bims-ectoca Biomed News
on Epigenetic control of Tolerance in Cancer
Issue of 2021‒07‒25
27 papers selected by
Ankita Daiya
BITS Pilani
  1. Chromatin Profiling Techniques: Exploring the Chromatin Environment and Its Contributions to Complex Traits.
  2. Histone mimics: more tales to read.
  3. Epigenetic Regulation of microRNAs in Cancer: Shortening the Distance from Bench to Bedside.
  4. Mitochondrial Heteroplasmy Shifting as a Potential Biomarker of Cancer Progression.
  5. Resistance to platinum-based cancer drugs: a special focus on epigenetic mechanisms.
  6. Epigenetic dysregulation in various types of cells exposed to extremely low-frequency magnetic fields.
  7. Characterizing the Metabolic and Immune Landscape of Non-small Cell Lung Cancer Reveals Prognostic Biomarkers Through Omics Data Integration.
  8. Single-cell analysis enters the multiomics age.
  9. A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data.
  10. Deciphering the PTM codes of the tumor suppressor p53.
  11. A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility.
  12. High-Throughput Characterization of Cell Adhesion Strength Using Long-Channel Constriction-Based Microfluidics.
  13. Chromatin and Epigenetic Dysregulation of Prostate Cancer Development, Progression, and Therapeutic Response.
  14. Yes-activated protein promotes primary resistance of BRAF V600E mutant metastatic colorectal cancer cells to mitogen-activated protein kinase pathway inhibitors.
  15. Deregulation of Transcriptional Enhancers in Cancer.
  16. Aberrant expression of WDR4 affects the clinical significance of cancer immunity in pan-cancer.
  17. Valproic Acid and Breast Cancer: State of the Art in 2021.
  18. The Crosstalk Between Long Non-Coding RNAs and Various Types of Death in Cancer Cells.
  19. A likelihood-based deconvolution of bulk gene expression data using single-cell references.
  20. Functional Roles of Bromodomain Proteins in Cancer.
  21. Visualisation of tumour cells in bone in vivo at single-cell resolution.
  22. MicroRNAs: understanding their role in gene expression and cancer.
  23. Single-Molecule Techniques to Study Chromatin.
  24. Novel germline variant in the histone demethylase and transcription regulator KDM4C induces a multi-cancer phenotype.
  25. Crosstalk between epitranscriptomic and epigenetic mechanisms in gene regulation.
  26. HDAC Inhibitors: Dissecting Mechanisms of Action to Counter Tumor Heterogeneity.
  27. Drugs and Epigenetic Molecular Functions. A Pharmacological Data Scientometric Analysis.
  1. Int J Mol Sci. 2021 Jul 16. pii: 7612. [Epub ahead of print]22(14):
    Chromatin Profiling Techniques: Exploring the Chromatin Environment and Its Contributions to Complex Traits.
    Anjali Chawla, Corina Nagy, Gustavo Turecki.
      The genetic architecture of complex traits is multifactorial. Genome-wide association studies (GWASs) have identified risk loci for complex traits and diseases that are disproportionately located at the non-coding regions of the genome. On the other hand, we have just begun to understand the regulatory roles of the non-coding genome, making it challenging to precisely interpret the functions of non-coding variants associated with complex diseases. Additionally, the epigenome plays an active role in mediating cellular responses to fluctuations of sensory or environmental stimuli. However, it remains unclear how exactly non-coding elements associate with epigenetic modifications to regulate gene expression changes and mediate phenotypic outcomes. Therefore, finer interrogations of the human epigenomic landscape in associating with non-coding variants are warranted. Recently, chromatin-profiling techniques have vastly improved our understanding of the numerous functions mediated by the epigenome and DNA structure. Here, we review various chromatin-profiling techniques, such as assays of chromatin accessibility, nucleosome distribution, histone modifications, and chromatin topology, and discuss their applications in unraveling the brain epigenome and etiology of complex traits at tissue homogenate and single-cell resolution. These techniques have elucidated compositional and structural organizing principles of the chromatin environment. Taken together, we believe that high-resolution epigenomic and DNA structure profiling will be one of the best ways to elucidate how non-coding genetic variations impact complex diseases, ultimately allowing us to pinpoint cell-type targets with therapeutic potential.
    Keywords:  DNA structure; brain; chromatin loops; complex diseases; complex traits; epigenome; histone modifications; non-coding; open chromatin; transcription factors
    DOI:  https://doi.org/10.3390/ijms22147612
  2. Biochem J. 2021 Jul 30. 478(14): 2789-2791
    Histone mimics: more tales to read.
    Yucong Yu, Hong Wen, Xiaobing Shi.
      Post-translational modifications (PTMs) on histone proteins are known as epigenetic marks that demarcate the status of chromatin. These modifications are 'read' by specific reader proteins, which in turn recruit additional factors to modulate chromatin accessibility and the activity of the underlying DNA. Accumulating evidence suggests that these modifications are not restricted solely to histones, many non-histone proteins may function in a similar way through mimicking the histones. In this commentary, we briefly discuss a systematic study of the discovery of histone H3 N-terminal mimicry proteins (H3TMs), and their implications in chromatin regulation and drug discoveries.
    DOI:  https://doi.org/10.1042/BCJ20210357
  3. Int J Mol Sci. 2021 Jul 08. pii: 7350. [Epub ahead of print]22(14):
    Epigenetic Regulation of microRNAs in Cancer: Shortening the Distance from Bench to Bedside.
