bims-ectoca 2022-03-27 papers

bims-ectoca

Biomed News

on Epigenetic control of tolerance in cancer

Issue of 2022–03–27
eightteen papers selected by
Ankita Daiya, Birla Institute of Technology and Science

Stem Cell Theory of Cancer: Implications for Drug Resistance and Chemosensitivity in Cancer Care.
p62 Promotes the Mitochondrial Localization of p53 through Its UBA Domain and Participates in Regulating the Sensitivity of Ovarian Cancer Cells to Cisplatin.
Calmodulin activates the Hippo signaling pathway by promoting LATS1 kinase-mediated inhibitory phosphorylation of the transcriptional coactivator YAP.
R code and downstream analysis objects for the scRNA-seq atlas of normal and tumorigenic human breast tissue.
Single-Cell RNA Sequencing with Spatial Transcriptomics of Cancer Tissues.
Chemotherapy Resistance: Role of Mitochondrial and Autophagic Components.
Single-Cell Image-Based Analysis Reveals Chromatin Changes during the Acquisition of Tamoxifen Drug Resistance.
Identification of histone deacetylase 10 (HDAC10) inhibitors that modulate autophagy in transformed cells.
Is Autophagy Always a Barrier to Cisplatin Therapy?
Acetylation, Phosphorylation, Ubiquitination (Oh My!): Following Post-Translational Modifications on the Ubiquitin Road.
The Emerging Significance of Histone Lysine Demethylases as Prognostic Markers and Therapeutic Targets in Head and Neck Cancers.
Systematic identification of biomarker-driven drug combinations to overcome resistance.
Is There a Role for Epigenetic Therapies in Modulating DNA Damage Repair Pathways to Enhance Chemotherapy and Overcome Drug Resistance?
Protein synthesis control in cancer: selectivity and therapeutic targeting.
Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro.
An epigenetic small molecule screen to target abnormal nuclear morphology in human cells.
The Role of Epigenetic Modifications in Human Cancers and the Use of Natural Compounds as Epidrugs: Mechanistic Pathways and Pharmacodynamic Actions.
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data.

Cancers (Basel). 2022 Mar 18. pii: 1548. [Epub ahead of print]14(6):

Stem Cell Theory of Cancer: Implications for Drug Resistance and Chemosensitivity in Cancer Care.

Shi-Ming Tu, Charles C Guo, Diana S-L Chow, Niki M Zacharias.

  When it concerns cancer care and cancer therapy, drug resistance is more than an obstacle to successful treatment; it is a major cause of frustration in our attempts to optimize drug development versus therapy development. Importantly, overcoming the challenges of drug resistance may provide invaluable clues about the origin and nature of cancer. From this perspective, we discuss how chemoresistance and chemosensitivity in cancer therapy could be directly linked to the stem cell origin of cancer. A stem cell theory of cancer stipulates that both normal stem cells and cancer stem cells are similarly endowed with robust efflux pumps, potent antiapoptotic mechanisms, redundant DNA repair systems, and abundant antioxidation reserves. Cancer stem cells, like their normal stem cell counterparts, are equipped with the same drug resistance phenotypes (e.g., ABC transporters, anti-apoptotic pathways, and DNA repair mechanisms). Drug resistance, like other cancer hallmarks (e.g., tumor heterogeneity and cancer dormancy), could be intrinsically ingrained and innately embedded within malignancy. We elaborate that cellular context and the microenvironment may attenuate the effects of cancer treatments. We examine the role of circadian rhythms and the value of chronotherapy to maximize efficacy and minimize toxicity. We propose that a stem cell theory of drug resistance and drug sensitivity will ultimately empower us to enhance drug development and enable us to improve therapy development in patient care.

Keywords:  cancer stem cells; chemosensitivity; chronotherapy; circadian rhythm; clonal origin; drug development; drug resistance; therapy development; unified theory

DOI:  https://doi.org/10.3390/cancers14061548
Int J Mol Sci. 2022 Mar 18. pii: 3290. [Epub ahead of print]23(6):

p62 Promotes the Mitochondrial Localization of p53 through Its UBA Domain and Participates in Regulating the Sensitivity of Ovarian Cancer Cells to Cisplatin.

