bims-ectoca 2022-05-29 papers

bims-ectoca

Biomed News

on Epigenetic control of tolerance in cancer

Issue of 2022‒05‒29
twenty-one papers selected by
Ankita Daiya
BITS Pilani

Cracking chromatin with proteomics: From chromatome to histone modifications.
Discovery of precision targeting EZH2 degraders for triple-negative breast cancer.
Evidence of histone modification affecting ARID1A expression in colorectal cancer cell lines.
How Phosphofructokinase-1 Promotes PI3K and YAP/TAZ in Cancer: Therapeutic Perspectives.
TEAD4 as an Oncogene and a Mitochondrial Modulator.
Deletion of Trp53 and Rb1 in Ctsk-expressing cells drives osteosarcoma progression by activating glucose metabolism and YAP signaling.
First fluorescent acetylspermidine deacetylation assay for HDAC10 identifies selective inhibitors with cellular target engagement.
Ha-RasV12-Induced Multilayer Cellular Aggregates Is Mediated by Rac1 Activation Rather Than YAP Activation.
Nuclear and Cytoplasmatic Players in Mitochondria-Related CNS Disorders: Chromatin Modifications and Subcellular Trafficking.
Implication of Different Tumor Biomarkers in Drug Resistance and Invasiveness in Primary and Metastatic Colorectal Cancer Cell Lines.
Mutational signatures are markers of drug sensitivity of cancer cells.
EZH2 enhances proliferation and migration of trophoblast cell lines by blocking GADD45A-mediated p38/MAPK signaling pathway.
The biology of YAP in programmed cell death.
Insights into a Cancer-Target Demethylase: Substrate Prediction through Systematic Specificity Analysis for KDM3A.
Cross talk between acetylation and methylation regulators reveals histone modifier expression patterns posing prognostic and therapeutic implications on patients with colon cancer.
Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation.
Osteosarcoma-Specific Genes as a Diagnostic Tool and Clinical Predictor of Tumor Progression.
A novel crosstalk between autophagosomes and phagosomes that facilitates the clearance of apoptotic cells.
The heterogeneity of cellular senescence: insights at the single-cell level.
Evaluation of synergism in drug combinations and reference models for future orientations in oncology.
Mechanical Cues Regulate Histone Modifications and Cell Behavior.

Proteomics. 2022 May 28. e2100206

Cracking chromatin with proteomics: From chromatome to histone modifications.

Gianluca Sigismondo, Dimitris N Papageorgiou, Jeroen Krijgsveld.

  Chromatin is the assembly of genomic DNA and proteins packaged in the nucleus of eukaryotic cells, which together are crucial in regulating a plethora of cellular processes. Histones may be the best known class of protein constituents in chromatin, which are decorated by a range of post-translational modifications to recruit accessory proteins and protein complexes to execute specific functions, ranging from DNA compaction, repair, transcription and duplication, all in a dynamic fashion and depending on the cellular state. The key role of chromatin in cellular fitness is emphasized by the deregulation of chromatin determinants predisposing to different diseases, including cancer. For this reason, deep investigation of chromatin composition is fundamental to better understand cellular physiology. Proteomic approaches have played a crucial role to understand critical aspects of this complex interplay, benefiting from the ability to identify and quantify proteins and their modifications in an unbiased manner. This review gives an overview of the proteomic approaches that have been developed by combining mass spectrometry-based with tailored biochemical and genetic methods to examine overall protein make-up of chromatin, to characterize chromatin domains, to determine protein interactions, and to decipher the broad spectrum of histone modifications that represent the quintessence of chromatin function. This article is protected by copyright. All rights reserved.

Keywords:  cell biology; post-translational modification analysis; sample preparation; signal transduction; technology; technology

DOI:  https://doi.org/10.1002/pmic.202100206
Eur J Med Chem. 2022 May 20. pii: S0223-5234(22)00364-6. [Epub ahead of print]238 114462

Discovery of precision targeting EZH2 degraders for triple-negative breast cancer.

Cheng Wang, Xinye Chen, Xingchen Liu, Dehua Lu, Shang Li, Lailiang Qu, Fucheng Yin, Heng Luo, Yonglei Zhang, Zhongwen Luo, Ningjie Cui, Lingyi Kong, Xiaobing Wang.