    María J Pajares, Ester Alemany-Cosme, Saioa Goñi, Eva Bandres, Cora Palanca-Ballester, Juan Sandoval.
      Cancer is a complex disease involving alterations of multiple processes, with both genetic and epigenetic features contributing as core factors to the disease. In recent years, it has become evident that non-coding RNAs (ncRNAs), an epigenetic factor, play a key role in the initiation and progression of cancer. MicroRNAs, the most studied non-coding RNAs subtype, are key controllers in a myriad of cellular processes, including proliferation, differentiation, and apoptosis. Furthermore, the expression of miRNAs is controlled, concomitantly, by other epigenetic factors, such as DNA methylation and histone modifications, resulting in aberrant patterns of expression upon the occurrence of cancer. In this sense, aberrant miRNA landscape evaluation has emerged as a promising strategy for cancer management. In this review, we have focused on the regulation (biogenesis, processing, and dysregulation) of miRNAs and their role as modulators of the epigenetic machinery. We have also highlighted their potential clinical value, such as validated diagnostic and prognostic biomarkers, and their relevant role as chromatin modifiers in cancer therapy.
    Keywords:  DNA methylation; biomarkers; cancer; clinical applications; epigenetics; microRNAs
    DOI:  https://doi.org/10.3390/ijms22147350
  4. Int J Mol Sci. 2021 Jul 09. pii: 7369. [Epub ahead of print]22(14):
    Mitochondrial Heteroplasmy Shifting as a Potential Biomarker of Cancer Progression.
    Carlos Jhovani Pérez-Amado, Amellalli Bazan-Cordoba, Alfredo Hidalgo-Miranda, Silvia Jiménez-Morales.
      Cancer is a serious health problem with a high mortality rate worldwide. Given the relevance of mitochondria in numerous physiological and pathological mechanisms, such as adenosine triphosphate (ATP) synthesis, apoptosis, metabolism, cancer progression and drug resistance, mitochondrial genome (mtDNA) analysis has become of great interest in the study of human diseases, including cancer. To date, a high number of variants and mutations have been identified in different types of tumors, which coexist with normal alleles, a phenomenon named heteroplasmy. This mechanism is considered an intermediate state between the fixation or elimination of the acquired mutations. It is suggested that mutations, which confer adaptive advantages to tumor growth and invasion, are enriched in malignant cells. Notably, many recent studies have reported a heteroplasmy-shifting phenomenon as a potential shaper in tumor progression and treatment response, and we suggest that each cancer type also has a unique mitochondrial heteroplasmy-shifting profile. So far, a plethora of data evidencing correlations among heteroplasmy and cancer-related phenotypes are available, but still, not authentic demonstrations, and whether the heteroplasmy or the variation in mtDNA copy number (mtCNV) in cancer are cause or consequence remained unknown. Further studies are needed to support these findings and decipher their clinical implications and impact in the field of drug discovery aimed at treating human cancer.
    Keywords:  cancer; heteroplasmy; heteroplasmy shifting; mitochondrial DNA; mitochondrial mutations
    DOI:  https://doi.org/10.3390/ijms22147369
  5. Pharmacogenomics. 2021 Jul 20.
    Resistance to platinum-based cancer drugs: a special focus on epigenetic mechanisms.
    Yuselin Mora, María Elena Reyes, Louise Zanella, Bárbara Mora, Kurt Buchegger, Carmen Ili, Priscilla Brebi.
      Chemoresistance is a significant clinical challenge, limiting the drug response in cancer. Several mechanisms associated with drug resistance have been characterized, and the role of epigenetics in generating resistance to platinum-based drugs has been clarified. Epigenetic mechanisms such as DNA methylation, histone modification, long noncoding RNA, and microRNA affect the expression of genes implicated in absorption, distribution, metabolism and excretion (ADME) of drugs, and other non-ADME genes that encode enzymes involved in the processes of cell proliferation, DNA repair, apoptosis and signal transduction key in the development of chemoresistance in cancer, specifically in platinum-based drugs. This review summarizes current discoveries in epigenetic regulation implicated in platinum drug resistance in cancer and the main clinical trials based on epigenetic therapy, evaluating their potential synergy with platinum-based drugs.
    Keywords:  ADME gene; cancer; drug resistance; epigenetics; non-ADME gene; platinum-based drugs
    DOI:  https://doi.org/10.2217/pgs-2021-0020
  6. Cell Tissue Res. 2021 Jul 21.
    Epigenetic dysregulation in various types of cells exposed to extremely low-frequency magnetic fields.
    Gianfranco Giorgi, Brunella Del Re.
      Epigenetic mechanisms regulate gene expression, without changing the DNA sequence, and establish cell-type-specific temporal and spatial expression patterns. Alterations of epigenetic marks have been observed in several pathological conditions, including cancer and neurological disorders. Emerging evidence indicates that a variety of environmental factors may cause epigenetic alterations and eventually influence disease risks. Humans are increasingly exposed to extremely low-frequency magnetic fields (ELF-MFs), which in 2002 were classified as possible carcinogens by the International Agency for Research on Cancer. This review summarizes the current knowledge of the link between the exposure to ELF-MFs and epigenetic alterations in various cell types. In spite of the limited number of publications, available evidence indicates that ELF-MF exposure can be associated with epigenetic changes, including DNA methylation, modifications of histones and microRNA expression. Further research is needed to investigate the molecular mechanisms underlying the observed phenomena.