Qinghuan Kong, Xiaoyu Yan, Meiyu Cheng, Xin Jiang, Long Xu, Luyan Shen, Huimei Yu, Liankun Sun.

  Chemotherapeutic drug-induced p53-dependent crosstalk among tumor cells affects the sensitivity of tumor cells to chemotherapeutic drugs, contributing to chemoresistance. Therefore, pharmacological targeting of p53 may contribute to overcoming drug resistance. The localization of p53 is closely related to its function. Thus, we assessed the effect of p62 on the coordination of p53 mitochondrial localization under chemotherapeutic drug treatment in ovarian cancer cells. We found that the combined use of the proteasome inhibitor epoxomicin and cisplatin led to the accumulation of p53 and sequestosome1(p62) in the mitochondria, downregulated mitochondrial DNA (mtDNA) transcription, inhibited mitochondrial functions, and ultimately promoted apoptosis by enhancing cisplatin sensitivity in ovarian cancer cells. Moreover, the ubiquitin-associated (UBA) domain of p62 was involved in regulating the mitochondrial localization of p53. Our findings suggest that the interaction between p62 and p53 may be a mechanism that determines the fate of tumor cells. In conclusion, p62 coordinated the mitochondrial localization of p53 through its UBA domain, inhibited mtDNA transcription, downregulated mitochondrial function, and promoted ovarian cancer cell death. Our study demonstrates the important role of p53 localization in tumor cell survival and apoptosis, and provides new insights into understanding the anti-tumor mechanism of targeting the ubiquitin-proteasome system in tumor cells.

Keywords:  drug resistance; mitochondria; ovarian cancer; p53; p62/SQSTM1

DOI:  https://doi.org/10.3390/ijms23063290
J Biol Chem. 2022 Mar 17. pii: S0021-9258(22)00279-4. [Epub ahead of print] 101839

Calmodulin activates the Hippo signaling pathway by promoting LATS1 kinase-mediated inhibitory phosphorylation of the transcriptional coactivator YAP.

Louise Thines, Laëtitia Gorisse, Zhigang Li, Samar Sayedyahossein, David B Sacks.

  The Hippo signaling pathway regulates tissue growth and cell fate, and its dysregulation can induce tumorigenesis. When Hippo is activated by cell-cell contact, extracellular signals, or cell polarity among others, the large tumor suppressor 1 (LATS1) kinase catalyzes inhibitory phosphorylation of the transcriptional coactivator Yes-associated protein (YAP) to maintain YAP in the cytoplasm or promote its degradation. Separately, calmodulin is a Ca2+-dependent protein that modulates the activity of target proteins and regulates several signaling cascades; however, its potential role in the Hippo pathway has not been identified. Here, using diverse experimental approaches including in vitro binding analyses, kinases assays, RT-PCR, and confocal microscopy, we reveal that calmodulin promotes Hippo signaling. We show that purified YAP and LATS1 bind directly to calmodulin and form a Ca2+-dependent ternary complex in vitro. Importantly, Ca2+/calmodulin directly stimulated the activity of LATS1 kinase. In cultured mammalian cells, we also demonstrated that endogenous YAP and LATS1 co-immunoprecipitate with endogenous calmodulin. In cells with activated Hippo signaling, we show that calmodulin antagonism significantly (i) decreases YAP phosphorylation, (ii) increases expression of two Hippo target genes (CTGF and CYR61) that regulate cell proliferation and tumor progression, and (iii) enhances the interaction of YAP with the transcription factor TEAD, which facilitates transcription of target genes. Collectively, our data demonstrate that calmodulin activates the Hippo kinase cascade and inhibits YAP activity via a direct interaction with LATS1 and YAP, thereby uncovering previously unidentified cross-talk between the Ca2+/calmodulin and Hippo signaling pathways.