  EZH2 is usually overexpressed in TNBC and other tumors, which has a great influence on the occurrence, development and prognosis of tumors. However, current EZH2 inhibitors, including Tazemetostat and GSK126, affect the methyl catalytic capacity of EZH2 and have little effect on the tumorigenic activity of EZH2 itself, resulting in poor efficacy against most solid tumors. Herein, we designed and optimized proteolytic targeting chimeras (PROTACs) precision targeting EZH2. The most active PROTAC molecule U3i has a high affinity for PRC2 complex (KD = 16.19 nM) and show good inhibitory effects on MDA-MB-231 (IC50 = 0.57 μM) and MDA-MB-468 (IC50 = 0.38 μM) cells. Compared with that of the GSK126, the growth inhibitory activities of U3i against these two TNBC cells increased by approximately 20- and 30-fold. Further studies showed that U3i can degrade PRC2 complex in TNBC cells, induce apoptosis, and cause little damage to normal cells. Therefore, U3i is a potential anticancer molecule for TNBC treatment.

Keywords:  Apoptosis; Enhancer of zeste homolog 2; Polycomb repressive complex 2; Proteolysis targeting chimeras; Triple-negative breast cancer

DOI:  https://doi.org/10.1016/j.ejmech.2022.114462
Gastroenterol Hepatol Bed Bench. 2022 ;15(1): 32-38

Evidence of histone modification affecting ARID1A expression in colorectal cancer cell lines.

Mehran Erfani, Mozhdeh Zamani, Pooneh Mokarram.

Aim: The current study aimed to focus on the role of histone deacetylation in reduced ARID1A expression in colorectal cancer cell lines.Background: ARID1A, a subunit of the switch/sucrose nonfermentable chromatin remodeling complex, has emerged as a bona fide tumor suppressor and is frequently downregulated and inactivated in multiple human cancers. Epigenetic modifications play an important role in dysregulation of gene expression in cancer. DNA methylation has been reported as an important regulator of ARID1A expression in colorectal cancer cell lines; however, the histone modification role in ARID1A suppression in colorectal cancer remains unclear.
Methods: The expression levels of ARID1A mRNA were determined using real-time quantitative PCR in colorectal cancer cell lines including HCT116, SW48, HT29, SW742, LS180, and SW480. To evaluate the effect of histone deacetylation on ARID1A expression, all cell lines were treated with trichostatin A (TSA), a histone deacetylase inhibitor. SPSS software (Version 23) and GraphPad Prism (Version 6.01) were applied for data analysis using one-way ANOVA, followed by Tukey's multiple comparison tests.
Results: Treatment of colorectal cancer cell lines with TSA increased ARID1A expression in a cell line-dependent manner, suggesting that histone deacetylation is at least one factor contributing to ARID1A downregulation in colorectal cancer.
Conclusion: Histone deacetylase inhibitors might provide a strategy to restore ARID1A expression and may bring benefits to the colorectal cancer patients with a broader range of genetic backgrounds.

Keywords: ARID1A; Colorectal cancer; Epigenetics; Histone acetylation
Cancers (Basel). 2022 May 18. pii: 2478. [Epub ahead of print]14(10):

How Phosphofructokinase-1 Promotes PI3K and YAP/TAZ in Cancer: Therapeutic Perspectives.

Luca Simula, Marco Alifano, Philippe Icard.

  PI3K/AKT is one of the most frequently altered signaling pathways in human cancers, supporting the activation of many proteins sustaining cell metabolism, proliferation, and aggressiveness. Another important pathway frequently altered in cancer cells is the one regulating the YAP/TAZ transcriptional coactivators, which promote the expression of genes sustaining aerobic glycolysis (such as WNT, MYC, HIF-1), EMT, and drug resistance. Of note, the PI3K/AKT pathway can also regulate the YAP/TAZ one. Unfortunately, although PI3K and YAP inhibitors are currently tested in highly resistant cancers (both solid and hematologic ones), several resistance mechanisms may arise. Resistance mechanisms to PI3K inhibitors may involve the stimulation of alternative pathways (such as RAS, HER, IGFR/AKT), the inactivation of PTEN (the physiologic inhibitor of PI3K), and the expression of anti-apoptotic Bcl-xL and MCL1 proteins. Therefore, it is important to improve current therapeutic strategies to overcome these limitations. Here, we want to highlight how the glycolytic enzyme PFK1 (and its product F-1,6-BP) promotes the activation of both PI3K/AKT and YAP/TAZ pathways by several direct and indirect mechanisms. In turn, PI3K/AKT and YAP/TAZ can promote PFK1 activity and F-1,6-BP production in a positive feedback loop, thus sustaining the Warburg effect and drug resistance. Thus, we propose that the inhibition of PFK1 (and of its key activator PFK2/PFKFB3) could potentiate the sensitivity to PI3K and YAP inhibitors currently tested. Awaiting the development of non-toxic inhibitors of these enzymes, we propose to test the administration of citrate at a high dosage, because citrate is a physiologic inhibitor of both PFK1 and PFK2/PFKFB3. Consistently, in various cultured cancer cells (including melanoma, sarcoma, hematologic, and epithelial cancer cells), this "citrate strategy" efficiently inhibits the IGFR1/AKT pathway, promotes PTEN activity, reduces Bcl-xL and MCL1 expression, and increases sensitivity to standard chemotherapy. It also inhibits the development of sarcoma, pancreatic, mammary HER+ and lung RAS-driven tumors in mice without apparent toxicities.