    Keywords:  DNA methylation; Electromagnetic; Epigenetics; Histone modifications; MicroRNA; magnetic field
    DOI:  https://doi.org/10.1007/s00441-021-03489-6
  7. Front Cell Dev Biol. 2021 ;9 702112
    Characterizing the Metabolic and Immune Landscape of Non-small Cell Lung Cancer Reveals Prognostic Biomarkers Through Omics Data Integration.
    Fengjiao Wang, Yuanfu Zhang, Yangyang Hao, Xuexin Li, Yue Qi, Mengyu Xin, Qifan Xiao, Peng Wang.
      Non-small cell lung cancer (NSCLC) is one of the most common malignancies worldwide. The development of high-throughput single-cell RNA-sequencing (RNA-seq) technology and the advent of multi-omics have provided a solid basis for a systematic understanding of the heterogeneity in cancers. Although numerous studies have revealed the molecular features of NSCLC, it is important to identify and validate the molecular biomarkers related to specific NSCLC phenotypes at single-cell resolution. In this study, we analyzed and validated single-cell RNA-seq data by integrating multi-level omics data to identify key metabolic features and prognostic biomarkers in NSCLC. High-throughput single-cell RNA-seq data, including 4887 cellular gene expression profiles from NSCLC tissues, were analyzed. After pre-processing, the cells were clustered into 12 clusters using the t-SNE clustering algorithm, and the cell types were defined according to the marker genes. Malignant epithelial cells exhibit individual differences in molecular features and intra-tissue metabolic heterogeneity. We found that oxidative phosphorylation (OXPHOS) and glycolytic pathway activity are major contributors to intra-tissue metabolic heterogeneity of malignant epithelial cells and T cells. Furthermore, we constructed T-cell differentiation trajectories and identified several key genes that regulate the cellular phenotype. By screening for genes associated with T-cell differentiation using the Lasso algorithm and Cox risk regression, we identified four prognostic marker genes for NSCLC. In summary, our study revealed metabolic features and prognostic markers of NSCLC at single-cell resolution, which provides novel findings on molecular biomarkers and signatures of cancers.
    Keywords:  NSCLC; cellular phenotypes; omics data integration; prognostic biomarkers; single cell sequencing
    DOI:  https://doi.org/10.3389/fcell.2021.702112
  8. Nature. 2021 Jul;595(7868): 614-616
    Single-cell analysis enters the multiomics age.
    Jeffrey M Perkel.
      
    Keywords:  Computational biology and bioinformatics; Epigenetics; Transcriptomics
    DOI:  https://doi.org/10.1038/d41586-021-01994-w
  9. Genome Res. 2021 Jul 22. pii: gr.271205.120. [Epub ahead of print]
    A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data.
    Norah Alghamdi, Wennan Chang, Pengtao Dang, Xiaoyu Lu, Changlin Wan, Silpa Gampala, Zhi Huang, Jiashi Wang, Qin Ma, Yong Zang, Melissa L Fishel, Sha Cao, Chi Zhang.
      The metabolic heterogeneity, and metabolic interplay between cells have been known as significant contributors to disease treatment resistance. However, with the lack of a mature high-throughput single-cell metabolomics technology, we have yet to establish systematic understanding of the intra-tissue metabolic heterogeneity and cooperative mechanisms. To mitigate this knowledge gap, we developed a novel computational method, namely scFEA (single-cell Flux Estimation Analysis), to infer cell-wise fluxome from single-cell RNA-sequencing (scRNA-seq) data. scFEA is empowered by a systematically reconstructed human metabolic map as a factor graph, a novel probabilistic model to leverage the flux balance constraints on scRNA-seq data, and a novel graph neural network based optimization solver. The intricate information cascade from transcriptome to metabolome was captured using multi-layer neural networks to capitulate the nonlinear dependency between enzymatic gene expressions and reaction rates. We experimentally validated scFEA by generating an scRNA-seq dataset with matched metabolomics data on cells of perturbed oxygen and genetic conditions. Application of scFEA on this dataset demonstrated the consistency between predicted flux and the observed variation of metabolite abundance in the matched metabolomics data. We also applied scFEA on five publicly available scRNA-seq and spatial transcriptomics datasets and identified context and cell group-specific metabolic variations. The cell-wise fluxome predicted by scFEA empowers a series of downstream analysis including identification of metabolic modules or cell groups that share common metabolic variations, sensitivity evaluation of enzymes with regards to their impact on the whole metabolic flux, and inference of cell-tissue and cell-cell metabolic communications.
    DOI:  https://doi.org/10.1101/gr.271205.120
  10. J Mol Cell Biol. 2021 Jul 21. pii: mjab047. [Epub ahead of print]
    Deciphering the PTM codes of the tumor suppressor p53.
    Jia Wen, Donglai Wang.
      The genome guardian p53 functions as a transcription factor that senses numerous cellular stresses and orchestrates the corresponding transcriptional events involved in determining various cellular outcomes, including cell cycle arrest, apoptosis, senescence, DNA repair, and metabolic regulation. In response to diverse stresses, p53 undergoes multiple posttranslational modifications (PTMs) that coordinate with intimate interdependencies to precisely modulate its diverse properties in given biological contexts. Notably, PTMs can recruit 'reader' proteins that exclusively recognize specific modifications and facilitate the functional readout of p53. Targeting PTM‒reader interplay has been developing into a promising cancer therapeutic strategy. In this review, we summarize the advances in deciphering the 'PTM codes' of p53, focusing particularly on the mechanisms by which the specific reader proteins functionally decipher the information harbored within these PTMs of p53. We also highlight the potential applications of intervention with p53 PTM‒reader interactions in cancer therapy and discuss perspectives on the 'PTMomic' study of p53 and other proteins.
