bims-ectoca 2021-08-29 papers

bims-ectoca

Biomed News

on Epigenetic control of tolerance in cancer

Issue of 2021–08–29
twelve papers selected by
Ankita Daiya, Birla Institute of Technology and Science

Naturally occurring small molecule compounds that target histone deacetylases and their potential applications in cancer therapy.
Emerging Single-Cell Technological Approaches to Investigate Chromatin Dynamics and Centromere Regulation in Human Health and Disease.
Autophagy Modulators in Cancer: Focus on Cancer Treatment.
Polycomb-dependent histone H2A ubiquitination links developmental disorders with cancer.
PARP1-modulated chromatin remodeling is a new target for cancer treatment.
Unraveling the Epigenetic Role and Clinical Impact of Histone Deacetylases in Neoplasia.
Adding Some "Splice" to Stress Eating: Autophagy, ESCRT and Alternative Splicing Orchestrate the Cellular Stress Response.
Arginine Methyltransferase PRMT1 Regulates p53 Activity in Breast Cancer.
A pan-cancer analysis revealed the role of the SLC16 family in cancer.
Circulating Long Non-Coding RNAs as Novel Potential Biomarkers for Osteogenic Sarcoma.
Pharmacological Inhibition of Core Regulatory Circuitry Liquid-liquid Phase Separation Suppresses Metastasis and Chemoresistance in Osteosarcoma.
Protein Aggregation and Disaggregation in Cells and Development.

J Antibiot (Tokyo). 2021 Aug 23.

Naturally occurring small molecule compounds that target histone deacetylases and their potential applications in cancer therapy.

Yuki Maemoto, Yuki Shimizu, Ryu Katoh, Akihiro Ito.

Epigenetics is defined as the heritable alteration of gene expression without change to the DNA sequence. Epigenetic abnormalities play a role in various diseases, including cancer. Epigenetic regulation of gene expression occurs through histone chemical modifications and DNA methylation. Lysine acetylation is one of the major histone chemical modifications essential for epigenetic gene expression. Histone acetylation is reversibly regulated by histone acetyltransferases and histone deacetylases, which are molecular targets for cancer therapy. There has been an explosion of research in epigenetic-related drug discovery, and accordingly many small molecule compounds have been developed. Notably, several small molecule inhibitors of histone deacetylases have been approved for the treatment of cancer. This review will introduce natural products, their derivative inhibitors of histone deacetylases, and their clinical development.

DOI: https://doi.org/10.1038/s41429-021-00459-6
Int J Mol Sci. 2021 Aug 16. pii: 8809. [Epub ahead of print]22(16):

Emerging Single-Cell Technological Approaches to Investigate Chromatin Dynamics and Centromere Regulation in Human Health and Disease.

Laura Leo, Nunzia Colonna Romano.

  Epigenetic regulators play a crucial role in establishing and maintaining gene expression states. To date, the main efforts to study cellular heterogeneity have focused on elucidating the variable nature of the chromatin landscape. Specific chromatin organisation is fundamental for normal organogenesis and developmental homeostasis and can be affected by different environmental factors. The latter can lead to detrimental alterations in gene transcription, as well as pathological conditions such as cancer. Epigenetic marks regulate the transcriptional output of cells. Centromeres are chromosome structures that are epigenetically regulated and are crucial for accurate segregation. The advent of single-cell epigenetic profiling has provided finer analytical resolution, exposing the intrinsic peculiarities of different cells within an apparently homogenous population. In this review, we discuss recent advances in methodologies applied to epigenetics, such as CUT&RUN and CUT&TAG. Then, we compare standard and emerging single-cell techniques and their relevance for investigating human diseases. Finally, we describe emerging methodologies that investigate centromeric chromatin specification and neocentromere formation.

Keywords:  centromere; chromatin regulation; emerging technologies; epigenetics; epigenetics in human health & disease; single-cell epigenetics

DOI:  https://doi.org/10.3390/ijms22168809
Life (Basel). 2021 Aug 17. pii: 839. [Epub ahead of print]11(8):

Autophagy Modulators in Cancer: Focus on Cancer Treatment.

Hye Jin Nam.

  Uncontrolled autophagy has been associated with the development and progression of various cancers that are resistant to cancer therapy. Therefore, many efforts to modulate uncontrolled autophagy as a cancer treatment have been attempted, from basic science to clinical trials. However, it remains difficult to equally apply autophagy modulators to cancer therapy because autophagy is a double-edged sword in cancer: it can be tumor-suppressive or tumor-protective. Therefore, the precise mechanisms of autophagy modulators and their varied responsiveness to each cancer type should be addressed in detail. This study will describe the precise mechanisms of developing various autophagy modulators, their current therapeutic applications and future perspectives.

