bims-ectoca 2021-10-24 papers

bims-ectoca

Biomed News

on Epigenetic control of tolerance in cancer

Issue of 2021–10–24
twelve papers selected by
Ankita Daiya, Birla Institute of Technology and Science

Single-cell RNA sequencing and bioinformatics as tools to decipher cancer heterogenicity and mechanisms of drug resistance.
Simple oligonucleotide-based multiplexing of single-cell chromatin accessibility.
Intrinsic and acquired drug resistance to LSD1 inhibitors in small cell lung cancer occurs through a TEAD4-driven transcriptional state.
Intermittent High Glucose Elevates Nuclear Localization of EZH2 to Cause H3K27me3-Dependent Repression of KLF2 Leading to Endothelial Inflammation.
The implications of ABCC3 in cancer drug resistance: can we use it as a therapeutic target?
LncRNAs in tumor microenvironment: the potential target for cancer treatment with natural compounds and chemical drugs.
Changing and stable chromatin accessibility supports transcriptional overhaul during neural stem cell activation and is altered with age.
Decoding the function of bivalent chromatin in development and cancer.
The anti-osteosarcoma effect from panax notoginseng saponins by inhibiting the G0 / G1 phase in the cell cycle and affecting p53-mediated autophagy and mitochondrial apoptosis.
Global Histone H3 Lysine 4 Trimethylation (H3K4me3) Landscape Changes in Response to TGFβ.
Hedgehog/GLI1 signaling pathway regulates the resistance to cisplatin in human osteosarcoma.
Tumor-suppressive function of EZH2 is through inhibiting glutaminase.

Biochem Pharmacol. 2021 Oct 18. pii: S0006-2952(21)00427-5. [Epub ahead of print] 114811

Single-cell RNA sequencing and bioinformatics as tools to decipher cancer heterogenicity and mechanisms of drug resistance.

Diletta Rosati, Antonio Giordano.

  It is well known that cancer is an aggressive disease, often associated with relapse, in many cases due to drug resistance. Cancer stem cell and clonal evolution are frequently causes of innate or acquired drug resistance. Current RNA sequencing technologies do not distinguish gene expression of different cell lineages because they are based on bulk cell studies. Single-cell RNA sequencing technologies and related bioinformatics clustering and differential expression analysis represent a turning point in cancer research. They are emerging as essential tools for dissecting tumors at single-cell resolution and represent novel tools to understand carcinogenesis and drug response. In this review, we will outline the role of these new technologies in addressing cancer heterogeneity and cell lineage-dependent drug resistance.

Keywords:  Bioinformatics data analysis; Cancer stem cells, Cancer clonal evolution; Drug resistance; scRNA-seq

DOI:  https://doi.org/10.1016/j.bcp.2021.114811
Mol Cell. 2021 Oct 21. pii: S1097-2765(21)00795-4. [Epub ahead of print]81(20): 4319-4332.e10

Simple oligonucleotide-based multiplexing of single-cell chromatin accessibility.

Kaile Wang, Zhenna Xiao, Yun Yan, Rui Ye, Min Hu, Shanshan Bai, Emi Sei, Yawei Qiao, Hui Chen, Bora Lim, Steven H Lin, Nicholas E Navin.

  Microdroplet single-cell ATAC-seq is widely used to measure chromatin accessibility, however, highly scalable and simple sample multiplexing procedures are not available. Here, we present a transposome-assisted single nucleus barcoding approach for ATAC-seq (SNuBar-ATAC) that utilizes a single oligonucleotide adaptor for multiplexing samples during the existing tagmentation step and does not require a pre-labeling procedure. The accuracy and scalability of SNuBar-ATAC was evaluated using cell line mixture experiments. We applied SNuBar-ATAC to investigate treatment-induced chromatin accessibility dynamics by multiplexing 28 mice with lung tumors that received different combinations of chemo, radiation, and targeted immunotherapy. We also applied SNuBar-ATAC to study spatial epigenetic heterogeneity by multiplexing 32 regions from a human breast tissue. Additionally, we show that SNuBar can multiplex single cell ATAC and RNA multiomic assays in cell lines and human breast tissue samples. Our data show that SNuBar is a highly accurate, easy-to-use, and scalable system for multiplexing scATAC-seq and scATAC and RNA co-assay experiments.

Keywords:  SNuBar; cell-type-specific transcription factors; multiplexing therapy combinations; single-cell ATAC sequencing; single-cell multiomics multiplexing; single-cell multiomics sequencing; single-cell multiplexing; spatial epigenetic heterogeneity

DOI:  https://doi.org/10.1016/j.molcel.2021.09.026
Mol Oncol. 2021 Oct 20.

