrent mutations and their possible involvement in cancer pathogenesis.
  7. Histone H3K4me1 and H3K27ac play roles in nucleosome eviction and eRNA transcription, respectively, at enhancers.
  8. Non-CpG methylation-a key epigenetic modification in cancer.
  9. p53 induces a survival transcriptional response after nucleolar stress.
  10. Research Progress of MicroRNA in Chemotherapy Resistance of Osteosarcoma.
  11. The small Cajal body-specific RNA 15 (SCARNA15) directs p53 and redox homeostasis via selective splicing in cancer cells.
  12. Cisplatin-induced hydroxyl radicals mediate pro-survival autophagy in human lung cancer H460 cells.
  13. Long Noncoding RNA DICER1-AS1 Functions in Methylation Regulation on the Multi-Drugresistance of Osteosarcoma Cells via miR-34a-5p and GADD45A.
  1. Microscopy (Oxf). 2021 Jul 30. pii: dfab030. [Epub ahead of print]
    Live-Cell Imaging Probes to Track Chromatin Modification Dynamics.
    Yuko Sato, Masaru Nakao, Hiroshi Kimura.
      The spatiotemporal organization of chromatin is regulated at different levels in the nucleus. Epigenetic modifications such as DNA methylation and histone modifications are involved in chromatin regulation and play fundamental roles in genome function. While the one-dimensional epigenomic landscape in many cell types has been revealed by chromatin immunoprecipitation and sequencing, the dynamic changes of chromatin modifications and their relevance to chromatin organization and genome function remain elusive. Live-cell probes to visualize chromatin and its modifications have become powerful tools to monitor dynamic chromatin regulation. Bulk chromatin can be visualized both by small fluorescent dyes and fluorescent proteins, and specific endogenous genomic loci have been detected by adapting genome-editing tools. To track chromatin modifications in living cells, various types of probes have been developed. Protein domains that bind to specific modifications weakly, such as chromodomains for histone methylation, can be repeated to create a tighter binding probe that can then be tagged with a fluorescent protein. It has also been demonstrated that antigen-binding fragments and single-chain variable fragments from modification-specific antibodies can serve as binding probes without disturbing cell division, development and, differentiation. These modification-binding modules are used in modification sensors based on fluorescence/Förster resonance energy transfer to measure the intramolecular conformation changes triggered by modifications. Other probes can be created using a bivalent binding system, such as fluorescence complementation, or luciferase chemiluminescence. Live-cell chromatin modification imaging using these probes will address dynamic chromatin regulation and will be useful for assaying and screening effective epigenome drugs in cells and organisms.
    Keywords:  DNA methylation; Live-cell imaging; epigenetics; fluorescence microscopy; histone modification; intrabodies
    DOI:  https://doi.org/10.1093/jmicro/dfab030
  2. Curr Opin Struct Biol. 2021 Jul 21. pii: S0959-440X(21)00094-4. [Epub ahead of print]71 116-122
    Recent advance in single-cell epigenomics.
    Akihito Harada, Hiroshi Kimura, Yasuyuki Ohkawa.
      The analysis of gene expression regulation, or the epigenome analysis, at the single-cell level is at the forefront of genomics research. To elucidate the mechanisms that regulate gene expression, chromatin immunoprecipitation has been conventionally used for determining the binding sites of DNA-binding proteins, such as histones and transcription factors. Now several new approaches have been emerged to reveal epigenome states at the single-cell level. Instead of using immunoprecipitation of fragmented chromatin, in situ reactions using cells or nuclei, combining with transposase tagging and other methods, have enabled single-cell analysis. Furthermore, single-cell multiomics techniques to simultaneously profiling transcriptome and open chromatin or histone modification have been developed. These single-cell analyses have the potential to identify different cell types in a cell population and reveal the dynamic changes of gene regulation, although those technologies have not yet reached a level for general application.
    DOI:  https://doi.org/10.1016/j.sbi.2021.06.010
  3. Clin Epigenetics. 2021 Jul 28. 13(1): 145
    Spatial epi-proteomics enabled by histone post-translational modification analysis from low-abundance clinical samples.
    Roberta Noberini, Evelyn Oliva Savoia, Stefania Brandini, Francesco Greco, Francesca Marra, Giovanni Bertalot, Giancarlo Pruneri, Liam A McDonnell, Tiziana Bonaldi.
       BACKGROUND: Increasing evidence linking epigenetic mechanisms and different diseases, including cancer, has prompted in the last 15 years the investigation of histone post-translational modifications (PTMs) in clinical samples. Methods allowing the isolation of histones from patient samples followed by the accurate and comprehensive quantification of their PTMs by mass spectrometry (MS) have been developed. However, the applicability of these methods is limited by the requirement for substantial amounts of material.