Keywords:  Calmodulin; Hippo pathway; Large Tumor Suppressor 1 (LATS1); Protein-protein interaction; Signaling; Yes-Associated Protein (YAP)

DOI:  https://doi.org/10.1016/j.jbc.2022.101839
Sci Data. 2022 Mar 23. 9(1): 96

R code and downstream analysis objects for the scRNA-seq atlas of normal and tumorigenic human breast tissue.

Yunshun Chen, Bhupinder Pal, Geoffrey J Lindeman, Jane E Visvader, Gordon K Smyth.

Breast cancer is a common and highly heterogeneous disease. Understanding cellular diversity in the mammary gland and its surrounding micro-environment across different states can provide insight into cancer development in the human breast. Recently, we published a large-scale single-cell RNA expression atlas of the human breast spanning normal, preneoplastic and tumorigenic states. Single-cell expression profiles of nearly 430,000 cells were obtained from 69 distinct surgical tissue specimens from 55 patients. This article extends the study by providing quality filtering thresholds, downstream processed R data objects, complete cell annotation and R code to reproduce all the analyses. Data quality assessment measures are presented and details are provided for all the bioinformatic analyses that produced results described in the study.

DOI: https://doi.org/10.1038/s41597-022-01236-2
Int J Mol Sci. 2022 Mar 11. pii: 3042. [Epub ahead of print]23(6):

Single-Cell RNA Sequencing with Spatial Transcriptomics of Cancer Tissues.

Rashid Ahmed, Tariq Zaman, Farhan Chowdhury, Fatima Mraiche, Muhammad Tariq, Irfan S Ahmad, Anwarul Hasan.

  Single-cell RNA sequencing (RNA-seq) techniques can perform analysis of transcriptome at the single-cell level and possess an unprecedented potential for exploring signatures involved in tumor development and progression. These techniques can perform sequence analysis of transcripts with a better resolution that could increase understanding of the cellular diversity found in the tumor microenvironment and how the cells interact with each other in complex heterogeneous cancerous tissues. Identifying the changes occurring in the genome and transcriptome in the spatial context is considered to increase knowledge of molecular factors fueling cancers. It may help develop better monitoring strategies and innovative approaches for cancer treatment. Recently, there has been a growing trend in the integration of RNA-seq techniques with contemporary omics technologies to study the tumor microenvironment. There has been a realization that this area of research has a huge scope of application in translational research. This review article presents an overview of various types of single-cell RNA-seq techniques used currently for analysis of cancer tissues, their pros and cons in bulk profiling of transcriptome, and recent advances in the techniques in exploring heterogeneity of various types of cancer tissues. Furthermore, we have highlighted the integration of single-cell RNA-seq techniques with other omics technologies for analysis of transcriptome in their spatial context, which is considered to revolutionize the understanding of tumor microenvironment.

Keywords:  intratumor heterogeneity; single-cell RNA sequencing techniques; spatial transcriptomics

DOI:  https://doi.org/10.3390/ijms23063042
Cancers (Basel). 2022 Mar 12. pii: 1462. [Epub ahead of print]14(6):

Chemotherapy Resistance: Role of Mitochondrial and Autophagic Components.

Entaz Bahar, Sun-Young Han, Ji-Ye Kim, Hyonok Yoon.

  Cancer chemotherapy resistance is one of the most critical obstacles in cancer therapy. One of the well-known mechanisms of chemotherapy resistance is the change in the mitochondrial death pathways which occur when cells are under stressful situations, such as chemotherapy. Mitophagy, or mitochondrial selective autophagy, is critical for cell quality control because it can efficiently break down, remove, and recycle defective or damaged mitochondria. As cancer cells use mitophagy to rapidly sweep away damaged mitochondria in order to mediate their own drug resistance, it influences the efficacy of tumor chemotherapy as well as the degree of drug resistance. Yet despite the importance of mitochondria and mitophagy in chemotherapy resistance, little is known about the precise mechanisms involved. As a consequence, identifying potential therapeutic targets by analyzing the signal pathways that govern mitophagy has become a vital research goal. In this paper, we review recent advances in mitochondrial research, mitophagy control mechanisms, and their implications for our understanding of chemotherapy resistance.