    Keywords:  PTM code; p53; posttranslational modification; reader; tumor therapy
    DOI:  https://doi.org/10.1093/jmcb/mjab047
  11. Nat Protoc. 2021 Jul 19.
    A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility.
    Wei Xu, Yi Wen, Yingying Liang, Qiushi Xu, Xuefei Wang, Wenfei Jin, Xi Chen.
      Profiling chromatin accessibility at the single-cell level provides critical information about cell type composition and cell-to-cell variation within a complex tissue. Emerging techniques for the interrogation of chromatin accessibility in individual cells allow investigation of the fundamental mechanisms that lead to the variability of different cells. This protocol describes a fast and robust method for single-cell chromatin accessibility profiling based on the assay for transposase-accessible chromatin using sequencing (ATAC-seq). The method combines up-front bulk Tn5 tagging of chromatin with flow cytometry to isolate single nuclei or cells. Reagents required to generate sequencing libraries are added to the same well in the plate where cells are sorted. The protocol described here generates data of high complexity and excellent signal-to-noise ratio and can be combined with index sorting for in-depth characterization of cell types. The whole experimental procedure can be finished within 1 or 2 d with a throughput of hundreds to thousands of nuclei, and the data can be processed by the provided computational pipeline. The execution of the protocol only requires basic techniques and equipment in a molecular biology laboratory with flow cytometry support.
    DOI:  https://doi.org/10.1038/s41596-021-00583-5
  12. ACS Sens. 2021 Jul 19.
    High-Throughput Characterization of Cell Adhesion Strength Using Long-Channel Constriction-Based Microfluidics.
    Mingji Wei, Fei Zhang, Rongbiao Zhang, Jin-Ming Lin, Ning Yang.
      The adhesion strength of a cancer cell is a valuable biophysical marker of its metastatic potential, tightly associated with various metastatic processes; for example, cancer cells escape from a primary tumor, and circulating tumor cells (CTCs) are anchored to the vessel wall. Although constriction-based microfluidics can realize the high-throughput characterization of single-cell deformability, due to the influence of cell size heterogeneity, accurately evaluating the adhesion strength of a cancer cell at high throughputs in constriction remains difficult. In this paper, we first proposed an approach for the assessment of adhesion strength of BGC-823 and SGC-7901 cell lines at high throughputs based on a friction coefficient using the constant velocity stage of cell transit in a long-channel constriction. Cell size was proven to be independent of adhesion strength by cell detachment assay; however, it has large effects on cell transit velocity in constriction. Therefore, the linear elasticity of a completely deformed cell in constriction is simplified as a compressed spring model, effectively reducing the influence of cell size heterogeneity. Theoretically, our proposed model can well offset the influence of cell size by cell transit velocity, while our experimental results indicate that the friction coefficient has a good linear relationship with the logarithm of the adhesion strength too. Therefore, our proposed approach can realize accurate characterization of cell adhesion strength at high throughputs using long-channel constriction-based microfluidics. Hence, this work might enrich the functions of constriction-based microfluidics and bring new insights into the characterization of mechanical phenotypes.
    Keywords:  cell adhesion strength; cell transit velocity; friction coefficient; long-channel constriction-based microfluidics; mechanical phenotype characterization; single cell
    DOI:  https://doi.org/10.1021/acssensors.1c01037
  13. Cancers (Basel). 2021 Jul 02. pii: 3325. [Epub ahead of print]13(13):
    Chromatin and Epigenetic Dysregulation of Prostate Cancer Development, Progression, and Therapeutic Response.
    Konsta Kukkonen, Sinja Taavitsainen, Laura Huhtala, Joonas Uusi-Makela, Kirsi J Granberg, Matti Nykter, Alfonso Urbanucci.
      The dysregulation of chromatin and epigenetics has been defined as the overarching cancer hallmark. By disrupting transcriptional regulation in normal cells and mediating tumor progression by promoting cancer cell plasticity, this process has the ability to mediate all defined hallmarks of cancer. In this review, we collect and assess evidence on the contribution of chromatin and epigenetic dysregulation in prostate cancer. We highlight important mechanisms leading to prostate carcinogenesis, the emergence of castration-resistance upon treatment with androgen deprivation therapy, and resistance to antiandrogens. We examine in particular the contribution of chromatin structure and epigenetics to cell lineage commitment, which is dysregulated during tumorigenesis, and cell plasticity, which is altered during tumor progression.
    Keywords:  androgen receptor signaling inhibitors; castration resistant prostate cancer; chromatin; chromatin regulators alterations; chromatin-associated factors; drug resistance; epigenetics; lineage commitment; lineage plasticity; prostate cancer
    DOI:  https://doi.org/10.3390/cancers13133325
  14. J Gastrointest Oncol. 2021 Jun;12(3): 953-963
    Yes-activated protein promotes primary resistance of BRAF V600E mutant metastatic colorectal cancer cells to mitogen-activated protein kinase pathway inhibitors.
    Meng Su, Lei Zhan, Yong Zhang, Jingdong Zhang.
      Background: Most colorectal cancer (CRC) patients with the BRAF V600E mutation display resistance to chemotherapy and targeted medicinal treatments. Thus, exploring new drugs and drug resistance mechanisms for the BRAF V600E mutation has become an urgent clinical priority.Methods: MTS experiment, cell cloning experiment, cell scratching experiment, Transwell experiment, chromatin immunoprecipitation (ChIP), quantitative polymerase chain reaction (qPCR) and flow cytometry are used. Detect the transcription and protein expression of YAP in colorectal cancer cell lines, establish a transient cell line with YAP gene overexpression and knockdown, and detect the effect of YAP gene expression on the biological functions of colorectal cancer cells RKO and HT-29. And further study the mechanism of YAP regulating the response of RAF and MEK targeted therapy.
