bims-ectoca Biomed News
on Epigenetic control of Tolerance in Cancer
Issue of 2021‒07‒11
38 papers selected by
Ankita Daiya
BITS Pilani
  1. Similarity and Dissimilarity Regularized Nonnegative Matrix Factorization for Single-Cell RNA-seq Analysis.
  2. Single-cell nucleic acid profiling in droplets (SNAPD) enables high-throughput analysis of heterogeneous cell populations.
  3. High-content single-cell combinatorial indexing.
  4. Multiplexing Methods for Simultaneous Large-Scale Transcriptomic Profiling of Samples at Single-Cell Resolution.
  5. [Methods and applications of single-cell proteomics analysis based on mass spectrometry].
  6. In Situ Single Cell Proteomics Reveals Circulating Tumor Cell Heterogeneity during Treatment.
  7. Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor.
  8. Single cells and transposable element heterogeneity in stem cells and development.
  9. Tumor-associated neutrophils: Orchestrating cancer pathobiology and therapeutic resistance.
  10. Applications and analytical tools of cell communication based on ligand-receptor interactions at single cell level.
  11. Single-cell classification using graph convolutional networks.
  12. Perinatal stress and epigenetics.
  13. Chromatin states shaped by an epigenetic code confer regenerative potential to the mouse liver.
  14. Key molecular alterations in endothelial cells in human glioblastoma uncovered through single-cell RNA sequencing.
  15. DNA Methylation Markers in Lung Cancer.
  16. Single-cell imaging of genome organization and dynamics.
  17. Hypothesis: Sam68 and Pygo2 mediate cell type-specific effects of the modulation of CBP-Wnt and p300-Wnt activities in Colorectal Cancer Cells.
  18. Remodeling the Epigenetic Landscape of Cancer-Application Potential of Flavonoids in the Prevention and Treatment of Cancer.
  19. Long non-coding RNAs and microorganism-associated cancers.
  20. Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data.
  21. HOXB5 Confers Tamoxifen Resistance in Breast Cancer Cells and Promotes Tumor Aggression and Progression.
  22. The proteolytic landscape of cells exposed to non-lethal stresses is shaped by executioner caspases.
  23. Cell migration guided by long-lived spatial memory.
  24. Lysine Demethylases: Promising Drug Targets in Melanoma and Other Cancers.
  25. PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity.
  26. Novel Post-Translational Modifications and Molecular Substrates in Glioma Identified by Bioinformatics.
  27. Spatial Organization of Chromatin: Emergence of Chromatin Structure During Development.
  28. Anti-cancer properties of quercetin in osteosarcoma.
  29. Regulation of autophagy by protein methylation and acetylation in cancer.
  30. Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors.
  31. Applying Peptide and Protein Synthesis to Study Post-translational Modifications in Epigenetics and Beyond.
  32. The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes.
  33. OASIS/CREB3L1 is a factor that responds to nuclear envelope stress.
  34. An easy-to-operate method for single-cell isolation and retrieval using a microfluidic static droplet array.
  35. Development and Validation of Epigenetic Modification-Related Signals for the Diagnosis and Prognosis of Hepatocellular Carcinoma.
  36. Phosphorylation of Ser1452 on BRG1 inhibits the function of the SWI/SNF complex in chromatin activation.
  37. Transcriptome and chromatin landscape changes associated with trastuzumab resistance in HER2+ breast cancer cells.
  38. AgDD System: A Chemical Controllable Protein Aggregates in Cells.
  1. Interdiscip Sci. 2021 Jul 06.
    Similarity and Dissimilarity Regularized Nonnegative Matrix Factorization for Single-Cell RNA-seq Analysis.
    Ya-Li Zhu, Sha-Sha Yuan, Jin-Xing Liu.
      In traditional sequencing techniques, the different functions of cells and the different roles they play in differentiation are often ignored. With the advancement of single-cell RNA sequencing (scRNA-seq) techniques, scientists can measure the gene expression value at the single-cell level, and it is helping to understand the heterogeneity hidden in cells. One of the most powerful ways to find heterogeneity is using the unsupervised clustering method to get separate subpopulations. In this paper, we propose a novel clustering method Similarity and Dissimilarity Regularized Nonnegative Matrix Factorization (SDCNMF) that simultaneously impose similarity and dissimilarity constraints on low-dimensional representations. SDCNMF both considers the similarity of closer cells and the dissimilarity of cells that are farther away. It can not only keep the similar cells getting closer in low-dimensional space, but also can push the dissimilar cells away from each other. We test the validity of our proposed method on five scRNA-seq datasets. Clustering results show that SDCNMF is better than other comparative methods, and the gene markers we find are also consistent with previous studies. Therefore, we can conclude that SDCNMF is effective in scRNA-seq data analysis. This paper proposes a novel clustering method Similarity and Dissimilarity Regularized Nonnegative Matrix Factorization (SDCNMF) that simultaneously impose similarity and dissimilarity constraints on low-dimensional representations. SDCNMF both considers the similarity of closer cells and the dissimilarity of cells that are farther away. It can not only keep the similar cells getting closer in low-dimensional space, but also can push the dissimilar cells away from each other. Clustering results show that SDCNMF is better than other comparative methods, and the gene markers we find are also consistent with previous studies.
    Keywords:  Clustering; Dimension reduction; Nonnegative matrix factorization; Single-cell RNA sequencing
    DOI:  https://doi.org/10.1007/s12539-021-00457-0
  2. Nucleic Acids Res. 2021 Jul 07. pii: gkab577. [Epub ahead of print]
    Single-cell nucleic acid profiling in droplets (SNAPD) enables high-throughput analysis of heterogeneous cell populations.
    Leland B Hyman, Clare R Christopher, Philip A Romero.
      Experimental methods that capture the individual properties of single cells are revealing the key role of cell-to-cell variability in countless biological processes. These single-cell methods are becoming increasingly important across the life sciences in fields such as immunology, regenerative medicine and cancer biology. In addition to high-dimensional transcriptomic techniques such as single-cell RNA sequencing, there is a need for fast, simple and high-throughput assays to enumerate cell samples based on RNA biomarkers. In this work, we present single-cell nucleic acid profiling in droplets (SNAPD) to analyze sets of transcriptional markers in tens of thousands of single mammalian cells. Individual cells are encapsulated in aqueous droplets on a microfluidic chip and the RNA markers in each cell are amplified. Molecular logic circuits then integrate these amplicons to categorize cells based on the transcriptional markers and produce a detectable fluorescence output. SNAPD is capable of analyzing over 100,000 cells per hour and can be used to quantify distinct cell types within heterogeneous populations, detect rare cells at frequencies down to 0.1% and enrich specific cell types using microfluidic sorting. SNAPD provides a simple, rapid, low cost and scalable approach to study complex phenotypes in heterogeneous cell populations.
    DOI:  https://doi.org/10.1093/nar/gkab577
  3. Nat Biotechnol. 2021 Jul 05.
    High-content single-cell combinatorial indexing.
    Ryan M Mulqueen, Dmitry Pokholok, Brendan L O'Connell, Casey A Thornton, Fan Zhang, Brian J O'Roak, Jason Link, Galip Gürkan Yardımcı, Rosalie C Sears, Frank J Steemers, Andrew C Adey.
      Single-cell combinatorial indexing (sci) with transposase-based library construction increases the throughput of single-cell genomics assays but produces sparse coverage in terms of usable reads per cell. We develop symmetrical strand sci ('s3'), a uracil-based adapter switching approach that improves the rate of conversion of source DNA into viable sequencing library fragments following tagmentation. We apply this chemistry to assay chromatin accessibility (s3-assay for transposase-accessible chromatin, s3-ATAC) in human cortical and mouse whole-brain tissues, with mouse datasets demonstrating a six- to 13-fold improvement in usable reads per cell compared with other available methods. Application of s3 to single-cell whole-genome sequencing (s3-WGS) and to whole-genome plus chromatin conformation (s3-GCC) yields 148- and 14.8-fold improvements, respectively, in usable reads per cell compared with sci-DNA-sequencing and sci-HiC. We show that s3-WGS and s3-GCC resolve subclonal genomic alterations in patient-derived pancreatic cancer cell lines. We expect that the s3 platform will be compatible with other transposase-based techniques, including sci-MET or CUT&Tag.