Keywords:  chemotherapy resistance; mitochondria; mitophagy

DOI:  https://doi.org/10.3390/cancers14061462
Life (Basel). 2022 Mar 17. pii: 438. [Epub ahead of print]12(3):

Single-Cell Image-Based Analysis Reveals Chromatin Changes during the Acquisition of Tamoxifen Drug Resistance.

Han Zhao, Li F Lin, Joshua Hahn, Junkai Xie, Harvey F Holman, Chongli Yuan.

  Cancer drug resistance is the leading cause of cancer related deaths. The development of drug resistance can be partially contributed to tumor heterogeneity and epigenetic plasticity. However, the detailed molecular mechanism underlying epigenetic modulated drug resistance remains elusive. In this work, we systematically analyzed epigenetic changes in tamoxifen (Tam) responsive and resistant breast cancer cell line MCF7, and adopted a data-driven approach to identify key epigenetic features distinguishing between these two cell types. Significantly, we revealed that DNA methylation and H3K9me3 marks that constitute the heterochromatin are distinctively different between Tam-resistant and -responsive cells. We then performed time-lapse imaging of 5mC and H3K9me3 features using engineered probes. After Tam treatment, we observed a slow transition of MCF7 cells from a drug-responsive to -resistant population based on DNA methylation features. A similar trend was not observed using H3K9me3 probes. Collectively, our results suggest that DNA methylation changes partake in the establishment of Tam-resistant breast cancer cell lines. Instead of global changes in the DNA methylation level, the distribution of DNA methylation features inside the nucleus can be one of the drivers that facilitates the establishment of a drug resistant phenotype in MCF7.

Keywords:  breast cancer; chromatin; drug resistance; epigenetics

DOI:  https://doi.org/10.3390/life12030438
Eur J Med Chem. 2022 Mar 11. pii: S0223-5234(22)00174-X. [Epub ahead of print]234 114272

Identification of histone deacetylase 10 (HDAC10) inhibitors that modulate autophagy in transformed cells.

Patrik Zeyen, Yanira Zeyn, Daniel Herp, Fereshteh Mahmoudi, Talha Z Yesiloglu, Frank Erdmann, Matthias Schmidt, Dina Robaa, Christophe Romier, Johannes Ridinger, Corey J Herbst-Gervasoni, David W Christianson, Ina Oehme, Manfred Jung, Oliver H Krämer, Wolfgang Sippl.

  Histone deacetylases (HDACs) are a family of 18 epigenetic modifiers that fall into 4 classes. Histone deacetylase inhibitors (HDACi) are valid tools to assess HDAC functions. HDAC6 and HDAC10 belong to the class IIb subgroup of the HDAC family. The targets and biological functions of HDAC10 are ill-defined. This lack of knowledge is due to a lack of specific and potent HDAC10 inhibitors with cellular activity. Here, we have synthesized and characterized piperidine-4-acrylhydroxamates as potent and highly selective inhibitors of HDAC10. This was achieved by targeting the acidic gatekeeper residue Glu274 of HDAC10 with a basic piperidine moiety that mimics the interaction of the polyamine substrate of HDAC10. We have confirmed the binding modes of selected inhibitors using X-ray crystallography. Promising candidates were selected based on their specificity by in vitro profiling using recombinant HDACs. The most promising HDAC10 inhibitors 10c and 13b were tested for specificity in acute myeloid leukemia (AML) cells with the FLT3-ITD oncogene. By immunoblot experiments we assessed the hyperacetylation of histones and tubulin-α, which are class I and HDAC6 substrates, respectively. As validated test for HDAC10 inhibition we used flow cytometry assessing autolysosome formation in neuroblastoma and AML cells. We demonstrate that 10c and 13b inhibit HDAC10 with high specificity over HDAC6 and with no significant impact on class I HDACs. The accumulation of autolysosomes is not a consequence of apoptosis and 10c and 13b are not toxic for normal human kidney cells. These data show that 10c and 13b are nanomolar inhibitors of HDAC10 with high specificity. Thus, our new HDAC10 inhibitors are tools to identify the downstream targets and functions of HDAC10 in cells.