    Results: In this study, for the first time, we verified that the expression of transcription factor yes-associated protein (YAP) was upregulated in BRAF V600E mutant CRC cells. After knocking down YAP, we observed a reduction in the growth rate, proliferation, and invasion ability of colon cancer cells. We further verified that YAP knockdown increased sensitivity of BRAF V600E mutant CRC cells to mitogen-activated protein kinase (MAPK) pathway inhibitors. In addition, we clarified the mechanism underlying YAP regulation of RAF and MAPK/extracellular signal-regulated kinase (MEK)-targeted therapy response: YAP cooperates with RAF→MEK pathway inhibitors to regulate the cell cycle, increase cell G1/S phase arrest, and increase apoptosis.
    Conclusions: These results suggest that YAP expression may be related to the primary resistance of MAPK inhibitors in metastatic CRC with the BRAF V600E mutation. Therefore, the combination of YAP and MAPK pathway inhibitors in BRAF V600E mutant metastatic CRC may present a promising treatment method.
    Keywords:  BRAF V600E mutation; Colorectal cancer (CRC); mitogen-activated protein kinase pathway (MAPK pathway); yes-activated protein
    DOI:  https://doi.org/10.21037/jgo-21-258
  15. Cancers (Basel). 2021 Jul 14. pii: 3532. [Epub ahead of print]13(14):
    Deregulation of Transcriptional Enhancers in Cancer.
    Fatemeh Mirzadeh Azad, Yaser Atlasi.
      Epigenetic regulations can shape a cell's identity by reversible modifications of the chromatin that ultimately control gene expression in response to internal and external cues. In this review, we first discuss the concept of cell plasticity in cancer, a process that is directly controlled by epigenetic mechanisms, with a particular focus on transcriptional enhancers as the cornerstone of epigenetic regulation. In the second part, we discuss mechanisms of enhancer deregulation in adult stem cells and epithelial-to-mesenchymal transition (EMT), as two paradigms of cell plasticity that are dependent on epigenetic regulation and serve as major sources of tumour heterogeneity. Finally, we review how genetic variations at enhancers and their epigenetic modifiers contribute to tumourigenesis, and we highlight examples of cancer drugs that target epigenetic modifications at enhancers.
    Keywords:  cancer; enhancer; epigenetic; plasticity; stem cell
    DOI:  https://doi.org/10.3390/cancers13143532
  16. Aging (Albany NY). 2021 Jul 19. 13(undefined):
    Aberrant expression of WDR4 affects the clinical significance of cancer immunity in pan-cancer.
    Hanqian Zeng, Shiwen Xu, Erjie Xia, Suzita Hirachan, Adheesh Bhandari, Yanyan Shen.
      Recent publications have presented research showing that WD repeat domain 4 (WDR4) plays a significant role in various kinds of malignant tumours. However, the expression profile of WDR4 is still unspecified, as is its significance in the analysis of human pan-cancer. We conducted an in-depth analysis of three aspects of WDR4 expression patterns from 33 types of cancer and determined the value of WDR4 for prognostic prediction and carcinoma drug resistance prediction. WDR4 was expressed in different cancer cell lines at inconsistent levels. Aberrant expression of WDR4 has been observed in various malignant cancers and is significantly implicated in overall survival outcomes. The expression level of WDR4 is also strongly associated with tumour immunity, such as immune scores and tumour-infiltrating immune cells. The level of WDR4 is related to microsatellite instability and tumour mutation burden in several types of malignancy, and validation studies implied that WDR4-associated terms and pathways are involved in malignancy. We explored the expression level of WDR4 across 33 types of cancer and showed that WDR4 plays a significant role during cancer development. More crucially, WDR4 is associated with immune infiltration, which suggests that WDR4 could be an immunotherapy target in cancers. In summary, our research showed that WDR4 plays a vital role in tumorigenesis and has the potential for to be targeted with treatments.
    Keywords:  WDR4; clinical significance; immune infiltration; pan-cancer; prognostic biomarker
    DOI:  https://doi.org/10.18632/aging.203284
  17. Cancers (Basel). 2021 Jul 07. pii: 3409. [Epub ahead of print]13(14):
    Valproic Acid and Breast Cancer: State of the Art in 2021.
    Anna Wawruszak, Marta Halasa, Estera Okon, Wirginia Kukula-Koch, Andrzej Stepulak.
      Valproic acid (2-propylpentanoic acid, VPA) is a short-chain fatty acid, a member of the group of histone deacetylase inhibitors (HDIs). VPA has been successfully used in the treatment of epilepsy, bipolar disorders, and schizophrenia for over 50 years. Numerous in vitro and in vivo pre-clinical studies suggest that this well-known anticonvulsant drug significantly inhibits cancer cell proliferation by modulating multiple signaling pathways. Breast cancer (BC) is the most common malignancy affecting women worldwide. Despite significant progress in the treatment of BC, serious adverse effects, high toxicity to normal cells, and the occurrence of multi-drug resistance (MDR) still limit the effective therapy of BC patients. Thus, new agents which improve the effectiveness of currently used methods, decrease the emergence of MDR, and increase disease-free survival are highly needed. This review focuses on in vitro and in vivo experimental data on VPA, applied individually or in combination with other anti-cancer agents, in the treatment of different histological subtypes of BC.