    DOI:  https://doi.org/10.1038/s41587-021-00962-z
  4. Adv Sci (Weinh). 2021 Jul 08. e2101229
    Multiplexing Methods for Simultaneous Large-Scale Transcriptomic Profiling of Samples at Single-Cell Resolution.
    Junyun Cheng, Jie Liao, Xin Shao, Xiaoyan Lu, Xiaohui Fan.
      Barcoding technology has greatly improved the throughput of cells and genes detected in single-cell RNA sequencing (scRNA-seq) studies. Recently, increasing studies have paid more attention to the use of this technology to increase the throughput of samples, as it has greatly reduced the processing time, technical batch effects, and library preparation costs, and lowered the per-sample cost. In this review, the various DNA-based barcoding methods for sample multiplexing are focused on, specifically, on the four major barcoding strategies. A detailed comparison of the barcoding methods is also presented, focusing on aspects such as sample/cell throughput and gene detection, and guidelines for choosing the most appropriate barcoding technique according to the personalized requirements are developed. Finally, the critical applications of sample multiplexing and technical challenges in combinatorial labeling, barcoding in vivo, and multimodal tagging at the spatially resolved resolution, as well as, the future prospects of multiplexed scRNA-seq, for example, prioritizing and predicting the severity of coronavirus disease 2019 (COVID-19) in patients of different gender and age are highlighted.
    Keywords:  DNA-based barcoding; sample multiplexing; single-cell RNA sequencing
    DOI:  https://doi.org/10.1002/advs.202101229
  5. Se Pu. 2021 Feb;39(2): 142-151
    [Methods and applications of single-cell proteomics analysis based on mass spectrometry].
    Shaojie Qin, Yu Bai, Huwei Liu.
      The cell is the smallest unit of living organisms. Although cells often assemble to serve a common function, intercellular heterogeneity often exists due to different genetic and environmental effects. Therefore, single-cell analysis has been regarded as an indispensable means to investigate cell heterogeneity, especially when researching cell differentiation, disease diagnosis, and therapy. As the chief factors influencing cell and biological activities, proteins have long been a major concern in biochemistry. However, due to their intrinsic lack of amplification characteristics, wide species variety, low abundance, and wide dynamic range, proteins are scarcely studied in single-cell research when compared with other biological macromolecules. Therefore, ultra-sensitive single-cell proteomics analysis methods are urgently required. Among all general measurement techniques, fluorescence methods possess high sensitivity and a capability of dynamic tracing, but low target numbers impose restrictions on their broad application in real "proteomic" studies. Similarly, electrochemical methods adapt to electrochemically active molecules, which miss the majority of proteins. Mass spectrometry (MS), as the core approach of proteomic studies, provides high-sensitivity and high-throughput analysis of proteins together with abundant structural information, which is unique in all the analytical instruments and has made great progress in single-cell proteomic research. Herein, the representative research methods for single-cell proteomics based on MS are reviewed. According to the different protein separation methods used prior to MS analysis, they are divided into three categories, including capillary electrophoresis (CE), liquid chromatography (LC), and direct infusion without the need for separation. First, CE has been widely used in the separation and analysis of complex biological samples owing to its low cost, high analysis speed, and high separation efficiency. Its unique feature is the extraction and transfer of contents from cellular or subcellular regions using capillaries smaller than a single cell size. This sampling method also offers less substrate interference and negligible oxidative damage to the cells. Nonetheless, single-cell analysis based on CE-MS mainly focuses on proteomic studies of large cells because of the considerable sample loss, interface instability, and reproducibility issues. Compared with CE, LC, especially nanoLC, is more widely used in single-cell proteomic research, which mainly depends on its good reproducibility, nanoliter injection volume, low flow rate, low sample loss, and good compatibility with mass spectrometry. In recent years, it has been increasingly applied in the study of large-volume embryos, germ cells, and even somatic cells. More than 1000 proteins have been identified in single HeLa cells using this state-of-the-art single-cell proteomics method. It is worth noting that the single-cell sampling volume based on LC gradually reduces to the nanoliter level, and that the sample loss can be reduced by integrating a series of proteomic sampling processes into small volumes, setting sealing conditions, and reducing washing steps. However, the adequacy of cell lysis, the completeness and efficiency of protein pretreatment, and the labeling of peptide segments are important factors affecting the number and types of protein identification. Compared with protein separation using CE or LC prior to MS analysis, the direct MS analysis, assisted by labelling and signal transformation, eliminates complicated sample pretreatment and simplifies the operation by reducing enzymatic hydrolysis and separation. It also renders higher resolution as well as multi-omics compatibility. So far, the number of proteins detected using this method is limited due to the complexity of the samples. In conclusion, the aspects of throughput, sensitivity, identified protein species, and applications are summarized for each method mentioned above, and the prospect of single-cell proteomic research based on MS in the future is also discussed.
    Keywords:  capillary electrophoresis (CE); liquid chromatography (LC); mass spectrometry (MS); microfluidic; proteomics; review; single cell
    DOI:  https://doi.org/10.3724/SP.J.1123.2020.08030
  6. ACS Nano. 2021 Jul 06.
    In Situ Single Cell Proteomics Reveals Circulating Tumor Cell Heterogeneity during Treatment.
    K Kamil Reza, Shuvashis Dey, Alain Wuethrich, Jing Wang, Andreas Behren, Fiach Antaw, Yuling Wang, Abu Ali Ibn Sina, Matt Trau.
      Cancer is a dynamic disease with heterogenic molecular signatures and constantly evolves during the course of the disease. Single cell proteomic analysis could offer a suitable pathway to monitor cancer cell heterogeneity and deliver critical information for the diagnosis, recurrence, and drug-resistant mechanisms in cancer. Current standard techniques for proteomic analysis such as ELISA, mass spectrometry, and Western blots are time-consuming, expensive, and often require fluorescence labeling that fails to provide accurate information about the multiple protein expression changes at the single cell level. Herein, we report a surface-enhanced Raman spectroscopy-based simple microfluidic device that enables the screening of single circulating tumor cells (CTC) in a dynamic state to precisely understand the heterogeneous expression of multiple protein biomarkers in response to therapy. It further enables identifying intercellular heterogeneous expression of CTC surface proteins which would be highly informative to identify the cancer cells surviving treatment and potentially responsible for drug resistance. Using a bead and cell line-based model system, we successfully detect single bead and single cell spectra when flowed through the device. Using SK-MEL-28 melanoma cells, we demonstrate that our system is capable of monitoring heterogeneous expressions of multiple surface protein markers (MCSP, MCAM, and LNGFR) before and during drug treatment. Integrating a label-free electrochemical system with the device, we also monitor the expression of an intracellular protein (here, BRAFV600E) under drug treatment. Finally, we perform a longitudinal study with 15 samples from five different melanoma patients who underwent therapy. We find that the average expression of receptor proteins in a patient fails to determine the therapy response particularly when the disease progresses. However, single CTC analysis with our device shows a high level of intercellular heterogeneity in the receptor expression profiles of patient-derived CTCs and identifies heterogeneity within CTCs. More importantly, we find that a fraction of CTCs still shows a high expression of these receptor proteins during and after therapy, indicating the presence of resistant CTCs which may evolve after a certain time and progress the disease. We believe this automated assay will have high clinical importance in disease diagnosis and monitoring treatment and will significantly advance the understanding of cancer heterogeneity on the single cell level.
    Keywords:  cancer diagnosis; cancer heterogeneity; circulating tumor cells; microfluidic immunoassay; single cell proteomics; surface-enhanced Raman spectroscopy; treatment monitoring
    DOI:  https://doi.org/10.1021/acsnano.0c10008
  7. Nat Protoc. 2021 Jul 07.
    Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor.