Keywords:  Acute myeloid leukemia (AML); Autophagy; Chronic lymphoid leukemia; Drug design; HDAC10; Histone deacetylases (HDAC); Ligand docking; Lysosomes

DOI:  https://doi.org/10.1016/j.ejmech.2022.114272
Biomolecules. 2022 Mar 17. pii: 463. [Epub ahead of print]12(3):

Is Autophagy Always a Barrier to Cisplatin Therapy?

Jingwen Xu, David A Gewirtz.

  Cisplatin has long been a first-line chemotherapeutic agent in the treatment of cancer, largely for solid tumors. During the course of the past two decades, autophagy has been identified in response to cancer treatments and almost uniformly detected in studies involving cisplatin. There has been increasing recognition of autophagy as a critical factor affecting tumor cell death and tumor chemoresistance. In this review and commentary, we introduce four mechanisms of resistance to cisplatin followed by a discussion of the factors that affect the role of autophagy in cisplatin-sensitive and resistant cells and explore the two-sided outcomes that occur when autophagy inhibitors are combined with cisplatin. Our goal is to analyze the potential for the combinatorial use of cisplatin and autophagy inhibitors in the clinic.

Keywords:  autophagy; chloroquine; cisplatin; p53; resistant

DOI:  https://doi.org/10.3390/biom12030463
Biomolecules. 2022 Mar 18. pii: 467. [Epub ahead of print]12(3):

Acetylation, Phosphorylation, Ubiquitination (Oh My!): Following Post-Translational Modifications on the Ubiquitin Road.

Rachel E Lacoursiere, Dania Hadi, Gary S Shaw.

  Ubiquitination is controlled by a series of E1, E2, and E3 enzymes that can ligate ubiquitin to cellular proteins and dictate the turnover of a substrate and the outcome of signalling events such as DNA damage repair and cell cycle. This process is complex due to the combinatorial power of ~35 E2 and ~1000 E3 enzymes involved and the multiple lysine residues on ubiquitin that can be used to assemble polyubiquitin chains. Recently, mass spectrometric methods have identified that most enzymes in the ubiquitination cascade can be further modified through acetylation or phosphorylation under particular cellular conditions and altered modifications have been noted in different cancers and neurodegenerative diseases. This review provides a cohesive summary of ubiquitination, acetylation, and phosphorylation sites in ubiquitin, the human E1 enzyme UBA1, all E2 enzymes, and some representative E3 enzymes. The potential impacts these post-translational modifications might have on each protein function are highlighted, as well as the observations from human disease.

Keywords:  acetylation; cancer; neurodegenerative disease; phosphorylation; protein structure; proteomics; ubiquitination

DOI:  https://doi.org/10.3390/biom12030467
Cells. 2022 Mar 17. pii: 1023. [Epub ahead of print]11(6):

The Emerging Significance of Histone Lysine Demethylases as Prognostic Markers and Therapeutic Targets in Head and Neck Cancers.

Dawid Dorna, Jarosław Paluszczak.

  Epigenetic aberrations, associated with altered DNA methylation profiles and global changes in the level of histone modifications, are commonly detected in head and neck squamous cell carcinomas (HNSCC). Recently, histone lysine demethylases have been implicated in the pathogenesis of HNSCC and emerged as potential molecular targets. Histone lysine demethylases (KDMs) catalyze the removal of methyl groups from lysine residues in histones. By affecting the methylation of H3K4, H3K9, H3K27, or H3K36, these enzymes take part in transcriptional regulation, which may result in changes in the level of expression of tumor suppressor genes and protooncogenes. KDMs are involved in many biological processes, including cell cycle control, senescence, DNA damage response, and heterochromatin formation. They are also important regulators of pluripotency. The overexpression of most KDMs has been observed in HNSCC, and their inhibition affects cell proliferation, apoptosis, cell motility, invasiveness, and stemness. Of all KDMs, KDM1, KDM4, KDM5, and KDM6 proteins are currently regarded as the most promising prognostic and therapeutic targets in head and neck cancers. The aim of this review is to present up-to-date knowledge on the significance of histone lysine demethylases in head and neck carcinogenesis and to discuss the possibility of using them as prognostic markers and pharmacological targets in patients' treatment.