Keywords:  F-1,6-BP; PFK1; PI3K; YAP/TAZ; citrate; drug resistance

DOI:  https://doi.org/10.3390/cancers14102478
Front Cell Dev Biol. 2022 ;10 890419

TEAD4 as an Oncogene and a Mitochondrial Modulator.

Sheng-Chieh Hsu, Ching-Yu Lin, Yen-Yi Lin, Colin C Collins, Chia-Lin Chen, Hsing-Jien Kung.

  TEAD4 (TEA Domain Transcription Factor 4) is well recognized as the DNA-anchor protein of YAP transcription complex, which is modulated by Hippo, a highly conserved pathway in Metazoa that controls organ size through regulating cell proliferation and apoptosis. To acquire full transcriptional activity, TEAD4 requires co-activator, YAP (Yes-associated protein) or its homolog TAZ (transcriptional coactivator with PDZ-binding motif) the signaling hub that relays the extracellular stimuli to the transcription of target genes. Growing evidence suggests that TEAD4 also exerts its function in a YAP-independent manner through other signal pathways. Although TEAD4 plays an essential role in determining that differentiation fate of the blastocyst, it also promotes tumorigenesis by enhancing metastasis, cancer stemness, and drug resistance. Upregulation of TEAD4 has been reported in several cancers, including colon cancer, gastric cancer, breast cancer, and prostate cancer and serves as a valuable prognostic marker. Recent studies show that TEAD4, but not other members of the TEAD family, engages in regulating mitochondrial dynamics and cell metabolism by modulating the expression of mitochondrial- and nuclear-encoded electron transport chain genes. TEAD4's functions including oncogenic activities are tightly controlled by its subcellular localization. As a predominantly nuclear protein, its cytoplasmic translocation is triggered by several signals, such as osmotic stress, cell confluency, and arginine availability. Intriguingly, TEAD4 is also localized in mitochondria, although the translocation mechanism remains unclear. In this report, we describe the current understanding of TEAD4 as an oncogene, epigenetic regulator and mitochondrial modulator. The contributing mechanisms will be discussed.

Keywords:  Tead4; cancer; epigenetics; mitochondria; oxphos

DOI:  https://doi.org/10.3389/fcell.2022.890419
MedComm (2020). 2022 Jun;3(2): e131

Deletion of Trp53 and Rb1 in Ctsk-expressing cells drives osteosarcoma progression by activating glucose metabolism and YAP signaling.

Yang Li, Shuting Yang, Yang Liu, Shuying Yang.

  Glucose metabolism reprogramming is a critical factor in the progression of multiple cancers and is directly regulated by many tumor suppressors. However, how glucose metabolism regulates osteosarcoma development and progression is largely unknown. Cathepsin K (Ctsk) has been reported to express in chondroprogenitor cells and stem cells besides osteoclasts. Moreover, mutations in the tumor suppressors transformation-related protein 53 (Trp53) and retinoblastoma protein (Rb1) are evident in approximately 50%-70% of human osteosarcoma. To understand how deletion of Trp53 and Rb1 in Ctsk-expressing cells drives tumorigenesis, we generated the Ctsk-Cre;Trp53f/f/Rb1f/f mouse model. Our data revealed that those mice developed osteosarcoma without formation of tumor in osteoclast lineage. The level of cortical bone destruction was gradually increased in parallel to the osteosarcoma progression rate. Through mechanistic studies, we found that loss of Trp53/Rb1 in Ctsk-expressing cells significantly elevated Yes-associated protein (YAP) expression and activity. YAP/TEAD1 complex binds to the glucose transporter 1 (Glut1) promoter to upregulate Glut1 expression. Upregulated Glut1 expression led to overactive glucose metabolism, increasing osteosarcoma progression. Ablation of YAP signaling inhibited energy metabolism and delayed osteosarcoma progression in Ctsk-Cre;Trp53f/f/Rb1f/f mice. Collectively, these findings provide proof of principle that inhibition of YAP activity may be a potential strategy for osteosarcoma treatment.