Intrinsic and acquired drug resistance to LSD1 inhibitors in small cell lung cancer occurs through a TEAD4-driven transcriptional state.

Wen Yan, Chi-Yeh Chung, Tao Xie, Mark Ozeck, Timothy C Nichols, Jessica Frey, Akshata R Udyavar, Shikhar Sharma, Thomas A Paul.

  Small cell lung cancer (SCLC) is a heterogeneous disease, consisting of intra-tumoral and inter-tumoral neuroendocrine (ASCL1 and/or NEUROD1), mesenchymal-like, and YAP-driven transcriptional states. Lysine-specific demethylase 1 (LSD1; also known as KDM1A) inhibitors have recently been progressed to clinical trials in SCLC based on a promising preclinical anti-tumor activity. A potential clinical limitation of LSD1 inhibitors is the heterogeneous drug responses that have been observed in SCLC cell lines and patient-derived models. Based on these observations, we studied molecular and transcriptional signatures that predict patient response to this class of drug. Employing SCLC patient-derived transcriptional signatures, we define that SCLC cell lines sensitive to LSD1 inhibitors are enriched in neuroendocrine transcriptional markers, whereas cell lines enriched in a mesenchymal-like transcriptional program demonstrate intrinsic resistance to LSD1 inhibitors. We have identified a reversible, adaptive resistance mechanism to LSD1 inhibitors through epigenetic reprogramming to a TEAD4-driven mesenchymal-like state. Our data suggest that only a segment of SCLC patients, with a defined neuroendocrine differentiation state, will likely benefit from LSD1 inhibitors. It provides novel evidence for the selection of a TEAD4-driven mesenchymal-like subpopulation resistant to LSD1 inhibitors in SCLC patients that may require effective drug combinations to sustain effective clinical responses.

Keywords:  KDM1A; LSD1; drug resistance; epigenetic therapy; small cell lung cancer (SCLC)

DOI:  https://doi.org/10.1002/1878-0261.13124
Cells. 2021 Sep 26. pii: 2548. [Epub ahead of print]10(10):

Intermittent High Glucose Elevates Nuclear Localization of EZH2 to Cause H3K27me3-Dependent Repression of KLF2 Leading to Endothelial Inflammation.

Sumukh Thakar, Yash T Katakia, Shyam Kumar Ramakrishnan, Niyati Pandya Thakkar, Syamantak Majumder.

  Epigenetic mechanisms have emerged as one of the key pathways promoting diabetes-associated complications. Herein, we explored the role of enhancer of zeste homolog 2 (EZH2) and its product histone 3 lysine 27 trimethylation (H3K27me3) in high glucose-mediated endothelial inflammation. To examine this, we treated cultured primary endothelial cells (EC) with different treatment conditions-namely, constant or intermittent or transient high glucose. Intermittent high glucose maximally induced endothelial inflammation by upregulating transcript and/or protein-level expression of ICAM1 and P-selectin and downregulating eNOS, KLF2, and KLF4 protein levels. We next investigated the underlining epigenetic mechanisms responsible for intermittent hyperglycemia-dependent endothelial inflammation. Compared with other high glucose treatment groups, intermittent high glucose-exposed EC exhibited an increased level of H3K27me3 caused by reduction in EZH2 threonine 367 phosphorylation and nuclear retention of EZH2. Intermittent high glucose also promoted polycomb repressive complex-2 (PRC2) assembly and EZH2's recruitment to histone H3. Abrupt enrichment of H3K27me3 on KLF2 and KLF4 gene promoters caused repression of these genes, further supporting endothelial inflammation. In contrast, reducing H3K27me3 through small molecule and/or siRNA-mediated inhibition of EZH2 rescued KLF2 level and inhibited endothelial inflammation in intermittent high glucose-challenged cultured EC and isolated rat aorta. These findings indicate that abrupt chromatin modifications cause high glucose-dependent inflammatory switch of EC.

Keywords:  H3K27me3; KLF2; endothelial cells; enhancer of zeste homolog 2; epigenetics; inflammation

DOI:  https://doi.org/10.3390/cells10102548
Am J Cancer Res. 2021 ;11(9): 4127-4140

The implications of ABCC3 in cancer drug resistance: can we use it as a therapeutic target?

Adriana Ramírez-Cosmes, Edilburga Reyes-Jiménez, Cecilia Zertuche-Martínez, Carlos A Hernández-Hernández, Rebeca García-Román, Roberto I Romero-Díaz, Adán E Manuel-Martínez, Jesús Elizarrarás-Rivas, Verónica R Vásquez-Garzón.