    Keywords:  breast cancer; epigenetics; histone acetylation; histone deacetylase inhibitor (HDI); histone deacetylases (HDACs); targeted therapy; valproic acid (VPA)
    DOI:  https://doi.org/10.3390/cancers13143409
  18. Technol Cancer Res Treat. 2021 Jan-Dec;20:20 15330338211033044
    The Crosstalk Between Long Non-Coding RNAs and Various Types of Death in Cancer Cells.
    Wenwen Tang, Shaomi Zhu, Xin Liang, Chi Liu, Linjiang Song.
      With the increasing aging population, cancer has become one of the leading causes of death worldwide, and the number of cancer cases and deaths is only anticipated to grow further. Long non-coding RNAs (lncRNAs), which are closely associated with the expression level of downstream genes and various types of bioactivity, are regarded as one of the key regulators of cancer cell proliferation and death. Cell death, including apoptosis, necrosis, autophagy, pyroptosis, and ferroptosis, plays a vital role in the progression of cancer. A better understanding of the regulatory relationships between lncRNAs and these various types of cancer cell death is therefore urgently required. The occurrence and development of tumors can be controlled by increasing or decreasing the expression of lncRNAs, a method which confers broad prospects for cancer treatment. Therefore, it is urgent for us to understand the influence of lncRNAs on the development of different modes of tumor death, and to evaluate whether lncRNAs have the potential to be used as biological targets for inducing cell death and predicting prognosis and recurrence of chemotherapy. The purpose of this review is to provide an overview of the various forms of cancer cell death, including apoptosis, necrosis, autophagy, pyroptosis, and ferroptosis, and to describe the mechanisms of different types of cancer cell death that are regulated by lncRNAs in order to explore potential targets for cancer therapy.
    Keywords:  apoptosis; autophagy; cancer; ferroptosis; lncRNAs; necrosis; pyroptosis
    DOI:  https://doi.org/10.1177/15330338211033044
  19. Genome Res. 2021 Jul 22. pii: gr.272344.120. [Epub ahead of print]
    A likelihood-based deconvolution of bulk gene expression data using single-cell references.
    Dan D Erdmann-Pham, Jonathan Fischer, Justin Hong, Yun S Song.
      Direct comparison of bulk gene expression profiles is complicated by distinct cell type mixtures in each sample which obscure whether observed differences are actually due to changes in expression levels themselves or simply due to differing cell type compositions. Single-cell technology has made it possible to measure gene expression in individual cells, achieving higher resolution at the expense of increased noise. If carefully incorporated, such single-cell data can be used to deconvolve bulk samples to yield accurate estimates of the true cell type proportions, thus enabling one to disentangle the effects of differential expression and cell type mixtures. Here, we propose a generative model and a likelihood-based inference method that uses asymptotic statistical theory and a novel optimization procedure to perform deconvolution of bulk RNA-seq data to produce accurate cell type proportion estimates. We demonstrate the effectiveness of our method, called RNA-Sieve, across a diverse array of scenarios involving real data and discuss extensions made uniquely possible by our probabilistic framework, including a demonstration of well-calibrated confidence intervals.
    DOI:  https://doi.org/10.1101/gr.272344.120
  20. Cancers (Basel). 2021 Jul 19. pii: 3606. [Epub ahead of print]13(14):
    Functional Roles of Bromodomain Proteins in Cancer.
    Samuel P Boyson, Cong Gao, Kathleen Quinn, Joseph Boyd, Hana Paculova, Seth Frietze, Karen C Glass.
      Histone acetylation is generally associated with an open chromatin configuration that facilitates many cellular processes including gene transcription, DNA repair, and DNA replication. Aberrant levels of histone lysine acetylation are associated with the development of cancer. Bromodomains represent a family of structurally well-characterized effector domains that recognize acetylated lysines in chromatin. As part of their fundamental reader activity, bromodomain-containing proteins play versatile roles in epigenetic regulation, and additional functional modules are often present in the same protein, or through the assembly of larger enzymatic complexes. Dysregulated gene expression, chromosomal translocations, and/or mutations in bromodomain-containing proteins have been correlated with poor patient outcomes in cancer. Thus, bromodomains have emerged as a highly tractable class of epigenetic targets due to their well-defined structural domains, and the increasing ease of designing or screening for molecules that modulate the reading process. Recent developments in pharmacological agents that target specific bromodomains has helped to understand the diverse mechanisms that bromodomains play with their interaction partners in a variety of chromatin processes, and provide the promise of applying bromodomain inhibitors into the clinical field of cancer treatment. In this review, we explore the expression and protein interactome profiles of bromodomain-containing proteins and discuss them in terms of functional groups. Furthermore, we highlight our current understanding of the roles of bromodomain-containing proteins in cancer, as well as emerging strategies to specifically target bromodomains, including combination therapies using bromodomain inhibitors alongside traditional therapeutic approaches designed to re-program tumorigenesis and metastasis.
    Keywords:  bromodomain; cancer; chromatin reader; epigenetic gene regulation; histone post-translational modifications; protein-protein interaction network
    DOI:  https://doi.org/10.3390/cancers13143606
  21. Bone. 2021 Jul 14. pii: S8756-3282(21)00278-7. [Epub ahead of print] 116113
    Visualisation of tumour cells in bone in vivo at single-cell resolution.
    Ryan C Chai, Michelle M McDonald.