    Stephan Fischer, Megan Crow, Benjamin D Harris, Jesse Gillis.
      Single-cell RNA-sequencing data have significantly advanced the characterization of cell-type diversity and composition. However, cell-type definitions vary across data and analysis pipelines, raising concerns about cell-type validity and generalizability. With MetaNeighbor, we proposed an efficient and robust quantification of cell-type replicability that preserves dataset independence and is highly scalable compared to dataset integration. In this protocol, we show how MetaNeighbor can be used to characterize cell-type replicability by following a simple three-step procedure: gene filtering, neighbor voting and visualization. We show how these steps can be tailored to quantify cell-type replicability, determine gene sets that contribute to cell-type identity and pretrain a model on a reference taxonomy to rapidly assess newly generated data. The protocol is based on an open-source R package available from Bioconductor and GitHub, requires basic familiarity with Rstudio or the R command line and can typically be run in <5 min for millions of cells.
    DOI:  https://doi.org/10.1038/s41596-021-00575-5
  8. Cell Regen. 2021 Jul 06. 10(1): 23
    Single cells and transposable element heterogeneity in stem cells and development.
    Andrew P Hutchins.
      Recent innovations in single cell sequencing-based technologies are shining a light on the heterogeneity of cellular populations in unprecedented detail. However, several cellular aspects are currently underutilized in single cell studies. One aspect is the expression and activity of transposable elements (TEs). TEs are selfish sequences of DNA that can replicate, and have been wildly successful in colonizing genomes. However, most TEs are mutated, fragmentary and incapable of transposition, yet they are actively bound by multiple transcription factors, host complex patterns of chromatin modifications, and are expressed in mRNAs as part of the transcriptome in both normal and diseased states. The contribution of TEs to development and cellular function remains unclear, and the routine inclusion of TEs in single cell sequencing analyses will potentially lead to insight into stem cells, development and human disease.
    DOI:  https://doi.org/10.1186/s13619-021-00085-5
  9. Expert Opin Ther Targets. 2021 Jul 08.
    Tumor-associated neutrophils: Orchestrating cancer pathobiology and therapeutic resistance.
    Triet M Bui, Lenore K Yalom, Ronen Sumagin.
      INTRODUCTION: Neutrophils or polymorphonuclear cells (PMNs) account for a considerable portion of the tumor immune stroma. Emerging single-cell transcriptomic analyses have elucidated the striking cellular heterogeneity of PMNs during homeostasis and pathologic conditions and have established their diverse roles in cancer. PMNs have emerged as important players in cancer pathobiology and therapeutic resistance. Tumor associated neutrophil (TANs) effector functions influence tumor development and resistance or response to therapy.AREAS COVERED: This review focuses on PMN heterogeneity and functional diversity in the context of carcinogenesis. TANs, by activating diverse signaling pathways, contribute to cancer progression and resistance to therapies. Mechanisms by which TANs impact therapeutic resistance include alterations of the tumoral DNA damage response, angiogenesis, reactivation of cancer dormancy, enhancement of tumor cell proliferation/survival and immune evasion.
    EXPERT OPINION: With the emerging phenotypic and function heterogeneity of TANs, targeting specific TAN functions in developing tumors can lead to translatable therapeutic approaches and limit drug resistance. We propose that combining specific targeting of TAN activity with standard cancer therapy can help patients achieving a complete response and prevent cancer relapse.
    Keywords:  Cancer; Drug Resistance; Heterogeneity; Immunotherapy; Migration; Neutrophils; Tumor-Associated Neutrophils
    DOI:  https://doi.org/10.1080/14728222.2021.1954162
  10. Cell Biosci. 2021 Jul 03. 11(1): 121
    Applications and analytical tools of cell communication based on ligand-receptor interactions at single cell level.
    Fen Ma, Siwei Zhang, Lianhao Song, Bozhi Wang, Lanlan Wei, Fengmin Zhang.
      BACKGROUND: Cellular communication is an essential feature of multicellular organisms. Binding of ligands to their homologous receptors, which activate specific cell signaling pathways, is a basic type of cellular communication and intimately linked to many degeneration processes leading to diseases.MAIN BODY: This study reviewed the history of ligand-receptor and presents the databases which store ligand-receptor pairs. The recently applications and research tools of ligand-receptor interactions for cell communication at single cell level by using single cell RNA sequencing have been sorted out.
    CONCLUSION: The summary of the advantages and disadvantages of analysis tools will greatly help researchers analyze cell communication at the single cell level. Learning cell communication based on ligand-receptor interactions by single cell RNA sequencing gives way to developing new target drugs and personalizing treatment.
    Keywords:  Cell communication; Ligand-receptor interactions; Single cell RNA sequencing; Target therapy; Tumor microenvironment
    DOI:  https://doi.org/10.1186/s13578-021-00635-z
  11. BMC Bioinformatics. 2021 Jul 08. 22(1): 364
    Single-cell classification using graph convolutional networks.
    Tianyu Wang, Jun Bai, Sheida Nabavi.
      BACKGROUND: Analyzing single-cell RNA sequencing (scRNAseq) data plays an important role in understanding the intrinsic and extrinsic cellular processes in biological and biomedical research. One significant effort in this area is the identification of cell types. With the availability of a huge amount of single cell sequencing data and discovering more and more cell types, classifying cells into known cell types has become a priority nowadays. Several methods have been introduced to classify cells utilizing gene expression data. However, incorporating biological gene interaction networks has been proved valuable in cell classification procedures.RESULTS: In this study, we propose a multimodal end-to-end deep learning model, named sigGCN, for cell classification that combines a graph convolutional network (GCN) and a neural network to exploit gene interaction networks. We used standard classification metrics to evaluate the performance of the proposed method on the within-dataset classification and the cross-dataset classification. We compared the performance of the proposed method with those of the existing cell classification tools and traditional machine learning classification methods.
    CONCLUSIONS: Results indicate that the proposed method outperforms other commonly used methods in terms of classification accuracy and F1 scores. This study shows that the integration of prior knowledge about gene interactions with gene expressions using GCN methodologies can extract effective features improving the performance of cell classification.
    Keywords:  Cell classification; Convolutional neural network; Deep learning; Graph convolutional neural network; Single cell RNA sequencing
    DOI:  https://doi.org/10.1186/s12859-021-04278-2
  12. Handb Clin Neurol. 2021 ;pii: B978-0-12-820107-7.00008-2. [Epub ahead of print]180 125-148
    Perinatal stress and epigenetics.
    Moshe Szyf.
      Animal and humans exposed to stress early in life are more likely to suffer from long-term behavioral, mental health, metabolic, immune, and cardiovascular health consequences. The hypothalamus plays a nodal role in programming, controlling, and regulating stress responses throughout the life course. Epigenetic reprogramming in the hippocampus and the hypothalamus play an important role in adapting genome function to experiences and exposures during the perinatal and early life periods and setting up stable phenotypic outcomes. Epigenetic programming during development enables one genome to express multiple cell type identities. The most proximal epigenetic mark to DNA is a covalent modification of the DNA itself by enzymatic addition of methyl moieties. Cell-type-specific DNA methylation profiles are generated during gestational development and define cell and tissue specific phenotypes. Programming of neuronal phenotypes and sex differences in the hypothalamus is achieved by developmentally timed rearrangement of DNA methylation profiles. Similarly, other stations in the life trajectory such as puberty and aging involve predictable and scheduled reorganization of DNA methylation profiles. DNA methylation and other epigenetic marks are critical for maintaining cell-type identity in the brain, across the body, and throughout life. Data that have emerged in the last 15 years suggest that like its role in defining cell-specific phenotype during development, DNA methylation might be involved in defining experiential identities, programming similar genes to perform differently in response to diverse experiential histories. Early life stress impact on lifelong phenotypes is proposed to be mediated by DNA methylation and other epigenetic marks. Epigenetic marks, as opposed to genetic mutations, are reversible by either pharmacological or behavioral strategies and therefore offer the potential for reversing or preventing disease including behavioral and mental health disorders. This chapter discusses data testing the hypothesis that DNA methylation modulations of the HPA axis mediate the impact of early life stress on lifelong behavioral and physical phenotypes.