Keywords:  autophagy; autophagy enhancer; autophagy inhibitor; cancer treatment

DOI:  https://doi.org/10.3390/life11080839
Trends Genet. 2021 Aug 20. pii: S0168-9525(21)00201-8. [Epub ahead of print]

Polycomb-dependent histone H2A ubiquitination links developmental disorders with cancer.

Simone Tamburri, Eric Conway, Diego Pasini.

  Cell identity is tightly controlled by specific transcriptional programs which require post-translational modifications of histones. These histone modifications allow the establishment and maintenance of active and repressed chromatin domains. Histone H2A lysine 119 ubiquitination (H2AK119ub1) has an essential role in building repressive chromatin domains during development. It is regulated by the counteracting activities of the Polycomb repressive complex 1 (PRC1) and the Polycomb repressive-deubiquitinase (PR-DUB) complexes, two multi-subunit ensembles that write and erase this modification, respectively. We have catalogued the recurrent genetic alterations in subunits of the PRC1 and PR-DUB complexes in both neurodevelopmental disorders and cancer. These genetic lesions are often shared across disorders, and we highlight common mechanisms of H2AK119ub1 dysregulation and how they affect development in multiple disease contexts.

Keywords:  Polycomb repressive complex 1 (PRC1); Polycomb repressive-deubiquitinase (PR-DUB) complex; cancer; chromatin; epigenetics; neurodevelopment; transcription

DOI:  https://doi.org/10.1016/j.tig.2021.07.011
Med Oncol. 2021 Aug 25. 38(10): 118

PARP1-modulated chromatin remodeling is a new target for cancer treatment.

Saptarshi Sinha, Sefinew Molla, Chanakya Nath Kundu.

  Cancer progression requires certain tumorigenic mutations in genes encoding for different cellular and nuclear proteins. Altered expressions of these mutated genes are mediated by post-translational modifications and chromatin remodeling. Chromatin remodeling is mainly regulated by the chromatin remodeling enzyme complexes and histone modifications. Upon DNA damage, Poly-(ADP-ribose) Polymerase1 (PARP1) plays a very important role in the induction of chromatin modifications and activation of DNA repair pathways to repair the DNA lesion. It has been targeted to develop different anti-cancer therapeutic interventions and PARP inhibitors have been approved by the U.S. Food and Drug Administration (FDA) for clinical use. But it has been found that the cancer cells often develop resistance to these PARP inhibitors and chromatin remodeling helps in enhancing this process. Hence, it may be beneficial to target PARP1-mediated chromatin remodeling, which may allow to reverse the drug resistance. In the current review, we have discussed the role of chromatin remodeling in DNA repair, how PARP1 regulates modifications of chromatin dynamics, and the role of chromatin modifications in cancer. It has also been discussed how the PARP1-mediated chromatin remodeling can be targeted by PARP inhibitors alone or in combination with other chemotherapeutic agents to establish novel anti-cancer therapeutics. We have also considered the use of PARG inhibitors that may enhance the action of PARP inhibitors to target different types of cancers.

Keywords:  Cancer; Chromatin remodeling; DNA repair; PARP inhibitors; PARP1

DOI:  https://doi.org/10.1007/s12032-021-01570-2
Diagnostics (Basel). 2021 Jul 26. pii: 1346. [Epub ahead of print]11(8):

Unraveling the Epigenetic Role and Clinical Impact of Histone Deacetylases in Neoplasia.

Dimitrios Goutas, Stamatios Theocharis, Gerasimos Tsourouflis.

  Histone deacetylases (HDACs) have long been implicated in tumorigenesis and tumor progression demonstrating their important participation in neoplasia. Therefore, numerous studies have been performed, highlighting the mechanism of HDACs action in tumor cells and demonstrating the potential role of HDAC inhibitors in the treatment of different cancer types. The outcome of these studies further delineated and strengthened the solid role that HDACs and epigenetic modifications exert in neoplasia. These results have spread promise regarding the potential use of HDACs as prospective therapeutic targets. Nevertheless, the clinical significance of HDAC expression and their use as biomarkers in cancer has not been extensively elucidated. The aim of our study is to emphasize the clinical significance of HDAC isoforms expression in different tumor types and the correlations noted between the clinicopathological parameters of tumors and patient outcomes. We further discuss the obstacles that the next generation HDAC inhibitors need to overcome, for them to become more potent.