    RESULTS: To address this issue, in this study we streamlined the protein extraction procedure from low-amount clinical samples and tested and implemented different in-gel digestion strategies, obtaining a protocol that allows the MS-based analysis of the most common histone PTMs from laser microdissected tissue areas containing as low as 1000 cells, an amount approximately 500 times lower than what is required by available methods. We then applied this protocol to breast cancer patient laser microdissected tissues in two proof-of-concept experiments, identifying differences in histone marks in heterogeneous regions selected by either morphological evaluation or MALDI MS imaging.
    CONCLUSIONS: These results demonstrate that analyzing histone PTMs from very small tissue areas and detecting differences from adjacent tumor regions is technically feasible. Our method opens the way for spatial epi-proteomics, namely the investigation of epigenetic features in the context of tissue and tumor heterogeneity, which will be instrumental for the identification of novel epigenetic biomarkers and aberrant epigenetic mechanisms.
    Keywords:  Epigenetics; Histone post-translational modifications; Laser microdissection; MALDI-MSI ; Mass spectrometry; Proteomics
    DOI:  https://doi.org/10.1186/s13148-021-01120-7
  4. Int J Biol Sci. 2021 ;17(10): 2590-2605
    Single-cell transcriptomics reveals heterogeneous progression and EGFR activation in pancreatic adenosquamous carcinoma.
    Xin Zhao, Han Li, Shaocheng Lyu, Jialei Zhai, Zhiwei Ji, Zhigang Zhang, Xinxue Zhang, Zhe Liu, Huaguang Wang, Junming Xu, Hua Fan, Jiantao Kou, Lixin Li, Ren Lang, Qiang He.
      Pancreatic adenosquamous carcinoma (PASC) - a rare pathological pancreatic cancer (PC) type - has a poor prognosis due to high malignancy. To examine the heterogeneity of PASC, we performed single-cell RNA sequencing (scRNA-seq) profiling with sample tissues from a healthy donor pancreas, an intraductal papillary mucinous neoplasm, and a patient with PASC. Of 9,887 individual cells, ten cell subpopulations were identified, including myeloid, immune, ductal, fibroblast, acinar, stellate, endothelial, and cancer cells. Cancer cells were divided into five clusters. Notably, cluster 1 exhibited stem-like phenotypes expressing UBE2C, ASPM, and TOP2A. We found that S100A2 is a potential biomarker for cancer cells. LGALS1, NPM1, RACK1, and PERP were upregulated from ductal to cancer cells. Furthermore, the copy number variations in ductal and cancer cells were greater than in the reference cells. The expression of EREG, FCGR2A, CCL4L2, and CTSC increased in myeloid cells from the normal pancreas to PASC. The gene sets expressed by cancer-associated fibroblasts were enriched in the immunosuppressive pathways. We demonstrate that EGFR-associated ligand-receptor pairs are activated in ductal-stromal cell communications. Hence, this study revealed the heterogeneous variations of ductal and stromal cells, defined cancer-associated signaling pathways, and deciphered intercellular interactions following PASC progression.
    Keywords:  cell-cell communication; heterogeneity; intraductal papillary mucinous neoplasm; pancreatic adenosquamous carcinoma; pancreatic cancer; single-cell RNA sequencing
    DOI:  https://doi.org/10.7150/ijbs.58886
  5. BMC Genomics. 2021 Jul 27. 22(1): 574
    LncGSEA: a versatile tool to infer lncRNA associated pathways from large-scale cancer transcriptome sequencing data.
    Yanan Ren, Ting-You Wang, Leah C Anderton, Qi Cao, Rendong Yang.
       BACKGROUND: Long non-coding RNAs (lncRNAs) are a growing focus in cancer research. Deciphering pathways influenced by lncRNAs is important to understand their role in cancer. Although knock-down or overexpression of lncRNAs followed by gene expression profiling in cancer cell lines are established approaches to address this problem, these experimental data are not available for a majority of the annotated lncRNAs.
    RESULTS: As a surrogate, we present lncGSEA, a convenient tool to predict the lncRNA associated pathways through Gene Set Enrichment Analysis of gene expression profiles from large-scale cancer patient samples. We demonstrate that lncGSEA is able to recapitulate lncRNA associated pathways supported by literature and experimental validations in multiple cancer types.