    Keywords:  DNA methylation; Early life stress; Epigenetics; Glucocorticoid receptor; HPA axis; Hippocampus; Hypothalamus; Maternal care; Socioeconomic status; Stress response
    DOI:  https://doi.org/10.1016/B978-0-12-820107-7.00008-2
  13. Nat Commun. 2021 07 05. 12(1): 4110
    Chromatin states shaped by an epigenetic code confer regenerative potential to the mouse liver.
    Chi Zhang, Filippo Macchi, Elena Magnani, Kirsten C Sadler.
      We hypothesized that the highly controlled pattern of gene expression that is essential for liver regeneration is encoded by an epigenetic code set in quiescent hepatocytes. Here we report that epigenetic and transcriptomic profiling of quiescent and regenerating mouse livers define chromatin states that dictate gene expression and transposon repression. We integrate ATACseq and DNA methylation profiling with ChIPseq for the histone marks H3K4me3, H3K27me3 and H3K9me3 and the histone variant H2AZ to identify 6 chromatin states with distinct functional characteristics. We show that genes involved in proliferation reside in active states, but are marked with H3K27me3 and silenced in quiescent livers. We find that during regeneration, H3K27me3 is depleted from their promoters, facilitating their dynamic expression. These findings demonstrate that hepatic chromatin states in quiescent livers predict gene expression and that pro-regenerative genes are maintained in active chromatin states, but are restrained by H3K27me3, permitting a rapid and synchronized response during regeneration.
    DOI:  https://doi.org/10.1038/s41467-021-24466-1
  14. JCI Insight. 2021 Jul 06. pii: 150861. [Epub ahead of print]
    Key molecular alterations in endothelial cells in human glioblastoma uncovered through single-cell RNA sequencing.
    Yuan Xie, Liqun He, Roberta Lugano, Yanyu Zhang, Haiyan Cao, Qiyuan He, Min Chao, Boxuan Liu, Qingze Cao, Jianhao Wang, Yang Jiao, Yaqin Hu, Liying Han, Yong Zhang, Hua Huang, Lene Uhrbom, Christer Betsholtz, Liang Wang, Anna Dimberg, Lei Zhang.
      Glioblastoma is the most aggressive type of brain tumor with poor therapeutic response and prognosis. Passage of systemically delivered pharmacological agents into the brain is largely blocked by the blood-brain-barrier (BBB), an organotypic specialization of brain endothelial cells (EC). Tumor vessels in GBM are abnormal and more permeable, but the heterogeneity of BBB breakdown in different parts of the tumor vasculature and at the tumor's invasive front is largely unknown. Here, through single-cell RNA sequencing (scRNA-seq) of freshly isolated ECs from human glioblastoma and paired tumor peripheral tissues, we have constructed a molecular atlas of human brain ECs providing unprecedented molecular insight into the heterogeneity of the human BBB and its molecular alteration in glioblastoma. We identified 5 distinct EC phenotypes representing different states of EC activation and BBB impairment, and associated with different anatomical locations within and around the tumor. This unique data resource provides key information for designing rational therapeutic regimens and optimizing drug delivery.
    Keywords:  Brain cancer; Endothelial cells; Vascular Biology
    DOI:  https://doi.org/10.1172/jci.insight.150861
  15. Curr Genomics. 2021 Feb;22(2): 79-87
    DNA Methylation Markers in Lung Cancer.
    Yoonki Hong, Woo Jin Kim.
      Lung cancer is the most common cancer and the leading cause of cancer-related morbidity and mortality worldwide. As early symptoms of lung cancer are minimal and non-specific, many patients are diagnosed at an advanced stage. Despite a concerted effort to diagnose lung cancer early, no biomarkers that can be used for lung cancer screening and prognosis prediction have been established so far. As global DNA demethylation and gene-specific promoter DNA methylation are present in lung cancer, DNA methylation biomarkers have become a major area of research as potential alternative diagnostic methods to detect lung cancer at an early stage. This review summarizes the emerging DNA methylation changes in lung cancer tumorigenesis, focusing on biomarkers for early detection and their potential clinical applications in lung cancer.
    Keywords:  DNA methylation; Non-small-cell lung cancer; biomarker; epigenetic; hypomethylation; tumorigenesis
    DOI:  https://doi.org/10.2174/1389202921999201013164110
  16. Mol Syst Biol. 2021 Jul;17(7): e9653
    Single-cell imaging of genome organization and dynamics.
    Liangqi Xie, Zhe Liu.
      Probing the architecture, mechanism, and dynamics of genome folding is fundamental to our understanding of genome function in homeostasis and disease. Most chromosome conformation capture studies dissect the genome architecture with population- and time-averaged snapshots and thus have limited capabilities to reveal 3D nuclear organization and dynamics at the single-cell level. Here, we discuss emerging imaging techniques ranging from light microscopy to electron microscopy that enable investigation of genome folding and dynamics at high spatial and temporal resolution. Results from these studies complement genomic data, unveiling principles underlying the spatial arrangement of the genome and its potential functional links to diverse biological activities in the nucleus.
    Keywords:  chromatin dynamics; genome organization; imaging; single cell; super-resolution
    DOI:  https://doi.org/10.15252/msb.20209653
  17. J Cancer. 2021 ;12(16): 5046-5052
    Hypothesis: Sam68 and Pygo2 mediate cell type-specific effects of the modulation of CBP-Wnt and p300-Wnt activities in Colorectal Cancer Cells.
    Michael Bordonaro.
      The preventive activity of dietary fiber against colorectal cancer (CRC) may be in part mediated by the fermentation product of fiber, butyrate, a histone deacetylase inhibitor (HDACi) that induces CRC cell growth arrest and apoptosis. This action of butyrate, and other HDACis, is in part due to the hyperactivation of the deregulated Wnt activity found in the relevant CRC cell lines. The histone acetylases CBP and p300 interact with beta-catenin; and the relative levels of CBP-Wnt vs. p300-Wnt activity influences CRC cell physiology. It has previously been observed that there are cell type-specific differences in how cotreatment with butyrate and ICG-001, an agent that blocks CBP-Wnt activity allowing for p300-Wnt activity, affects CRC cell physiology. These differences may have clinical significance in dealing with treatment of CRC patients with ICG-001-like agents. Sam68 is a factor differentially expressed in cancer cells, with higher expression in cancer cell lines that have cancer stem cell (CSC)-like properties. Sam68 expression sensitizes cancer cells to ICG-001 treatment, as ICG-001 enhances nuclear localization of Sam68, where binding between Sam68 and CBP diminishes CBP-beta-catenin binding and thus CBP-Wnt activity. Pygo2 is a chromatin effector involved with Wnt signaling that is differentially acetylated by CBP and p300; thus CBP-mediated acetylation localized Pygo2 to the nucleus where it functions in transcriptional activation, while p300-mediated acetylation localizes Pygo2 to the cytoplasm. This paper proposes the hypothesis that Sam68 and Pygo2 are responsible for cell type-specific response of CRC cell lines cotreated with ICG-001 and butyrate as well as other HDACis. Further, experiments are proposed to evaluate this hypothesis and consider possible expected results that could be obtained from such studies.
    Keywords:  CBP; ICG-001; Sam68; Wnt signaling; butyrate; colorectal cancer; p300
    DOI:  https://doi.org/10.7150/jca.59726
  18. Front Oncol. 2021 ;11 705903
    Remodeling the Epigenetic Landscape of Cancer-Application Potential of Flavonoids in the Prevention and Treatment of Cancer.
    Weiyi Jiang, Tingting Xia, Cun Liu, Jie Li, Wenfeng Zhang, Changgang Sun.