Drug resistance is one of the main causes of chemotherapy failure. Although several factors are involved in cancer drug resistant, the exporter pumps overexpression that mediates the drugs flow to outside the cells and reduces both the drugs intracellular concentration and effectiveness, has been one of the most important challenges. Overexpression of ABCC3, a member of the ABCC subfamily, has been strongly associated to the resistance to multiple drugs. ABCC3 has been found highly expressed in different types of cancers and is associated with poor prognosis and resistance to treatments. In this review, we summarize the molecular mechanisms involved in cancer drug resistance and discuss the current knowledge about the structure, function and role of ABCC3 in drug resistance, as well as, the expression status of ABCC3 in different types of cancer. We also provide evidences that place ABCC3 as a potential therapeutic target for improving the cancer treatment by focusing on the need of developing more effective cancer therapies to target ABCC3 in translational researches.

Keywords: ABCC3; Cancer; drug resistance; therapeutic target; transporters
Biochem Pharmacol. 2021 Oct 19. pii: S0006-2952(21)00418-4. [Epub ahead of print] 114802

LncRNAs in tumor microenvironment: the potential target for cancer treatment with natural compounds and chemical drugs.

Qiu-Ping Liu, Jia-Yi Lin, Pei An, Yu-Ying Chen, Xin Luan, Hong Zhang.

  It was thought that originally long non-coding RNAs (lncRNAs) were a kind of RNAs without any encoding function. Recently, a variety of studies have shown that lncRNAs play important roles in many life activities. The abnormal expression of lncRNAs in tumor microenvironment (TME) usually promotes the proliferation, migration, and drug resistance of tumor cells through direct or indirect effects, which also usually predicts the poor prognosis. The regulation of lncRNAs expression in TME could significantly inhibit tumor progress. However, the interaction between lncRNAs and TME has not been fully defined at present. Therefore, this paper provided the systemic summary of their interaction and natural products and chemicals targeting lncRNAs in cancer treatment. Currently, the strategies of cancer treatment still have their limits. Understanding the relationship between TME and lncRNAs can help us to realize breakthrough strategy for tumor treatment.

Keywords:  LncRNAs; drug; stromal cells; tumor; tumor microenvironment (TME)

DOI:  https://doi.org/10.1016/j.bcp.2021.114802
Aging Cell. 2021 Oct 23. e13499

Changing and stable chromatin accessibility supports transcriptional overhaul during neural stem cell activation and is altered with age.

Sun Y Maybury-Lewis, Abigail K Brown, Mitchell Yeary, Anna Sloutskin, Shleshma Dhakal, Tamar Juven-Gershon, Ashley E Webb.

  Neural stem cells (NSCs) in the adult and aged brain are largely quiescent, and require transcriptional reprogramming to re-enter the cell cycle. However, the mechanisms underlying these changes and how they are altered with age remain undefined. Here, we identify the chromatin accessibility differences between primary neural stem/progenitor cells in quiescent and activated states. These distinct cellular states exhibit shared and unique chromatin profiles, both associated with gene regulation. Accessible chromatin states specific to activation or quiescence are active enhancers bound by key pro-neurogenic and quiescence factors. In contrast, shared sites are enriched for core promoter elements associated with translation and metabolism. Unexpectedly, through integrated analysis, we find that many sites that become accessible during NSC activation are linked to gene repression and associated with pro-quiescence factors, revealing a novel mechanism that may preserve quiescence re-entry. Furthermore, we report that in aged NSCs, chromatin regions associated with metabolic and transcriptional functions bound by key pro-quiescence transcription factors lose accessibility, suggesting a novel mechanism of age-associated NSC dysfunction. Together, our findings reveal how accessible chromatin states regulate the transcriptional switch between NSC quiescence and activation, and how this switch is affected with age.

Keywords:  aging; chromatin accessibility; neural stem cells; stem cell activation

DOI:  https://doi.org/10.1111/acel.13499
Genome Res. 2021 Oct 19. pii: gr.275736.121. [Epub ahead of print]

Decoding the function of bivalent chromatin in development and cancer.

Dhirendra Kumar, Senthilkumar Cinghu, Andrew J Oldfield, Pengyi Yang, Raja Jothi.