    CONCLUSIONS: LncGSEA allows researchers to infer lncRNA regulatory pathways directly from clinical samples in oncology. LncGSEA is written in R, and is freely accessible at https://github.com/ylab-hi/lncGSEA .
    Keywords:  Cancer transcriptome; GSEA; Long non-coding RNA; Pathway analysis; RNA-seq; TCGA
    DOI:  https://doi.org/10.1186/s12864-021-07900-y
  6. NAR Cancer. 2021 Mar;3(1): zcab008
    Pan-cancer analysis of non-coding recurrent mutations and their possible involvement in cancer pathogenesis.
    Chie Kikutake, Minako Yoshihara, Mikita Suyama.
      Cancer-related mutations have been mainly identified in protein-coding regions. Recent studies have demonstrated that mutations in non-coding regions of the genome could also be a risk factor for cancer. However, the non-coding regions comprise 98% of the total length of the human genome and contain a huge number of mutations, making it difficult to interpret their impacts on pathogenesis of cancer. To comprehensively identify cancer-related non-coding mutations, we focused on recurrent mutations in non-coding regions using somatic mutation data from COSMIC and whole-genome sequencing data from The Cancer Genome Atlas (TCGA). We identified 21 574 recurrent mutations in non-coding regions that were shared by at least two different samples from both COSMIC and TCGA databases. Among them, 580 candidate cancer-related non-coding recurrent mutations were identified based on epigenomic and chromatin structure datasets. One of such mutation was located in RREB1 binding site that is thought to interact with TEAD1 promoter. Our results suggest that mutations may disrupt the binding of RREB1 to the candidate enhancer region and increase TEAD1 expression levels. Our findings demonstrate that non-coding recurrent mutations and coding mutations may contribute to the pathogenesis of cancer.
    DOI:  https://doi.org/10.1093/narcan/zcab008
  7. FASEB J. 2021 08;35(8): e21781
    Histone H3K4me1 and H3K27ac play roles in nucleosome eviction and eRNA transcription, respectively, at enhancers.
    Yujin Kang, Yea Woon Kim, Jin Kang, AeRi Kim.
      Histone H3K4me1 and H3K27ac are enhancer-specific modifications and are required for enhancers to activate transcription of target genes. However, the reciprocal effects of these histone modifications on each other and their roles in enhancers are not clear. Here to comparatively analyze the role of these modifications, we inhibited H3K4me1 and H3K27ac by deleting the SET domains of histone methyltransferases MLL3 and MLL4 and the HAT domain of histone acetyltransferase p300, respectively, in erythroid K562 cells. The loss of H3K4me1 reduced H3K27ac at the β-globin enhancer LCR HSs, but H3K27ac reduction did not affect H3K4me1. This unequal relationship between two modifications was revealed in putative enhancers by genome-wide analysis using ChIP-seq. Histone H3 eviction at putative enhancers was weakened by the loss of H3K4me1 but not by the loss of H3K27ac. Chromatin remodeling complexes were recruited into the β-globin LCR HSs in a H3K4me1-dependent manner. In contrast, H3K27ac was required for enhancer RNA (eRNA) transcription, and H3K4me1 was not enough for it. Forced H3K27ac-induced eRNA transcription without affecting H3K4me1 at the β-globin LCR HSs. These results indicate that H3K4me1 and H3K27ac affect each other in different ways and play more direct roles in nucleosome eviction and eRNA transcription, respectively, at enhancers.
    Keywords:  H3K27ac; H3K4me1; eRNA transcription; enhancers; nucleosome eviction
    DOI:  https://doi.org/10.1096/fj.202100488R
  8. Brief Funct Genomics. 2021 Jul 27. pii: elab035. [Epub ahead of print]
    Non-CpG methylation-a key epigenetic modification in cancer.
    Deepa Ramasamy, Arunagiri Kuha Deva Magendhra Rao, Thangarajan Rajkumar, Samson Mani.
      The methylation of cytosine residues that precede adenine/thymine or other cytosine nucleotides instead of guanine in DNA is known as non-CpG methylation. It is a pronounced epigenetic modification with a central role in gene regulation similar to CpG methylation. Due to technological limitations, the locus-specific role of non-CpG methylation was scarcely understood. At present, high-throughput analyses and improved enrichment methods can elucidate the role of genome-wide non-CpG methylation distributions. Although the functional basis of non-CpG methylation in regulating gene expression control is known, its role in cancer development is yet to be ascertained. This review sheds light on the possible mechanism of non-CpG methylation in embryos and developed tissues with a special focus on cancer development and progression. In particular, the maintenance and alteration of non-CpG methylation levels and the crucial factors that determine this level of non-CpG methylation and its functional role in cancer are discussed.