Keywords:  biomarkers; cancer; epigenetics; histone deacetylase; histone deacetylase inhibitors; histones; prognosis; survival

DOI:  https://doi.org/10.3390/diagnostics11081346
Genes (Basel). 2021 Jul 31. pii: 1196. [Epub ahead of print]12(8):

Adding Some "Splice" to Stress Eating: Autophagy, ESCRT and Alternative Splicing Orchestrate the Cellular Stress Response.

Elias Habib, Allyson Cook, Sabateeshan Mathavarajah, Graham Dellaire.

  Autophagy is a widely studied self-renewal pathway that is essential for degrading damaged cellular organelles or recycling biomolecules to maintain cellular homeostasis, particularly under cellular stress. This pathway initiates with formation of an autophagosome, which is a double-membrane structure that envelopes cytosolic components and fuses with a lysosome to facilitate degradation of the contents. The endosomal sorting complexes required for transport (ESCRT) proteins play an integral role in controlling autophagosome fusion events and disruption to this machinery leads to autophagosome accumulation. Given the central role of autophagy in maintaining cellular health, it is unsurprising that dysfunction of this process is associated with many human maladies including cancer and neurodegenerative diseases. The cell can also rapidly respond to cellular stress through alternative pre-mRNA splicing that enables adaptive changes to the cell's proteome in response to stress. Thus, alternative pre-mRNA splicing of genes that are involved in autophagy adds another layer of complexity to the cell's stress response. Consequently, the dysregulation of alternative splicing of genes associated with autophagy and ESCRT may also precipitate disease states by either reducing the ability of the cell to respond to stress or triggering a maladaptive response that is pathogenic. In this review, we summarize the diverse roles of the ESCRT machinery and alternative splicing in regulating autophagy and how their dysfunction can have implications for human disease.

Keywords:  ESCRT; alternative splicing; autophagy; cancer; neurodegenerative and eye disease

DOI:  https://doi.org/10.3390/genes12081196
Life (Basel). 2021 Aug 05. pii: 789. [Epub ahead of print]11(8):

Arginine Methyltransferase PRMT1 Regulates p53 Activity in Breast Cancer.

Li-Ming Liu, Qiang Tang, Xin Hu, Jing-Jing Zhao, Yuan Zhang, Guo-Guang Ying, Fei Zhang.

  The protein p53 is one of the most important tumor suppressors, responding to a variety of stress signals. Mutations in p53 occur in about half of human cancer cases, and dysregulation of the p53 function by epigenetic modifiers and modifications is prevalent in a large proportion of the remainder. PRMT1 is the main enzyme responsible for the generation of asymmetric-dimethylarginine, whose upregulation or aberrant splicing has been observed in many types of malignancies. Here, we demonstrate that p53 function is regulated by PRMT1 in breast cancer cells. PRMT1 knockdown activated the p53 signal pathway and induced cell growth-arrest and senescence. PRMT1 could directly bind to p53 and inhibit the transcriptional activity of p53 in an enzymatically dependent manner, resulting in a decrease in the expression levels of several key downstream targets of the p53 pathway. We were able to detect p53 asymmetric-dimethylarginine signals in breast cancer cells and breast cancer tissues from patients, and the signals could be significantly weakened by silencing of PRMT1 with shRNA, or inhibiting PRMT1 activity with a specific inhibitor. Furthermore, PRMT1 inhibitors significantly impeded cell growth and promoted cellular senescence in breast cancer cells and primary tumor cells. These results indicate an important role of PRMT1 in the regulation of p53 function in breast tumorigenesis.

Keywords:  PRMT1; arginine methylation; breast cancer; p53

DOI:  https://doi.org/10.3390/life11080789
Channels (Austin). 2021 Dec;15(1): 528-540

A pan-cancer analysis revealed the role of the SLC16 family in cancer.

Jun Li, Jiaheng Xie, Dan Wu, Liang Chen, Zetian Gong, Rui Wu, Yiming Hu, Jiangning Zhao, Yetao Xu.

  Cancer is one of the serious diseases that endanger human health and bring a heavy burden to world economic development. Although the current targeted therapy and immunotherapy have achieved initial results, the emergence of drug resistance shows that the existing research is far from enough. In recent years, the tumor microenvironment has been found to be an important condition for tumor development and has profound research value. The SLC16 family is a group of monocarboxylic acid transporters involved in cancer metabolism and the formation of the tumor microenvironment. However, there have been no generalized cancer studies in the SLC16 family. In this study, we conducted a pan-cancer analysis of the SLC16 family. The results showed that multiple members of the SLC16 family could be used as prognostic indicators for many tumors, and were associated with immune invasion and tumor stem cells. Therefore, the SLC16 family has extensive exploration value in the future.