      Epigenetics, including DNA methylation, histone modification, and noncoding RNA regulation, are physiological regulatory changes that affect gene expression without modifying the DNA sequence. Although epigenetic disorders are considered a sign of cell carcinogenesis and malignant events that affect tumor progression and drug resistance, in view of the reversible nature of epigenetic modifications, clinicians believe that associated mechanisms can be a key target for cancer prevention and treatment. In contrast, epidemiological and preclinical studies indicated that the epigenome is constantly reprogrammed by intake of natural organic compounds and the environment, suggesting the possibility of utilizing natural compounds to influence epigenetics in cancer therapy. Flavonoids, although not synthesized in the human body, can be consumed daily and are common in medicinal plants, vegetables, fruits, and tea. Recently, numerous reports provided evidence for the regulation of cancer epigenetics by flavonoids. Considering their origin in natural and food sources, few side effects, and remarkable biological activity, the epigenetic antitumor effects of flavonoids warrant further investigation. In this article, we summarized and analyzed the multi-dimensional epigenetic effects of all 6 subtypes of flavonoids (including flavonols, flavones, isoflavones, flavanones, flavanols, and anthocyanidin) in different cancer types. Additionally, our report also provides new insights and a promising direction for future research and development of flavonoids in tumor prevention and treatment via epigenetic modification, in order to realize their potential as cancer therapeutic agents.
    Keywords:  DNMT; HDAC; cancer; epigenetic; epigenome; flavonoids; natural compounds; phytochemicals
    DOI:  https://doi.org/10.3389/fonc.2021.705903
  19. Cell Biochem Funct. 2021 Jul 05.
    Long non-coding RNAs and microorganism-associated cancers.
    Reza Ranjbar, Mojtaba Behjatfar, Ali Teimouri, Arad Aghaie Fard, Mahmood Maniati, Mortaza Taheri-Anganeh.
      Cancerous cells are abnormal cells characterized by aberrant growth and proliferation, which can involve various types of cells and tissues. Through numerous signalling pathways, many mechanisms are involved in cells that keep them normal. These signalling pathways are tightly set by different proteins whose expression is regulated by a large number of factors. In other words, when a regulating factor does not act properly or undergoes a change in its function or expression, the result will be that the subordinate gene and subsequently the related protein will show deranged expression and activity. This leads to disordered signalling pathways which bring about uncontrolled proliferation in cells. One of the most significant factors in adjusting the expression of genes is noncoding RNAs. It should be noted that all underlying causes initiating malignancy try to alter the main regulatory factors in cellular processes and gene expression and direct the cell to an unregulated state. Microorganisms have been identified as one of the important elements to direct normal cells to abnormality. That is, they probably agitate the malignant traits through manipulating significant factors such as ncRNAs in given cells using their own or host-related factors. The present study is aimed at examining how the long noncoding RNAs are involved in microorganism-mediated cancers.
    Keywords:  cancer; epigenetics; long non-coding RNA; microorganism; oncogene
    DOI:  https://doi.org/10.1002/cbf.3657
  20. Nucleic Acids Res. 2021 Jul 06. pii: gkab552. [Epub ahead of print]
    Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data.
    Eric R Reed, Stefano Monti.
      As high-throughput genomics assays become more efficient and cost effective, their utilization has become standard in large-scale biomedical projects. These studies are often explorative, in that relationships between samples are not explicitly defined a priori, but rather emerge from data-driven discovery and annotation of molecular subtypes, thereby informing hypotheses and independent evaluation. Here, we present K2Taxonomer, a novel unsupervised recursive partitioning algorithm and associated R package that utilize ensemble learning to identify robust subgroups in a 'taxonomy-like' structure. K2Taxonomer was devised to accommodate different data paradigms, and is suitable for the analysis of both bulk and single-cell transcriptomics, and other '-omics', data. For each of these data types, we demonstrate the power of K2Taxonomer to discover known relationships in both simulated and human tissue data. We conclude with a practical application on breast cancer tumor infiltrating lymphocyte (TIL) single-cell profiles, in which we identified co-expression of translational machinery genes as a dominant transcriptional program shared by T cells subtypes, associated with better prognosis in breast cancer tissue bulk expression data.
    DOI:  https://doi.org/10.1093/nar/gkab552
  21. Anticancer Res. 2021 Jul;41(7): 3409-3417
    HOXB5 Confers Tamoxifen Resistance in Breast Cancer Cells and Promotes Tumor Aggression and Progression.
    Clara Yuri Kim, Yu Cheon Kim, Ji Hoon Oh, Myoung Hee Kim.
      BACKGROUND/AIM: ER-positive breast cancer patients commonly undergo endocrine therapy with drugs such as tamoxifen. Despite tamoxifen being a highly effective drug, long-term treatment results in resistance in one-third of the patients. Although many explanations for the development of tamoxifen resistance have been put forward, a clearly defined underlying mechanism is still lacking.MATERIALS AND METHODS: The expression level of HOXB5 was evaluated between MCF7 breast cancer cells and tamoxifen-resistant MCF7 (TAMR) cells by RT-PCR. Then, the effect of HOXB5 on invasion and migration abilities as well as on cancer stemness were investigated through 3D culture and spheroid formation assay.
    RESULTS: In this study, we provide evidence that HOXB5 is up-regulated in TAMR cells. EGFR is concurrently overexpressed, and the EGFR signaling cascade is activated, resulting in migratory and invasive phenotypes in TAMR cells compared to MCF7 cells. However, HOXB5 knockdown in TAMR cells resulted in the de-activation of the EGFR signaling pathway, less aggressive phenotypes and restoration of sensitivity to tamoxifen treatment. More interestingly, TAMR cells expressed higher levels of stem cell markers, and as a result, their enhanced stemness allowed for a better formation of spheroids than MCF7 cells. When HOXB5 was overexpressed in MCF7 cells, they were able to form a larger number of spheroids as in TAMR cells.
    CONCLUSION: HOXB5 is one of the key factors involved in tumor aggression and progression in tamoxifen-resistant breast cancer cells.
    Keywords:  Breast cancer; EGFR; HOXB5; cancer stem cell; endocrine-resistance
    DOI:  https://doi.org/10.21873/anticanres.15128
  22. Cell Death Discov. 2021 Jun 19. 7(1): 164
    The proteolytic landscape of cells exposed to non-lethal stresses is shaped by executioner caspases.
    María Del Carmen Conde-Rubio, Roman Mylonas, Christian Widmann.
      Cells are in constant adaptation to environmental changes to insure their proper functioning. When exposed to stresses, cells activate specific pathways to elicit adaptive modifications. Those changes can be mediated by selective modulation of gene and protein expression as well as by post-translational modifications, such as phosphorylation and proteolytic processing. Protein cleavage, as a controlled and limited post-translational modification, is involved in diverse physiological processes such as the maintenance of protein homeostasis, activation of repair pathways, apoptosis and the regulation of proliferation. Here we assessed by quantitative proteomics the proteolytic landscape in two cell lines subjected to low cisplatin concentrations used as a mild non-lethal stress paradigm. This landscape was compared to the one obtained in the same cells stimulated with cisplatin concentrations inducing apoptosis. These analyses were performed in wild-type cells and in cells lacking the two main executioner caspases: caspase-3 and caspase-7. Ninety-two proteins were found to be cleaved at one or a few sites (discrete cleavage) in low stress conditions compared to four hundred and fifty-three in apoptotic cells. Many of the cleaved proteins in stressed cells were also found to be cleaved in apoptotic conditions. As expected, ~90% of the cleavage events were dependent on caspase-3/caspase-7 in apoptotic cells. Strikingly, upon exposure to non-lethal stresses, no discrete cleavage was detected in cells lacking caspase-3 and caspase-7. This indicates that the proteolytic landscape in stressed viable cells fully depends on the activity of executioner caspases. These results suggest that the so-called executioner caspases fulfill important stress adaptive responses distinct from their role in apoptosis. Mass spectrometry data are available via ProteomeXchange with identifier PXD023488.