Bivalent chromatin is characterized by the simultaneous presence of H3K4me3 and H3K27me3, histone modifications generally associated with transcriptionally active and repressed chromatin, respectively. Prevalent in embryonic stem cells (ESCs), bivalency is postulated to poise/prime lineage-controlling developmental genes for rapid activation during embryogenesis while maintaining a transcriptionally repressed state in the absence of activation cues; however, this hypothesis remains to be directly tested. Most gene promoters DNA-hypermethylated in adult human cancers are bivalently marked in ESCs, and it was speculated that bivalency predisposes them for aberrant de novo DNA methylation and irreversible silencing in cancer, but evidence supporting this model is largely lacking. Here we show that bivalent chromatin does not poise genes for rapid activation but protects promoters from de novo DNA methylation. Genome-wide studies in differentiating ESCs reveal that activation of bivalent genes is no more rapid than that of other transcriptionally silent genes, challenging the premise that H3K4me3 is instructive for transcription. H3K4me3 at bivalent promoters, a product of the underlying DNA sequence, persists in nearly all cell types irrespective of gene expression and confers protection from de novo DNA methylation. Bivalent genes in ESCs that are frequent targets of aberrant hypermethylation in cancer are particularly strongly associated with loss of H3K4me3/bivalency in cancer. Altogether, our findings suggest that bivalency protects reversibly repressed genes from irreversible silencing and that loss of H3K4me3 may make them more susceptible to aberrant DNA methylation in diseases such as cancer. Bivalency may thus represent a distinct regulatory mechanism for maintaining epigenetic plasticity.

DOI: https://doi.org/10.1101/gr.275736.121
J Cancer. 2021 ;12(21): 6383-6392

The anti-osteosarcoma effect from panax notoginseng saponins by inhibiting the G0 / G1 phase in the cell cycle and affecting p53-mediated autophagy and mitochondrial apoptosis.

Guangtao Han, Yubiao Zhang, Ting Liu, Jianping Li, Haohuan Li.

  Osteosarcoma is the most common primary bone malignancy, and current chemotherapy sessions against it often induce severe complications in patients. Thus, it is necessary to develop new and effective antineoplastic agents with fewer side effects. Panax notoginseng saponins (PNS) are the active components in panax notoginseng and were reported to be capable of inhibiting the growth of several tumors both in vitro and in vivo. However, its effects on osteosarcoma have not been studied yet, which is addressed in this study for the first time. Our results indicated that PNS can inhibit proliferation, invasion and migration of the osteosarcoma cells, while promoting their apoptosis simultaneously. Specifically, PNS caused an increase in mitochondrial membrane potential and the amount of reactive oxygen species. The cell cycle in osteosarcoma cells was arrested in the G0 / G1 phase after PNS treatment. The expression of p53 and other apoptosis-related mitochondrial proteins were promoted. Nevertheless, it was observed that autophagy became less active in osteosarcoma cells when PNS was administered. In a word, PNS were of potential therapeutic significance for osteosarcoma.

Keywords:  G0 / G1 phase; apoptosis; autophagy; osteosarcoma; p53; panax notoginseng saponins

DOI:  https://doi.org/10.7150/jca.54602
Epigenet Insights. 2021 ;14 25168657211051755

Global Histone H3 Lysine 4 Trimethylation (H3K4me3) Landscape Changes in Response to TGFβ.

Ankit Naik, Nidhi Dalpatraj, Noopur Thakur.

  TGFβ expression acts as a biomarker of poor prognosis in prostate cancer. It plays a dual functional role in prostate cancer. In the early stages of the tumor, it acts as a tumor suppressor while at the later stages of tumor development, it promotes metastasis. The molecular mechanisms of action of TGFβ are largely understood through the canonical and non-canonical signal transduction pathways. Our understanding of the mechanisms that establish transient TGFβ stimulation into stable gene expression patterns remains incomplete. Epigenetic marks like histone H3 modifications are directly linked with gene expression and they play an important role in tumorigenesis. In this report, we performed chromatin immunoprecipitation-sequencing (ChIP-Seq) to identify the genome-wide regions that undergo changes in histone H3 Lysine 4 trimethylation (H3K4me3) occupancy in response to TGFβ stimulation. We also show that TGFβ stimulation can induce acute epigenetic changes through the modulation of H3K4me3 signals at genes belonging to special functional categories in prostate cancer. TGFβ induces the H3K4me3 on its own ligands like TGFβ, GDF1, INHBB, GDF3, GDF6, BMP5 suggesting a positive feedback loop. The majority of genes were found to be involved in the positive regulation of transcription from the RNA polymerase II promoter in response to TGFβ. Other functional categories were intracellular protein transport, brain development, EMT, angiogenesis, antigen processing, antigen presentation via MHC class II, lipid transport, embryo development, histone H4 acetylation, positive regulation of cell cycle arrest, and genes involved in mitotic G2 DNA damage checkpoints. Our results link TGFβ stimulation to acute changes in gene expression through an epigenetic mechanism. These findings have broader implications on epigenetic bases of acute gene expression changes caused by growth factor stimulation.