      The skeleton is a common site for the establishment of distant metastases. Once cancers occupy bone, the prognosis is poor as disease recurrence and visceral spread is imminent. Understanding the pathways and cellular interactions, which regulate tumour cell seeding, dormancy and growth in bone, is pertinent to improving outcomes for patients with advanced cancers. Advances in imaging techniques have facilitated the development of the concept that the behavior of bone marrow resident cells dictate the fate of tumour cells upon arrival in bone. This review summarises recent findings achieved through intravital imaging. It highlights the importance of developing both longitudinal static and acute dynamic data to develop our understanding of tumour cell engraftment, dormancy, activation and the subsequent establishment of metastases. We also describe how imaging techniques have developed our knowledge of the elements that make up the complex bone microenvironment which tumour cells interact with to survive and grow. We also discuss how through combining these imaging insights with single cell RNA sequencing data, we are entering a new era of research which has the power to define the cell-cell interactions which control tumour cell growth in bone.
    Keywords:  Bone cancer; Bone metastasis; Bone tumour cell interactions; Imaging bone cells; Imaging tumour cells; Intravital imaging; Single cell RNA sequencing; Tumour dormancy
    DOI:  https://doi.org/10.1016/j.bone.2021.116113
  22. Einstein (Sao Paulo). 2021 ;pii: S1679-45082021000100601. [Epub ahead of print]19 eRB5996
    MicroRNAs: understanding their role in gene expression and cancer.
    Ariany Lima Jorge, Erik Ribeiro Pereira, Christian Sousa de Oliveira, Eduardo Dos Santos Ferreira, Edmara Toledo Ninzoli Menon, Susana Nogueira Diniz, Julia Alejandra Pezuk.
      MicroRNAs are small RNA molecules that regulate gene expression in cells. These small molecules comprise 17 to 25 nucleotides and are able to recognize target messenger RNAs by sequence complementarity and regulate their protein translation. Different microRNAs are expressed in all human cells. There is over 2,500 microRNAs described in humans that are involved in virtually all biological processes. Given their role as gene expression regulators, these molecules have been widely investigated and are thought to be associated with some specific physiological and pathological conditions, being proposed as biomarkers. It has recently been reported that microRNAs are secreted outside cells and are involved in intercellular communication. MicroRNAs in biological fluids are named circulating and have been detected in all body fluids, although the expression profile is specific for each type. The major advantages of using circulating microRNAs as biological markers are the high stability of those molecules and the wide availability of samples. Also, given the individual nature of microRNA expression changes, these molecules have a high potential for use in personalized medicine. In fact, microRNA expression profile determination may support disease recognition and diagnosis, and can be used to monitor therapeutic responses and establish patient prognosis, assisting in choice of treatment. This review provides a general overview of microRNAs and discusses the importance of those molecules in cancer, for deeper understanding of their role in this disease.
    DOI:  https://doi.org/10.31744/einstein_journal/2021RB5996
  23. Front Cell Dev Biol. 2021 ;9 699771
    Single-Molecule Techniques to Study Chromatin.
    Anna Chanou, Stephan Hamperl.
      Besides the basic organization in nucleosome core particles (NCPs), eukaryotic chromatin is further packed through interactions with numerous protein complexes including transcription factors, chromatin remodeling and modifying enzymes. This nucleoprotein complex provides the template for many important biological processes, such as DNA replication, transcription, and DNA repair. Thus, to understand the molecular basis of these DNA transactions, it is critical to define individual changes of the chromatin structure at precise genomic regions where these machineries assemble and drive biological reactions. Single-molecule approaches provide the only possible solution to overcome the heterogenous nature of chromatin and monitor the behavior of individual chromatin transactions in real-time. In this review, we will give an overview of currently available single-molecule methods to obtain mechanistic insights into nucleosome positioning, histone modifications and DNA replication and transcription analysis-previously unattainable with population-based assays.
    Keywords:  DNA fiber analysis; chromatin accessibility; chromatin replication/transcription; electron microscopy; histone modifications; magnetic/optical tweezers; single-molecule techniques; third-generation sequencing
    DOI:  https://doi.org/10.3389/fcell.2021.699771
  24. J Med Genet. 2021 Jul 19. pii: jmedgenet-2021-107747. [Epub ahead of print]
    Novel germline variant in the histone demethylase and transcription regulator KDM4C induces a multi-cancer phenotype.
    Riku Katainen, Iikki Donner, Maritta Räisänen, Davide Berta, Anna Kuosmanen, Eevi Kaasinen, Marja Hietala, Lauri A Aaltonen.
      BACKGROUND: Genes involved in epigenetic regulation are central for chromatin structure and gene expression. Specific mutations in these might promote carcinogenesis in several tissue types.METHODS: We used exome, whole-genome and Sanger sequencing to detect rare variants shared by seven affected individuals in a striking early-onset multi-cancer family. The only variant that segregated with malignancy resided in a histone demethylase KDM4C. Consequently, we went on to study the epigenetic landscape of the mutation carriers with ATAC, ChIP (chromatin immunoprecipitation) and RNA-sequencing from lymphoblastoid cell lines to identify possible pathogenic effects.
    RESULTS: A novel variant in KDM4C, encoding a H3K9me3 histone demethylase and transcription regulator, was found to segregate with malignancy in the family. Based on Roadmap Epigenomics Project data, differentially accessible chromatin regions between the variant carriers and controls enrich to normally H3K9me3-marked chromatin. We could not detect a difference in global H3K9 trimethylation levels. However, carriers of the variant seemed to have more trimethylated H3K9 at transcription start sites. Pathway analyses of ChIP-seq and differential gene expression data suggested that genes regulated through KDM4C interaction partner EZH2 and its interaction partner PLZF are aberrantly expressed in mutation carriers.