Keywords:  KDM inhibitors; KDM1; KDM4; KDM5; KDM6; epigenetics; head and neck cancer; histone lysine demethylases

DOI:  https://doi.org/10.3390/cells11061023
Nat Chem Biol. 2022 Mar 24.

Systematic identification of biomarker-driven drug combinations to overcome resistance.

Matthew G Rees, Lisa Brenan, Mariana do Carmo, Patrick Duggan, Besnik Bajrami, Michael Arciprete, Andrew Boghossian, Emma Vaimberg, Steven J Ferrara, Timothy A Lewis, Danny Rosenberg, Tenzin Sangpo, Jennifer A Roth, Virendar K Kaushik, Federica Piccioni, John G Doench, David E Root, Cory M Johannessen.

The ability to understand and predict variable responses to therapeutic agents may improve outcomes in patients with cancer. We hypothesized that the basal gene-transcription state of cancer cell lines, coupled with cell viability profiles of small molecules, might be leveraged to nominate specific mechanisms of intrinsic resistance and to predict drug combinations that overcome resistance. We analyzed 564,424 sensitivity profiles to identify candidate gene-compound pairs, and validated nine such relationships. We determined the mechanism of a novel relationship, in which expression of the serine hydrolase enzymes monoacylglycerol lipase (MGLL) or carboxylesterase 1 (CES1) confers resistance to the histone lysine demethylase inhibitor GSK-J4 by direct enzymatic modification. Insensitive cell lines could be sensitized to GSK-J4 by inhibition or gene knockout. These analytical and mechanistic studies highlight the potential of integrating gene-expression features with small-molecule response to identify patient populations that are likely to benefit from treatment, to nominate rational candidates for combinations and to provide insights into mechanisms of action.

DOI: https://doi.org/10.1038/s41589-022-00996-7
Cancers (Basel). 2022 Mar 16. pii: 1533. [Epub ahead of print]14(6):

Is There a Role for Epigenetic Therapies in Modulating DNA Damage Repair Pathways to Enhance Chemotherapy and Overcome Drug Resistance?

Ian Matthew Garner, Robert Brown.

  Epigenetic therapies describe drug molecules such as DNA methyltransferase, histone methyltransferase and histone acetylase/deacetylase inhibitors, which target epigenetic mechanisms such as DNA methylation and histone modifications. Many DNA damage response (DDR) genes are epigenetically regulated in cancer leading to transcriptional silencing and the loss of DNA repair capacity. Epigenetic marks at DDR genes, such as DNA methylation at gene promoters, have the potential to be used as stratification biomarkers, identifying which patients may benefit from particular chemotherapy treatments. For genes such as MGMT and BRCA1, promoter DNA methylation is associated with chemosensitivity to alkylating agents and platinum coordination complexes, respectively, and they have use as biomarkers directing patient treatment options. In contrast to epigenetic change leading to chemosensitivity, DNA methylation of DDR genes involved in engaging cell death responses, such as MLH1, are associated with chemoresistance. This contrasting functional effect of epigenetic modification on chemosensitivity raises challenges in using DNA-demethylating agents, and other epigenetic approaches, to sensitise tumours to DNA-damaging chemotherapies and molecularly targeted agents. Demethylation of MGMT/BRCA1 could lead to drug resistance whereas demethylation of MLH1 could sensitise cells to chemotherapy. Patient selection based on a solid understanding of the disease pathway will be one means to tackle these challenges. The role of epigenetic modification of DDR genes during tumour development, such as causing a mutator phenotype, has different selective pressures and outcomes compared to epigenetic adaptation during treatment. The prevention of epigenetic adaptation during the acquisition of drug resistance will be a potential strategy to improve the treatment of patients using epigenetic therapies.