    DOI:  https://doi.org/10.1038/s41420-021-00539-4
  23. Nat Commun. 2021 07 05. 12(1): 4118
    Cell migration guided by long-lived spatial memory.
    Joseph d'Alessandro, Alex Barbier-Chebbah, Victor Cellerin, Olivier Benichou, René Marc Mège, Raphaël Voituriez, Benoît Ladoux.
      Living cells actively migrate in their environment to perform key biological functions-from unicellular organisms looking for food to single cells such as fibroblasts, leukocytes or cancer cells that can shape, patrol or invade tissues. Cell migration results from complex intracellular processes that enable cell self-propulsion, and has been shown to also integrate various chemical or physical extracellular signals. While it is established that cells can modify their environment by depositing biochemical signals or mechanically remodelling the extracellular matrix, the impact of such self-induced environmental perturbations on cell trajectories at various scales remains unexplored. Here, we show that cells can retrieve their path: by confining motile cells on 1D and 2D micropatterned surfaces, we demonstrate that they leave long-lived physicochemical footprints along their way, which determine their future path. On this basis, we argue that cell trajectories belong to the general class of self-interacting random walks, and show that self-interactions can rule large scale exploration by inducing long-lived ageing, subdiffusion and anomalous first-passage statistics. Altogether, our joint experimental and theoretical approach points to a generic coupling between motile cells and their environment, which endows cells with a spatial memory of their path and can dramatically change their space exploration.
    DOI:  https://doi.org/10.1038/s41467-021-24249-8
  24. Front Genet. 2021 ;12 680633
    Lysine Demethylases: Promising Drug Targets in Melanoma and Other Cancers.
    Gaya Punnia-Moorthy, Peter Hersey, Abdullah Al Emran, Jessamy Tiffen.
      Epigenetic dysregulation has been implicated in a variety of pathological processes including carcinogenesis. A major group of enzymes that influence epigenetic modifications are lysine demethylases (KDMs) also known as "erasers" which remove methyl groups on lysine (K) amino acids of histones. Numerous studies have implicated aberrant lysine demethylase activity in a variety of cancers, including melanoma. This review will focus on the structure, classification and functions of KDMs in normal biology and the current knowledge of how KDMs are deregulated in cancer pathogenesis, emphasizing our interest in melanoma. We highlight the current knowledge gaps of KDMs in melanoma pathobiology and describe opportunities to increases our understanding of their importance in this disease. We summarize the progress of several pre-clinical compounds that inhibit KDMs and represent promising candidates for further investigation in oncology.
    Keywords:  cancer; epigenetics; histones; lysine demethylases; melanoma; small molecule inhibitors
    DOI:  https://doi.org/10.3389/fgene.2021.680633
  25. BMC Bioinformatics. 2021 Jul 03. 22(1): 360
    PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity.
    Marilisa Montemurro, Elena Grassi, Carmelo Gabriele Pizzino, Andrea Bertotti, Elisa Ficarra, Gianvito Urgese.
      BACKGROUND: Tumors are composed by a number of cancer cell subpopulations (subclones), characterized by a distinguishable set of mutations. This phenomenon, known as intra-tumor heterogeneity (ITH), may be studied using Copy Number Aberrations (CNAs). Nowadays ITH can be assessed at the highest possible resolution using single-cell DNA (scDNA) sequencing technology. Additionally, single-cell CNA (scCNA) profiles from multiple samples of the same tumor can in principle be exploited to study the spatial distribution of subclones within a tumor mass. However, since the technology required to generate large scDNA sequencing datasets is relatively recent, dedicated analytical approaches are still lacking.RESULTS: We present PhyliCS, the first tool which exploits scCNA data from multiple samples from the same tumor to estimate whether the different clones of a tumor are well mixed or spatially separated. Starting from the CNA data produced with third party instruments, it computes a score, the Spatial Heterogeneity score, aimed at distinguishing spatially intermixed cell populations from spatially segregated ones. Additionally, it provides functionalities to facilitate scDNA analysis, such as feature selection and dimensionality reduction methods, visualization tools and a flexible clustering module.
    CONCLUSIONS: PhyliCS represents a valuable instrument to explore the extent of spatial heterogeneity in multi-regional tumour sampling, exploiting the potential of scCNA data.
    Keywords:  Algorithms; Cancer evolution; Clones; DNA; Intra-tumor heterogeneity; Single-cell sequencing
    DOI:  https://doi.org/10.1186/s12859-021-04277-3
  26. OMICS. 2021 Jul 06.
    Novel Post-Translational Modifications and Molecular Substrates in Glioma Identified by Bioinformatics.
    Devasahayam Arokia Balaya Rex, Sumaithangi Thattai Arun Kumar, Akhila Balakrishna Rai, Chinmaya Narayana Kotimoole, Prashant Kumar Modi, Thottethodi Subrahmanya Keshava Prasad.
      Glioma is the most common type of brain cancer that originates from the glial cells. It constitutes about one-third of all brain cancers. Recently, transcriptomics, proteomics, and multiomics approaches have been harnessed to discover potential biomarkers and therapeutic targets in glioma. Moreover, post-translational modifications (PTMs) of proteins play a major role in cell biology and function and offer new avenues of research in cancer. Using unbiased multi-PTM bioinformatics analyses of two proteomic datasets of glioma available in the public domain, we identified 866 proteins with common PTMs from both studies. Out of these 866 proteins, 19 proteins were identified with the common PTMs, with the same site modifications pertaining to glioma. Importantly, the identified PTMs belonged to proteins involved in integrin PI3K/Akt/mTOR, JAK/STAT, and Ras/Raf/MAPK pathways. These pathways are essential for cell proliferation in tumor cells and thus involved in glioma progression. Taken together, these findings call for validation in larger datasets in glioma and brain cancers and with an eye to future drug discovery and diagnostic innovation. Bioinformatics-guided discovery of novel PTMs from the publicly available proteomic data can offer new avenues for innovation in cancer research.
    Keywords:  diagnostics; drug targets; glioblastoma; mass spectrometry; post-translational modification; proteomics
    DOI:  https://doi.org/10.1089/omi.2021.0050
  27. Annu Rev Cell Dev Biol. 2021 Jul 06.
    Spatial Organization of Chromatin: Emergence of Chromatin Structure During Development.
    Rajarshi P Ghosh, Barbara J Meyer.
      Nuclei are central hubs for information processing in eukaryotic cells. The need to fit large genomes into small nuclei imposes severe restrictions on genome organization and the mechanisms that drive genome-wide regulatory processes. How a disordered polymer such as chromatin, which has vast heterogeneity in its DNA and histone modification profiles, folds into discernibly consistent patterns is a fundamental question in biology. Outstanding questions include how genomes are spatially and temporally organized to regulate cellular processes with high precision and whether genome organization is causally linked to transcription regulation. The advent of next-generation sequencing, super-resolution imaging, multiplexed fluorescent in situ hybridization, and single-molecule imaging in individual living cells has caused a resurgence in efforts to understand the spatiotemporal organization of the genome. In this review, we discuss structural and mechanistic properties of genome organization at different length scales and examine changes in higher-order chromatin organization during important developmental transitions. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-cellbio-032321-035734
  28. Cancer Cell Int. 2021 Jul 05. 21(1): 349
    Anti-cancer properties of quercetin in osteosarcoma.
    Parisa Maleki Dana, Fatemeh Sadoughi, Zatollah Asemi, Bahman Yousefi.
      Osteosarcoma is a primary bone tumor. Although it is a rare disease in general, it is the most common primary bone tumor among children. Despite the significant advances made in the field of osteosarcoma treatment, the outcomes of this disease are still unfavorable. Besides, there is still no targeted therapy for osteosarcoma that can be used in clinical settings. Quercetin is a member of the phytochemical family which is used for different diseases including cardiovascular diseases, diabetes, and cancer. Its anti-cancer effects are examined in many types of cancer including breast, colon, lung, prostate, and pancreatic cancers and have shown promising results. Herein, the studies dealing with the antitumor roles of quercetin in osteosarcoma are reviewed in this article. We take a look into quercetin's ability to affect proliferation, apoptosis, invasion, and chemo-resistance of the osteosarcoma cells through regulating protein expression and signaling pathways.