Keywords:  Glut1; Rb1; Trp53; YAP; bone; osteosarcoma

DOI:  https://doi.org/10.1002/mco2.131
Chembiochem. 2022 May 24.

First fluorescent acetylspermidine deacetylation assay for HDAC10 identifies selective inhibitors with cellular target engagement.

Daniel Herp, Johannes Ridinger, Dina Robaa, Stephen A Shinsky, Karin Schmidtkunz, Talha Z Yesiloglu, Theresa Bayer, Raphael R Steimbach, Corey J Herbst-Gervasoni, Annika Merz, Christophe Romier, Peter Sehr, Nikolas Gunkel, Aubry K Miller, David W Christianson, Ina Oehme, Wolfgang Sippl, Manfred Jung.

  Histone deacetylases (HDACs) are key epigenetic regulators involved in many diseases, especially cancer. Five HDAC inhibitors have been approved as drugs and many are in clinical trials. Among the 11 zinc-dependent HDACs, HDAC10 has received relatively little attention by drug discovery campaigns, despite its involvement, e.g., in the pathogenesis of neuroblastoma. This is due in part to a lack of robust enzymatic conversion assays. HDAC10 has strong preferences for deacetylation of oligoamine substrates like acetyl-putrescine or -spermidine. Hence, it is also termed as a polyamine deacetylase (PDAC). Here, we present the first fluorescent conversion assay for HDAC10 using an aminocoumarin-labelled acetyl-spermidine derivative to measure its PDAC activity. Using this assay, we identified potent inhibitors of HDAC10-mediated spermidine deacetylation in vitro. Based on the oligoamine preference of HDAC10, we also designed inhibitors with a basic moiety in appropriate distance to the zinc binding hydroxamate that showed potent inhibition of HDAC10 with high selectivity, and we solved a HDAC10-inhibitor structure using X-ray crystallography. We could demonstrate selective cellular target engagement for HDAC10 but a lysosomal phenotype in neuroblastoma cells that was previously associated with HDAC10 inhibition was not observed. Thus, we have developed new chemical probes for HDAC10 that allow further clarification of the biological role of this enzyme.

Keywords:  HDAC; HDAC10; histone deacetylases; inhibitors; polyamine

DOI:  https://doi.org/10.1002/cbic.202200180
Biomedicines. 2022 Apr 23. pii: 977. [Epub ahead of print]10(5):

Ha-RasV12-Induced Multilayer Cellular Aggregates Is Mediated by Rac1 Activation Rather Than YAP Activation.

Li-Ying Wu, Chia-Lin Han, Hsi-Hui Lin, Ming-Jer Tang.

  We demonstrate that Ha-RasV12 overexpression induces the nuclear translocation of Hippo effector Yes-associated protein (YAP) in MDCK cells via the hippo-independent pathway at the confluent stage. Ha-RasV12 overexpression leads to the downregulation of Caveolin-1 (Cav1) and the disruption of junction integrity. It has been shown that the disruption of actin belt integrity causes YAP nuclear translocation in epithelial cells at high density. Therefore, we hypothesized that Ha-RasV12-decreased Cav1 leads to the disruption of cell junction integrity, which subsequently facilitates YAP nuclear retention. We revealed that Ha-RasV12 downregulated Cav1 through the ERK pathway. Furthermore, the distribution and expression of Cav1 mediated the cell junction integrity and YAP nuclear localization. This suggests that the downregulation of Cav1 induced by Ha-RasV12 disrupted the cell junction integrity and promoted YAP nuclear translocation. We further indicated the consequence of Ha-RasV12-induced YAP activation. Surprisingly, the activation of YAP is not required for Ha-RasV12-induced multilayer cellular aggregates. Instead, Ha-RasV12 triggered the ERK-Rac pathway to promote cellular aggregate formation. Moreover, the overexpression of constitutively active Rac is sufficient to trigger cellular aggregation in MDCK cells at the confluent stage. This highlights that Rac activity is essential for cellular aggregates.