    Keywords:  DNA methylation; DNA methyltransferases; cancer; mitochondrial DNA; non-CpG methylation
    DOI:  https://doi.org/10.1093/bfgp/elab035
  9. Mol Biol Cell. 2021 Jul 28. mbcE21050251
    p53 induces a survival transcriptional response after nucleolar stress.
    Han Liao, Anushri Gaur, Claire Mauvais, Catherine Denicourt.
      Accumulating evidence indicate that increased ribosome biogenesis is a hallmark of cancer. It is well established that inhibition of any steps of ribosome biogenesis induces a nucleolar stress characterized by p53 activation and subsequent cell cycle arrest and/or cell death. However, cells derived from solid tumors have demonstrated different degree of sensitivity to ribosome biogenesis inhibition, where cytostatic effects rather than apoptosis are observed. The reason for this is not clear and the p53-specific transcriptional program induced after nucleolar stress has not been previously investigated. Here we demonstrate that blocking rRNA synthesis by depletion of essential rRNA processing factors such as LAS1L, PELP1, and NOP2 or by inhibition of RNA Pol I with the specific small molecule inhibitor CX-5461, mainly induce cell cycle arrest accompanied with autophagy in solid tumor-derived cell lines. Using gene expression analysis, we find that p53 orchestrates a transcriptional program involved in promoting metabolic remodeling and autophagy to help cells survive under nucleolar stress. Importantly, our study demonstrates that blocking autophagy significantly sensitizes cancer cells to RNA Pol I inhibition by CX-5461, suggesting that interfering with autophagy should be considered a strategy to heighten the responsiveness of ribosome biogenesis-targeted therapies in p53-positive tumors.
    DOI:  https://doi.org/10.1091/mbc.E21-05-0251
  10. Technol Cancer Res Treat. 2021 Jan-Dec;20:20 15330338211034262
    Research Progress of MicroRNA in Chemotherapy Resistance of Osteosarcoma.
    Zhaopeng Tang, Yubao Lu, Yutong Chen, Jiarui Zhang, Zhijun Chen, Qianfeng Wang.
      Osteosarcoma (OS) is a malignant tumor prevalent in adolescents; however, a clinically effective treatment for this malignancy is lacking. The lack of effective treatment methods and factors, such as recurrence and drug resistance, further dampen the prospect of clinically treating OS. In recent years, small molecule microRNAs (miRNAs) with a length of approximately 20-24 nucleotides have gradually attracted the attention of the medical community. Studies have found that miRNAs can regulate the cell cycle, apoptosis, cell proliferation, and cell proliferation. The metabolic response of cancer cells, invasion and metastasis of cancer cells, and angiogenesis play an important role in the process of tumorigenesis. miRNAs regulate gene expression by regulating mRNA expression after transcription. A large amount of data from many studies indicate that they have diagnostic and prognostic biomarker effects in OS and are involved in regulating the metabolism of cancer cells and resistance or sensitivity to chemotherapy drugs. Chemotherapy resistance is one of the most critical problems in clinically treating OS. A large number of basic studies and systematic summaries are required to provide a theoretical basis for elucidating the mechanism and drug development of chemotherapeutic agents. Therefore, this article discusses the role of miRNAs in OS resistance. Herein, the related research progress of the studies is reviewed to provide more useful information for the development of effective therapy.
    Keywords:  chemotherapeutic drugs; drug resistance; malignant; microRNA; osteosarcoma; prognostic marker
    DOI:  https://doi.org/10.1177/15330338211034262
  11. NAR Cancer. 2021 Sep;3(3): zcab026
    The small Cajal body-specific RNA 15 (SCARNA15) directs p53 and redox homeostasis via selective splicing in cancer cells.
    Giulia Beneventi, Roberto Munita, Phuong Cao Thi Ngoc, Magdalena Madej, Maciej Cieśla, Sowndarya Muthukumar, Nicolai Krogh, Henrik Nielsen, Vinay Swaminathan, Cristian Bellodi.
      Small Cajal body-specific RNAs (scaRNAs) guide post-transcriptional modification of spliceosomal RNA and, while commonly altered in cancer, have poorly defined roles in tumorigenesis. Here, we uncover that SCARNA15 directs alternative splicing (AS) and stress adaptation in cancer cells. Specifically, we find that SCARNA15 guides critical pseudouridylation (Ψ) of U2 spliceosomal RNA to fine-tune AS of distinct transcripts enriched for chromatin and transcriptional regulators in malignant cells. This critically impacts the expression and function of the key tumor suppressors ATRX and p53. Significantly, SCARNA15 loss impairs p53-mediated redox homeostasis and hampers cancer cell survival, motility and anchorage-independent growth. In sum, these findings highlight an unanticipated role for SCARNA15 and Ψ in directing cancer-associated splicing programs.