Keywords:  DNA methylation; DNA repair; cancer; epigenetics

DOI:  https://doi.org/10.3390/cancers14061533
EMBO J. 2022 Mar 22. e109823

Protein synthesis control in cancer: selectivity and therapeutic targeting.

Joanna R Kovalski, Duygu Kuzuoglu-Ozturk, Davide Ruggero.

  Translational control of mRNAs is a point of convergence for many oncogenic signals through which cancer cells tune protein expression in tumorigenesis. Cancer cells rely on translational control to appropriately adapt to limited resources while maintaining cell growth and survival, which creates a selective therapeutic window compared to non-transformed cells. In this review, we first discuss how cancer cells modulate the translational machinery to rapidly and selectively synthesize proteins in response to internal oncogenic demands and external factors in the tumor microenvironment. We highlight the clinical potential of compounds that target different translation factors as anti-cancer therapies. Next, we detail how RNA sequence and structural elements interface with the translational machinery and RNA-binding proteins to coordinate the translation of specific pro-survival and pro-growth programs. Finally, we provide an overview of the current and emerging technologies that can be used to illuminate the mechanisms of selective translational control in cancer cells as well as within the microenvironment.

Keywords:  cancer; protein synthesis; translation and protein quality; translation inhibitors; translational control

DOI:  https://doi.org/10.15252/embj.2021109823
Nat Biotechnol. 2022 Mar 24.

Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro.

Bingjie Zhang, Avi Srivastava, Eleni Mimitou, Tim Stuart, Ivan Raimondi, Yuhan Hao, Peter Smibert, Rahul Satija.

Technologies that profile chromatin modifications at single-cell resolution offer enormous promise for functional genomic characterization, but the sparsity of the measurements and integrating multiple binding maps represent substantial challenges. Here we introduce single-cell (sc)CUT&Tag-pro, a multimodal assay for profiling protein-DNA interactions coupled with the abundance of surface proteins in single cells. In addition, we introduce single-cell ChromHMM, which integrates data from multiple experiments to infer and annotate chromatin states based on combinatorial histone modification patterns. We apply these tools to perform an integrated analysis across nine different molecular modalities in circulating human immune cells. We demonstrate how these two approaches can characterize dynamic changes in the function of individual genomic elements across both discrete cell states and continuous developmental trajectories, nominate associated motifs and regulators that establish chromatin states and identify extensive and cell-type-specific regulatory priming. Finally, we demonstrate how our integrated reference can serve as a scaffold to map and improve the interpretation of additional scCUT&Tag datasets.

DOI: https://doi.org/10.1038/s41587-022-01250-0
Mol Biol Cell. 2022 Mar 24. mbcE21100528

An epigenetic small molecule screen to target abnormal nuclear morphology in human cells.

Kalina R Atanasova, Saptarshi Chakraborty, Ranjala Ratnayake, Kshitij D Khare, Hendrik Luesch, Tanmay P Lele.

Irregular nuclear shapes are a hallmark of human cancers. Recent studies suggest that alterations to chromatin regulators may cause irregular nuclear morphologies. Here we screened an epigenetic small molecule library consisting of 145 compounds against chromatin regulators, for their ability to revert abnormal nuclear shapes that were induced by gene knockdown in non-cancerous MCF10A human mammary breast epithelial cells. We leveraged a previously validated quantitative Fourier approach to quantify the elliptical Fourier coefficient (EFC ratio) as a measure of nuclear irregularities, which allowed us to perform rigorous statistical analyses of screening data. Top hit compounds fell into three major mode of action categories, targeting three separate epigenetic modulation routes: 1) Histone deacetylase (HDAC) inhibitors; 2) Bromodomain and extra-terminal domain (BET) protein inhibitors; and 3) Methyl-transferase inhibitors. Some of the top hit compounds were also efficacious in reverting nuclear irregularities in MDA-MB-231 triple negative breast cancer cells and in PANC-1 pancreatic cancer cells in a cell type dependent manner. Regularization of nuclear shapes was compound-specific, cell-type specific, and dependent on the specific molecular perturbation that induced nuclear irregularities. Our approach of targeting nuclear abnormalities may be potentially useful in screening new types of cancer therapies targeted toward chromatin structure.