Keywords:  SLC; bioinformatics; cancer; immunology; transporter

DOI:  https://doi.org/10.1080/19336950.2021.1965422
Cancers (Basel). 2021 Aug 21. pii: 4214. [Epub ahead of print]13(16):

Circulating Long Non-Coding RNAs as Novel Potential Biomarkers for Osteogenic Sarcoma.

Sutpirat Moonmuang, Parunya Chaiyawat, Salinee Jantrapirom, Dumnoensun Pruksakorn, Luca Lo Piccolo.

  Circulating cell-free nucleic acids recently became attractive targets to develop non-invasive diagnostic tools for cancer detection. Along with DNA and mRNAs, transcripts lacking coding potential (non-coding RNAs, ncRNAs) directly involved in the process of tumor pathogenesis have been recently detected in liquid biopsies. Interestingly, circulating ncRNAs exhibit specific expression patterns associated with cancer and suggest their role as novel biomarkers. However, the potential of circulating long ncRNAs (c-lncRNAs) to be markers in osteosarcoma (OS) is still elusive. In this study we performed a systematic review to identify thirteen c-lncRNAs whose altered expression in blood associate with OS. We herein discuss the potential impact that these c-lncRNAs may have on clinical decision-making in the management of OS. Overall, we aimed to provide novel insights that can contribute to the development of future precision medicine in oncology.

Keywords:  biomarkers; circulating long non-coding RNA; liquid biopsy; osteosarcoma

DOI:  https://doi.org/10.3390/cancers13164214
Adv Sci (Weinh). 2021 Aug 25. e2101895

Pharmacological Inhibition of Core Regulatory Circuitry Liquid-liquid Phase Separation Suppresses Metastasis and Chemoresistance in Osteosarcoma.

Bing Lu, Changye Zou, Meiling Yang, Yangyang He, Jincan He, Chuanxia Zhang, Siyun Chen, Jiaming Yu, Kilia Yun Liu, Qi Cao, Wei Zhao.

  Liquid-liquid phase-separated (LLPS) transcriptional factor assemblies at super-enhancers (SEs) provide a conceptual framework for underlying transcriptional control in mammal cells. However, the mechanistic understanding of LLPS in aberrant transcription driven by dysregulation of SEs in human malignancies is still elusive. By integrating SE profiling and core regulatory circuitry (CRC) calling algorithm, the CRC of metastatic and chemo-resistant osteosarcoma is delineated. CRC components, HOXB8 and FOSL1, produce dense and dynamic phase-separated droplets in vitro and liquid-like puncta in cell nuclei. Disruption of CRC phase separation decreases the chromatin accessibility in SE regions and inhibits the release of RNA polymerase II from the promoter of SE-driven genes. Importantly, absence of CRC key component causes a reduction in osteosarcoma tumor growth and metastasis. Moreover, it is shown that CRC condensates can be specifically attenuated by the H3K27 demethylase inhibitor, GSK-J4. Pharmacological inhibition of the CRC phase separation results in metastasis suppression and re-sensitivity to chemotherapy drugs in patient-derived xenograft model. Taken together, this study reveals a previously unknown mechanism that CRC factors formed LLPS condensates, and provides a phase separation-based pharmacological strategy to target undruggable CRC components for the treatment of metastatic and chemo-resistant osteosarcoma.

Keywords:  HOXB8; core regulatory circuitry; liquid-liquid phase separation; osteosarcoma; super-enhancer

DOI:  https://doi.org/10.1002/advs.202101895
J Mol Biol. 2021 Aug 24. pii: S0022-2836(21)00448-4. [Epub ahead of print] 167215

Protein Aggregation and Disaggregation in Cells and Development.

Jan S Fassler, Sydney Skuodas, Daniel L Weeks, Bryan T Phillips.

  Protein aggregation is a feature of numerous neurodegenerative diseases. However, regulated, often reversible formation of protein aggregates, also known as condensates, helps control a wide range of cellular activities including stress response, gene expression, memory, cell development and differentiation. This review presents examples of aggregates found in biological systems, how they are used, and cellular strategies that control aggregation and disaggregation. We include features of the aggregating proteins themselves, environmental factors, co-aggregates, post-translational modifications and well-known aggregation-directed activities that influence their formation, material state, stability and dissolution. We highlight the emerging roles of biomolecular condensates in early animal development, and disaggregation processing proteins that have recently been shown to play key roles in gametogenesis and embryogenesis.

Keywords:  ABCF gene family; Amyloid; RuvBL gene family; biomolecular condensate; chaperone

DOI:  https://doi.org/10.1016/j.jmb.2021.167215