    Keywords:  Apoptosis; Cell viability; Osteosarcoma; Proliferation; Quercetin
    DOI:  https://doi.org/10.1186/s12935-021-02067-8
  29. J Cell Physiol. 2021 Jul 08.
    Regulation of autophagy by protein methylation and acetylation in cancer.
    Minsol Jeon, Jisu Park, Eunbi Yang, Hee-Ji Baek, Hyunkyung Kim.
      Autophagy is a highly conserved mechanism responsible for cellular homeostasis and integrity in a variety of physiological conditions. Materials targeted for degradation are directed to autophagosomes and autolysosomes, where they are broken down into their base components. Aberrant regulation of autophagy is significantly associated with various cancers and neurodegenerative diseases. Recently, accumulating evidence has revealed that the coordinated regulation of histone and non-histone protein modification is associated with autophagy. In this review, we highlight the recent progress that has been made in elucidating the molecular basis of protein methylation and acetylation associated with autophagy at the transcriptional and posttranslational levels. Furthermore, we discuss the importance of describing causality between protein methylation/acetylation and autophagy regulation as compelling therapeutic opportunities in cancer pathogenesis and progression.
    Keywords:  autophagy; cancer; protein acetylation; protein methylation
    DOI:  https://doi.org/10.1002/jcp.30502
  30. Algorithms Mol Biol. 2021 Jul 06. 16(1): 14
    Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors.
    Leah L Weber, Mohammed El-Kebir.
      BACKGROUND: Cancer arises from an evolutionary process where somatic mutations give rise to clonal expansions. Reconstructing this evolutionary process is useful for treatment decision-making as well as understanding evolutionary patterns across patients and cancer types. In particular, classifying a tumor's evolutionary process as either linear or branched and understanding what cancer types and which patients have each of these trajectories could provide useful insights for both clinicians and researchers. While comprehensive cancer phylogeny inference from single-cell DNA sequencing data is challenging due to limitations with current sequencing technology and the complexity of the resulting problem, current data might provide sufficient signal to accurately classify a tumor's evolutionary history as either linear or branched.RESULTS: We introduce the Linear Perfect Phylogeny Flipping (LPPF) problem as a means of testing two alternative hypotheses for the pattern of evolution, which we prove to be NP-hard. We develop Phyolin, which uses constraint programming to solve the LPPF problem. Through both in silico experiments and real data application, we demonstrate the performance of our method, outperforming a competing machine learning approach.
    CONCLUSION: Phyolin is an accurate, easy to use and fast method for classifying an evolutionary trajectory as linear or branched given a tumor's single-cell DNA sequencing data.
    Keywords:  Constraint programming; Intra-tumor heterogeneity; Perfect phylogeny; Single-cell DNA sequencing
    DOI:  https://doi.org/10.1186/s13015-021-00194-5
  31. Chimia (Aarau). 2021 Jun 30. 75(6): 484-488
    Applying Peptide and Protein Synthesis to Study Post-translational Modifications in Epigenetics and Beyond.
    Beat Fierz.
      Epigenetics research focuses on the study of heritable gene regulatory mechanisms that do not involve changes of the DNA sequence. Such mechanisms include post-translational modifications of histone proteins that organize the genome in the nucleus into a nucleoprotein complex called chromatin, and which are of key importance in development and disease. Chemical biology tools as developed by my group, in particular synthetic peptide and protein chemistry, have been critical to elucidate epigenetic signaling mechanisms. As outlined below, they allow the reconstitution of chromatin carrying defined modifications and thus the elucidation of detailed molecular mechanisms.
    DOI:  https://doi.org/10.2533/chimia.2021.484
  32. Clin Epigenetics. 2021 Jul 08. 13(1): 138
    The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes.
    Tasnim H Beacon, Geneviève P Delcuve, Camila López, Gino Nardocci, Igor Kovalchuk, Andre J van Wijnen, James R Davie.
      Transcriptionally active chromatin is marked by tri-methylation of histone H3 at lysine 4 (H3K4me3) located after first exons and around transcription start sites. This epigenetic mark is typically restricted to narrow regions at the 5`end of the gene body, though a small subset of genes have a broad H3K4me3 domain which extensively covers the coding region. Although most studies focus on the H3K4me3 mark, the broad H3K4me3 domain is associated with a plethora of histone modifications (e.g., H3 acetylated at K27) and is therein termed broad epigenetic domain. Genes marked with the broad epigenetic domain are involved in cell identity and essential cell functions and have clinical potential as biomarkers for patient stratification. Reducing expression of genes with the broad epigenetic domain may increase the metastatic potential of cancer cells. Enhancers and super-enhancers interact with the broad epigenetic domain marked genes forming a hub of interactions involving nucleosome-depleted regions. Together, the regulatory elements coalesce with transcription factors, chromatin modifying/remodeling enzymes, coactivators, and the Mediator and/or Integrator complex into a transcription factory which may be analogous to a liquid-liquid phase-separated condensate. The broad epigenetic domain has a dynamic chromatin structure which supports frequent transcription bursts. In this review, we present the current knowledge of broad epigenetic domains.
    Keywords:  Broad H3K4me3 domains; Cell identity genes; Enhancers; Epigenetics; Histone modifications; Tumor suppressor genes
    DOI:  https://doi.org/10.1186/s13148-021-01126-1
  33. Cell Death Discov. 2021 Jun 29. 7(1): 152
    OASIS/CREB3L1 is a factor that responds to nuclear envelope stress.
    Yasunao Kamikawa, Atsushi Saito, Koji Matsuhisa, Masayuki Kaneko, Rie Asada, Yasunori Horikoshi, Satoshi Tashiro, Kazunori Imaizumi.
      The nuclear envelope (NE) safeguards the genome and is pivotal for regulating genome activity as the structural scaffold of higher-order chromatin organization. NE had been thought as the stable during the interphase of cell cycle. However, recent studies have revealed that the NE can be damaged by various stresses such as mechanical stress and cellular senescence. These types of stresses are called NE stress. It has been proposed that NE stress is closely related to cellular dysfunctions such as genome instability and cell death. Here, we found that an endoplasmic reticulum (ER)-resident transmembrane transcription factor, OASIS, accumulates at damaged NE. Notably, the major components of nuclear lamina, Lamin proteins were depleted at the NE where OASIS accumulates. We previously demonstrated that OASIS is cleaved at the membrane domain in response to ER stress. In contrast, OASIS accumulates as the full-length form to damaged NE in response to NE stress. The accumulation to damaged NE is specific for OASIS among OASIS family members. Intriguingly, OASIS colocalizes with the components of linker of nucleoskeleton and cytoskeleton complexes, SUN2 and Nesprin-2 at the damaged NE. OASIS partially colocalizes with BAF, LEM domain proteins, and a component of ESCRT III, which are involved in the repair of ruptured NE. Furthermore, OASIS suppresses DNA damage induced by NE stress and restores nuclear deformation under NE stress conditions. Our findings reveal a novel NE stress response pathway mediated by OASIS.
    DOI:  https://doi.org/10.1038/s41420-021-00540-x
  34. Mikrochim Acta. 2021 Jul 06. 188(8): 242
    An easy-to-operate method for single-cell isolation and retrieval using a microfluidic static droplet array.
    Lin Ding, Payar Radfar, Meysam Rezaei, Majid Ebrahimi Warkiani.
      In-depth study of cellular heterogeneity of rare cells (e.g. circulating tumour cells (CTCs) and circulating foetal cells (CFCs)) is greatly needed in disease management but has never been completely explored due to the current technological limitations. We have developed a retrieval method for single-cell detection using a static droplet array (SDA) device through liquid segmentation with almost no sample loss. We explored the potential of using SDA for low sample input and retrieving the cells of interest using everyday laboratory equipment for downstream molecular analysis. This single-cell isolation and retrieval method is low-cost, rapid and provides a solution to the remaining challenge for single rare cell detection. The entire process takes less than 15 min, is easy to fabricate and allows for on-chip analysis of cells in nanolitre droplets and retrieval of desired droplets. To validate the applicability of our device and method, we mimicked detection of single CTCs by isolating and retrieving single cells and perform real-time PCR on their mRNA contents.