Keywords:  ChIP-sequencing; H3K4me3; TGFβ; epigenetic; histone modification

DOI:  https://doi.org/10.1177/25168657211051755
J Cancer. 2021 ;12(22): 6676-6684

Hedgehog/GLI1 signaling pathway regulates the resistance to cisplatin in human osteosarcoma.

Daosen Chen, Xiaodiao Kang, Zhenxing Li, Liang Chen, Qiong Ma, Pei Fan.

  Purpose: This study aimed to investigate the role and mechanism of Hedgehog/GLI1 signaling pathway in regulating the resistance to cisplatin in osteosarcoma (OS). Materials and methods: Immunohistochemistry, western blotting and qRT-PCR assay were performed to analyze and compare the expression of GLI1 in OS tumor tissue and normal bone tissue as well as in cisplatin sensitive and resistant cell lines (SOSP-9607 and SOSP-9607/CR). Meanwhile, the biological role of GLI1 in OS was investigated by using down-regulated expression of GLI1 and functional assays, including CCK-8, colony formation assay, flow cytometry, and wound healing assay. Moreover, the relationship between GLI1 and γ-H2AX (DNA damage protein) in cells treated with GLI1 siRNA and cisplatin was examined using western blot analysis. In addition, GANT61, a inhibitor of Hedgehog pathway was used in xenograft tumor model to further verify the effect and mechanism of GLI1 on cisplatin resistance in OS. Results: We showed that GLI1 expression was up-regulated in OS patients and cisplatin-resistant cells. Silencing GLI1 significantly restored the sensitivity of OS to cisplatin, reduced proliferation, migration and cloning capacity of cisplatin sensitive and resistant cells, and increased the apoptosis rate in vitro. Furthermore, combined administration of GANT61 and cisplatin markedly inhibitted tumor growth in the mouse model. Mechanitic studies found that γ-H2AX is involved in the cisplatin resistance, and blockade of Hedgehog/GLI1 pathway increased the expression of γ-H2AX. Conclusion: Abnormal activation of Hedgehog-GLI1 pathway can regulate the expression of γ-H2AX, thus affecting DNA damage and repair functions, and promoting acquired cisplatin resistance of OS.

Keywords:  GLI1; Hedgehog pathway; cisplatin resistance; osteosarcoma; γ-H2AX

DOI:  https://doi.org/10.7150/jca.61591
Cell Death Dis. 2021 Oct 20. 12(11): 975

Tumor-suppressive function of EZH2 is through inhibiting glutaminase.

Yongfeng Liu, Cheng-E Tu, Xuxue Guo, Changjie Wu, Chuncai Gu, Qiuhua Lai, Yuxin Fang, Junqi Huang, Zhizhang Wang, Aimin Li, Side Liu.

Tumors can use metabolic reprogramming to survive nutrient stress. Epigenetic regulators play a critical role in metabolic adaptation. Here we screened a sgRNA library to identify epigenetic regulators responsible for the vulnerability of colorectal cancer (CRC) cells to glucose deprivation and found that more EZH2-knockout cells survived glucose deprivation. Then, we showed that EZH2 expression was significantly downregulated in response to glucose deprivation in a glucose-sensitive CRC cell line, and EZH2-knockdown cells were more resistant to glucose deprivation. Mechanistically, EZH2 deficiency upregulated the expression of glutaminase (GLS) and promoted the production of glutamate, which in turn led to increased synthesis of intracellular glutathione (GSH) and eventually attenuated the reactive oxygen species (ROS)-mediated cell death induced by glucose deprivation. Although EZH2 functioned as an oncogene in cancer progression and EZH2 knockout abolished colorectal cancer development in a mouse model, here we revealed a mechanistic link between EZH2 and metabolic reprogramming via the direct regulation of GLS expression and observed a negative correlation between EZH2 and GLS expression in colorectal cancer tissues. These findings further confirmed the importance of heterogeneity, provided an explanation for the clinical tolerance of cancer cells to EZH2 inhibitors from the perspective of metabolism, and proposed the possibility of combining EZH2 inhibitors and glutamine metabolism inhibitors for the treatment of cancer.

DOI: https://doi.org/10.1038/s41419-021-04212-7