    DOI:  https://doi.org/10.1093/narcan/zcab026
  12. Biol Res. 2021 Jul 28. 54(1): 22
    Cisplatin-induced hydroxyl radicals mediate pro-survival autophagy in human lung cancer H460 cells.
    Somruethai Sumkhemthong, Eakachai Prompetchara, Pithi Chanvorachote, Chatchai Chaotham.
       BACKGROUND: Accumulated evidence demonstrates cisplatin, a recommended chemotherapy, modulating pro-survival autophagic response that contributes to treatment failure in lung cancer patients. However, distinct mechanisms involved in cisplatin-induced autophagy in human lung cancer cells are still unclear.
    RESULTS: Herein, role of autophagy in cisplatin resistance was indicated by a decreased cell viability and increased apoptosis in lung cancer H460 cells pre-incubated with wortmannin, an autophagy inhibitor, prior to treatment with 50 µM cisplatin for 24 h. The elevated level of hydroxyl radicals detected via flow-cytometry corresponded to autophagic response, as evidenced by the formation of autophagosomes and autolysosomes in cisplatin-treated cells. Interestingly, apoptosis resistance, autophagosome formation, and the alteration of the autophagic markers, LC3-II/LC3-I and p62, as well as autophagy-regulating proteins Atg7 and Atg3, induced by cisplatin was abrogated by pretreatment of H460 cells with deferoxamine, a specific hydroxyl radical scavenger. The modulations in autophagic response were also indicated in the cells treated with hydroxyl radicals generated via Fenton reaction, and likewise inhibited by pretreatment with deferoxamine.
    CONCLUSIONS: In summary, the possible role of hydroxyl radicals as a key mediator in the autophagic response to cisplatin treatment, which was firstly revealed in this study would benefit for the further development of novel therapies for lung cancer.
    Keywords:  Autophagy; Cisplatin; Drug resistance; Hydroxyl radicals; Lung cancer
    DOI:  https://doi.org/10.1186/s40659-021-00346-2
  13. Front Oncol. 2021 ;11 685881
    Long Noncoding RNA DICER1-AS1 Functions in Methylation Regulation on the Multi-Drugresistance of Osteosarcoma Cells via miR-34a-5p and GADD45A.
    Feng Wang, Lingsuo Kong, Youguang Pu, Fengmei Chao, Chunbao Zang, Wei Qin, Fangfang Zhao, Shanbao Cai.
      Osteosarcoma (OS) is a common malignant bone tumor that commonly occurs in children and adolescents. Long noncoding RNAs (lncRNAs) are recognized as a novel class of regulators of gene expression associated with tumorigenesis. However, the effect and mechanism of lncRNAs in OS tumorigenesis and drug resistance have not been characterized. The purpose of the study is to screen potential biomarker and therapeutic target against OS. We compared the lncRNA expression profiles between OS cell lines with different drug resistance levels using RNA-seq analysis and found that lncRNA DICER1-AS1 was significantly differentially expressed in multi-drugresistant OS cells SJSA-1 versus multi-drugsensitive OS cells G-292. Bisulfite Sequencing PCR (BSP) assay was performed to analyze the differential methylation status of the promoter region of DICER1-AS1 in four OS cells. Subsequently, in vitro gain- and loss-of-function experiments demonstrated the roles of DICER1-AS1 and miR-34a-5p in the multi-drugresistance of OS cells. The main findings is that DICER1-AS1 directly binds to miR-34a-5p, and their expression has a negative correlation with each other. The hypermethylation of the promoter region of DICER1-AS1 silenced its expression in the drugresistant cells SJSA-1 and MNNG/HOS. Moreover, we found that growth arrest and DNA damage-inducible alpha (GADD45A) participates in the DICER1-AS1/miR-34a-5p-regulated drug resistance of OS cells, probably via the cell cycle/pRb-E2F pathway. Our results revealed DICER1-AS1/miR-34a-5p-regulated drug resistance of OS cells, a new lncRNA-regulated network in OS tumorigenesis, suggested that DICER1-AS1 can be considered as a potential biomarker and therapeutic target against OS cells.
    Keywords:  DICER1-AS1; GADD45A; drug resistance; miR-34a-5p; osteosarcoma
    DOI:  https://doi.org/10.3389/fonc.2021.685881
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