DOI: https://doi.org/10.1091/mbc.E21-10-0528
Biomolecules. 2022 Feb 25. pii: 367. [Epub ahead of print]12(3):

The Role of Epigenetic Modifications in Human Cancers and the Use of Natural Compounds as Epidrugs: Mechanistic Pathways and Pharmacodynamic Actions.

Abdelhakim Bouyahya, Hamza Mechchate, Loubna Oumeslakht, Ikrame Zeouk, Sara Aboulaghras, Abdelaali Balahbib, Gokhan Zengin, Mohammad Amjad Kamal, Monica Gallo, Domenico Montesano, Nasreddine El Omari.

  Cancer is a complex disease resulting from the genetic and epigenetic disruption of normal cells. The mechanistic understanding of the pathways involved in tumor transformation has implicated a priori predominance of epigenetic perturbations and a posteriori genetic instability. In this work, we aimed to explain the mechanistic involvement of epigenetic pathways in the cancer process, as well as the abilities of natural bioactive compounds isolated from medicinal plants (flavonoids, phenolic acids, stilbenes, and ketones) to specifically target the epigenome of tumor cells. The molecular events leading to transformation, angiogenesis, and dissemination are often complex, stochastic, and take turns. On the other hand, the decisive advances in genomics, epigenomics, transcriptomics, and proteomics have allowed, in recent years, for the mechanistic decryption of the molecular pathways of the cancerization process. This could explain the possibility of specifically targeting this or that mechanism leading to cancerization. With the plasticity and flexibility of epigenetic modifications, some studies have started the pharmacological screening of natural substances against different epigenetic pathways (DNA methylation, histone acetylation, histone methylation, and chromatin remodeling) to restore the cellular memory lost during tumor transformation. These substances can inhibit DNMTs, modify chromatin remodeling, and adjust histone modifications in favor of pre-established cell identity by the differentiation program. Epidrugs are molecules that target the epigenome program and can therefore restore cell memory in cancerous diseases. Natural products isolated from medicinal plants such as flavonoids and phenolic acids have shown their ability to exhibit several actions on epigenetic modifiers, such as the inhibition of DNMT, HMT, and HAT. The mechanisms of these substances are specific and pleiotropic and can sometimes be stochastic, and their use as anticancer epidrugs is currently a remarkable avenue in the fight against human cancers.

Keywords:  DNMT; HDAC; cancer; cancer therapy; epidrugs; pharmacodynamic

DOI:  https://doi.org/10.3390/biom12030367
Nucleic Acids Res. 2022 Mar 24. pii: gkac199. [Epub ahead of print]

ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data.

Zhaonan Zou, Tazro Ohta, Fumihito Miura, Shinya Oki.

ChIP-Atlas (https://chip-atlas.org) is a web service providing both GUI- and API-based data-mining tools to reveal the architecture of the transcription regulatory landscape. ChIP-Atlas is powered by comprehensively integrating all data sets from high-throughput ChIP-seq and DNase-seq, a method for profiling chromatin regions accessible to DNase. In this update, we further collected all the ATAC-seq and whole-genome bisulfite-seq data for six model organisms (human, mouse, rat, fruit fly, nematode, and budding yeast) with the latest genome assemblies. These together with ChIP-seq data can be visualized with the Peak Browser tool and a genome browser to explore the epigenomic landscape of a query genomic locus, such as its chromatin accessibility, DNA methylation status, and protein-genome interactions. This epigenomic landscape can also be characterized for multiple genes and genomic loci by querying with the Enrichment Analysis tool, which, for example, revealed that inflammatory bowel disease-associated SNPs are the most significantly hypo-methylated in neutrophils. Therefore, ChIP-Atlas provides a panoramic view of the whole epigenomic landscape. All datasets are free to download via either a simple button on the web page or an API.

DOI: https://doi.org/10.1093/nar/gkac199