    Keywords:  Cancer; Cellular heterogeneity; Circulating tumour cells; Droplet microfluidics; Microfluidic system; Single cell detection
    DOI:  https://doi.org/10.1007/s00604-021-04897-9
  35. Front Oncol. 2021 ;11 649093
    Development and Validation of Epigenetic Modification-Related Signals for the Diagnosis and Prognosis of Hepatocellular Carcinoma.
    Maoqing Lu, Sheng Qiu, Xianyao Jiang, Diguang Wen, Ronggui Zhang, Zuojin Liu.
      Background: Increasing evidence has indicated that abnormal epigenetic factors such as RNA m6A modification, histone modification, DNA methylation, RNA binding proteins and transcription factors are correlated with hepatocarcinogenesis. However, it is unknown how epigenetic modification-associated genes contribute to the occurrence and clinical outcome of hepatocellular carcinoma (HCC). Thus, we constructed the epigenetic modification-associated models that may enhance the diagnosis and prognosis of HCC.Methods: In this study, we focused on the clinical value of epigenetic modification-associated genes for HCC. Our gene expression data were collected from TCGA and HCC data sets from the GEO database to ensure the reliability of the data. Their functions were analyzed by bioinformatics methods. We used lasso regression, Support vector machine (SVM), logistic regression and Cox regression to construct the diagnostic and prognostic models. We also constructed a nomogram of the practicability of the above-mentioned prognostic model. The above results were verified in an independent liver cancer data set from the ICGC database and clinical samples. Furthermore, we carried out pan-cancer analysis to verify the specificity of the above model and screened a wide range of drug candidates.
    Results: Many epigenetic modification-associated genes were significantly different in HCC and normal liver tissues. The gene signatures showed a good ability to predict the occurrence and survival of HCC patients, as verified by DCA and ROC curve analysis.
    Conclusion: Gene signatures based on epigenetic modification-associated genes can be used to identify the occurrence and prognosis of liver cancer.
    Keywords:  bioinformatics; candidate drugs; diagnosis; epigenetic modification; hepatocellular carcinoma; prognosis
    DOI:  https://doi.org/10.3389/fonc.2021.649093
  36. J Proteomics. 2021 Jul 05. pii: S1874-3919(21)00218-9. [Epub ahead of print] 104319
    Phosphorylation of Ser1452 on BRG1 inhibits the function of the SWI/SNF complex in chromatin activation.
    Ayuko Kimura, Noriaki Arakawa, Hiroyuki Kagawa, Yayoi Kimura, Hisashi Hirano.
      BRG1, one of core subunits of the SWI/SNF chromatin remodeling complex, is frequently mutated in cancers. Previously, we reported significant downregulation of the phosphorylation level of BRG1 on Ser1452 (<10%) in cell lines derived from ovarian clear cell carcinoma with frequent recurrence and acquired drug resistance. In this study, we tried to elucidate the roles of BRG1 phosphorylation, using cell lines expressing wild-type, phosphorylation-mimic (brg1-S1452D), or non-phosphorylatable (brg1-S1452A) BRG1. Quantitative proteomic analyses revealed upregulation of proteins and phosphoproteins related to linker histone H1s, histone methylation, and protein ubiquitylation in brg1-S1452D cells, which may coordinately promote the chromatin inactivation and ubiquitin-dependent degradation of target proteins. Consistent with these results, brg1-S1452D cells exhibited an increase in condensed chromatin and polyubiquitylated proteins. In brg1-S1452D cells, we also detected downregulation of various cancer-related proteins (e.g., EGFR and MET) as well as decreased migration, proliferation, and sensitivity to taxanes and oxaliplatin. Together, our results reveal that BRG1 phosphorylation drives tumor malignancy by inhibiting the functions of SWI/SNF complex in chromatin activation, thereby promoting expression of various cancer-related proteins. SIGNIFICANCE: For the first time we demonstrated that the mutation on Ser1452 phosphorylation site of BRG1, a component of SWI/SNF chromatin remodeling complex, changed protein and phosphoprotein levels of linker histone H1s, binding competitor of histone H1s, and histone methylase/demethylase involved in the heterochromatic histone modifications to promote the chromatin inactivation. In phosphorylation-mimic mutant, significant decrease of various cancer-related proteins as well as migration, proliferation, and sensitivity to specific antitumor agents were detected. Our results reveal that BRG1 phosphorylation drives tumor malignancy by inhibiting the functions of SWI/SNF complex in chromatin activation, thereby promoting expression of various cancer-related proteins.
    Keywords:  BRG1; Linker histone; Ovarian cancer; Phosphorylation; SWI/SNF complex; Ubiquitin
    DOI:  https://doi.org/10.1016/j.jprot.2021.104319
  37. Gene. 2021 Jul 02. pii: S0378-1119(21)00403-0. [Epub ahead of print] 145808
    Transcriptome and chromatin landscape changes associated with trastuzumab resistance in HER2+ breast cancer cells.
    Rabi Murad, Arabo Avanes, Xinyi Ma, Shuhui Geng, Ali Mortazavi, Jamil Momand.
      We set out to uncover transcriptome and chromatin landscape changes that occur in HER2+ breast cancer (BC) cells upon acquiring resistance to trastuzumab. RNA-seq analysis was applied to two independently-derived BC cell lines with acquired resistance to trastuzumab (SKBr3.HerR and BT-474HerR) and their parental drug-sensitive cell lines (SKBr3 and BT-474). Chromatin landscape analysis indicated that the most significant increase in accessibility in resistant cells occurs in PPP1R1B within a segment spanning introns 1b through intron 3. Footprint analysis of this segment revealed that FoxJ3 (within intron 2) and Pou5A1/Sox2 (within inton 3) transcription factor motifs are protected in resistant cells. Overall, 344 shared genes were upregulated in both resistant cell lines relative to their parental counterparts and 453 shared genes were downregulated in both resistant cell lines relative to their parental counterparts. In resistant cells, genes associated with autophagy and mitochondria organization are upregulated and genes associated with ribosome assembly and cell cycle are downregulated relative to parental cells. The five top upregulated genes in drug-resistant breast cancer cells are APOD, AZGP1, ETV5, ALPP, and PPP1R1B. This is the first report of increased chromatin accessibility within PPP1R1B associated with its t-Darpp transcript increase, and points to a possible mechanism for its activation in trastuzumab-resistant cells.
    Keywords:  ATAC-seq; Breast cancer; FoxJ3; Herceptin; PPP1R1B; Pou5A1; Sox2; differentially expressed genes; drug resistance; trastuzumab
    DOI:  https://doi.org/10.1016/j.gene.2021.145808
  38. Methods Mol Biol. 2021 ;2312 277-285
    AgDD System: A Chemical Controllable Protein Aggregates in Cells.
    Yusuke Miyazaki.
      There are increasing evidence and growing interest in the relationship between protein aggregates/phase separation and various human diseases, especially neurodegenerative diseases. However, we do not entirely comprehend how aggregates generate or the clearance network of chaperones, proteasomes, ubiquitin ligases, and other factors interact with aggregates. Here, we describe chemically controllable systems compose with a genetically engineered cell and a small drug that enables us to rapidly induce protein aggregates' formation by withdrawing the small molecule. This trigger does not activate global stress responses induced by stimuli, such as proteasome inhibitors or heat shock. This method can produce aggregates in a specific compartment and diverse experimental systems, including live animals.
    Keywords:  Chaperones; Chemical biology; Destabilizing domain; Phase separation; Proteasome; Protein aggregates
    DOI:  https://doi.org/10.1007/978-1-0716-1441-9_16
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