    CONCLUSIONS: The apparent dysregulation of H3K9 trimethylation and KDM4C-associated genes in lymphoblastoid cells supports the hypothesis that the KDM4C variant is causative of the multi-cancer susceptibility in the family. As the variant is ultrarare, located in the conserved catalytic JmjC domain and predicted pathogenic by the majority of available in silico tools, further studies on the role of KDM4C in cancer predisposition are warranted.
    Keywords:  epigenomics; gene expression; genetic predisposition to disease; genetic research; human genetics
    DOI:  https://doi.org/10.1136/jmedgenet-2021-107747
  25. Trends Genet. 2021 Jul 19. pii: S0168-9525(21)00170-0. [Epub ahead of print]
    Crosstalk between epitranscriptomic and epigenetic mechanisms in gene regulation.
    Ryan L Kan, Jianjun Chen, Tamer Sallam.
      Epigenetic modifications occur on genomic DNA and histones to influence gene expression. More recently, the discovery that mRNA undergoes similar chemical modifications that powerfully impact transcript turnover and translation adds another layer of dynamic gene regulation. Central to precise and synchronized regulation of gene expression is intricate crosstalk between multiple checkpoints involved in transcript biosynthesis and processing. There are more than 100 internal modifications of RNA in mammalian cells. The most common is N6-methyladenosine (m6A) methylation. Although m6A is established to influence RNA stability dynamics and translation efficiency, rapidly accumulating evidence shows significant crosstalk between RNA methylation and histone/DNA epigenetic mechanisms. These interactions specify transcriptional outputs, translation, recruitment of chromatin modifiers, as well as the deployment of the m6A methyltransferase complex (MTC) at target sites. In this review, we dissect m6A-orchestrated feedback circuits that regulate histone modifications and the activity of regulatory RNAs, such as long noncoding (lnc)RNA and chromosome-associated regulatory RNA. Collectively, this body of evidence suggests that m6A acts as a versatile checkpoint that can couple different layers of gene regulation with one another.
    Keywords:  RNA methylation; RNA modification; epigenetics; gene regulation
    DOI:  https://doi.org/10.1016/j.tig.2021.06.014
  26. Cancers (Basel). 2021 Jul 16. pii: 3575. [Epub ahead of print]13(14):
    HDAC Inhibitors: Dissecting Mechanisms of Action to Counter Tumor Heterogeneity.
    Dimitris Karagiannis, Theodoros Rampias.
      Intra-tumoral heterogeneity presents a major obstacle to cancer therapeutics, including conventional chemotherapy, immunotherapy, and targeted therapies. Stochastic events such as mutations, chromosomal aberrations, and epigenetic dysregulation, as well as micro-environmental selection pressures related to nutrient and oxygen availability, immune infiltration, and immunoediting processes can drive immense phenotypic variability in tumor cells. Here, we discuss how histone deacetylase inhibitors, a prominent class of epigenetic drugs, can be leveraged to counter tumor heterogeneity. We examine their effects on cellular processes that contribute to heterogeneity and provide insights on their mechanisms of action that could assist in the development of future therapeutic approaches.
    Keywords:  HDAC inhibitors; cancer; epigenetic drugs; tumor heterogeneity
    DOI:  https://doi.org/10.3390/cancers13143575
  27. Int J Mol Sci. 2021 Jul 06. pii: 7250. [Epub ahead of print]22(14):
    Drugs and Epigenetic Molecular Functions. A Pharmacological Data Scientometric Analysis.
    Dario Kringel, Sebastian Malkusch, Jörn Lötsch.
      Interactions of drugs with the classical epigenetic mechanism of DNA methylation or histone modification are increasingly being elucidated mechanistically and used to develop novel classes of epigenetic therapeutics. A data science approach is used to synthesize current knowledge on the pharmacological implications of epigenetic regulation of gene expression. Computer-aided knowledge discovery for epigenetic implications of current approved or investigational drugs was performed by querying information from multiple publicly available gold-standard sources to (i) identify enzymes involved in classical epigenetic processes, (ii) screen original biomedical scientific publications including bibliometric analyses, (iii) identify drugs that interact with epigenetic enzymes, including their additional non-epigenetic targets, and (iv) analyze computational functional genomics of drugs with epigenetic interactions. PubMed database search yielded 3051 hits on epigenetics and drugs, starting in 1992 and peaking in 2016. Annual citations increased to a plateau in 2000 and show a downward trend since 2008. Approved and investigational drugs in the DrugBank database included 122 compounds that interacted with 68 unique epigenetic enzymes. Additional molecular functions modulated by these drugs included other enzyme interactions, whereas modulation of ion channels or G-protein-coupled receptors were underrepresented. Epigenetic interactions included (i) drug-induced modulation of DNA methylation, (ii) drug-induced modulation of histone conformations, and (iii) epigenetic modulation of drug effects by interference with pharmacokinetics or pharmacodynamics. Interactions of epigenetic molecular functions and drugs are mutual. Recent research activities on the discovery and development of novel epigenetic therapeutics have passed successfully, whereas epigenetic effects of non-epigenetic drugs or epigenetically induced changes in the targets of common drugs have not yet received the necessary systematic attention in the context of pharmacological plasticity.
    Keywords:  computational knowledge-discovery; pharmacoepigenetics; pharmacological data science; pharmacological plasticity
    DOI:  https://doi.org/10.3390/ijms22147250
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