Keywords:  Caveolin-1; Ha-RasV12; Rac; YAP; cell aggregates; myosin IIB

DOI:  https://doi.org/10.3390/biomedicines10050977
Biomolecules. 2022 Apr 23. pii: 625. [Epub ahead of print]12(5):

Nuclear and Cytoplasmatic Players in Mitochondria-Related CNS Disorders: Chromatin Modifications and Subcellular Trafficking.

Matteo Gasparotto, Yi-Shin Lee, Alessandra Palazzi, Marcella Vacca, Francesco Filippini.

  Aberrant mitochondrial phenotypes are common to many central nervous system (CNS) disorders, including neurodegenerative and neurodevelopmental diseases. Mitochondrial function and homeostasis depend on proper control of several biological processes such as chromatin remodeling and transcriptional control, post-transcriptional events, vesicle and organelle subcellular trafficking, fusion, and morphogenesis. Mutation or impaired regulation of major players that orchestrate such processes can disrupt cellular and mitochondrial dynamics, contributing to neurological disorders. The first part of this review provides an overview of a functional relationship between chromatin players and mitochondria. Specifically, we relied on specific monogenic CNS disorders which share features with mitochondrial diseases. On the other hand, subcellular trafficking is coordinated directly or indirectly through evolutionarily conserved domains and proteins that regulate the dynamics of membrane compartments and organelles, including mitochondria. Among these "building blocks", longin domains and small GTPases are involved in autophagy and mitophagy, cell reshaping, and organelle fusion. Impairments in those processes significantly impact CNS as well and are discussed in the second part of the review. Hopefully, in filling the functional gap between the nucleus and cytoplasmic organelles new routes for therapy could be disclosed.

Keywords:  MeCP2; Rab; SNARE; VAMP; autophagy; chromatin remodeling; longin domain; mitochondria; mitophagy; small GTPase; subcellular trafficking

DOI:  https://doi.org/10.3390/biom12050625
Biomedicines. 2022 May 06. pii: 1083. [Epub ahead of print]10(5):

Implication of Different Tumor Biomarkers in Drug Resistance and Invasiveness in Primary and Metastatic Colorectal Cancer Cell Lines.

Marta Sánchez-Díez, Nicolás Alegría-Aravena, Marta López-Montes, Josefa Quiroz-Troncoso, Raquel González-Martos, Adrián Menéndez-Rey, José Luis Sánchez-Sánchez, Juan Manuel Pastor, Carmen Ramírez-Castillejo.

  Protein expression profiles are directly related to the different properties of cells and are conditioned by the cellular niche. As an example, they are the cause of the characteristic cell plasticity, epithelium-mesenchymal transition (EMT), and drug resistance of cancer cells. This article characterizes ten biomarkers related to these features in three human colorectal cancer cell lines: SW-480, SW-620, and DLD-1, evaluated by flow cytometry; and in turn, resistance to oxaliplatin is studied through dose-response trials. The main biomarkers present in the three studied lines correspond to EpCAM, CD-133, and AC-133, with the latter two in low proportions in the DLD-1 line. The biomarker CD166 is present in greater amounts in SW-620 and DLD-1 compared to SW-480. Finally, DLD-1 shows high values of Trop2, which may explain the aggressiveness and resistance of these cells to oxaliplatin treatments, as EpCAM is also highly expressed. Exposure to oxaliplatin slows cell growth but also helps generate resistance to the treatment. In conclusion, the response of the cell lines is variable, due to their genetic variability, which will condition protein expression and cell growth. Further analyses in this area will provide important information for better understanding of patients' cellular response and how to prevent resistance.

Keywords:  cancer stem cells; cell plasticity; chemotherapy; epithelium–mesenchymal transition; oxaliplatin; resistance; tumor biomarkers

DOI:  https://doi.org/10.3390/biomedicines10051083
Nat Commun. 2022 May 25. 13(1): 2926

Mutational signatures are markers of drug sensitivity of cancer cells.

Jurica Levatić, Marina Salvadores, Francisco Fuster-Tormo, Fran Supek.

Genomic analyses have revealed mutational footprints associated with DNA maintenance gone awry, or with mutagen exposures. Because cancer therapeutics often target DNA synthesis or repair, we asked if mutational signatures make useful markers of drug sensitivity. We detect mutational signatures in cancer cell line exomes (where matched healthy tissues are not available) by adjusting for the confounding germline mutation spectra across ancestries. We identify robust associations between various mutational signatures and drug activity across cancer cell lines; these are as numerous as associations with established genetic markers such as driver gene alterations. Signatures of prior exposures to DNA damaging agents - including chemotherapy - tend to associate with drug resistance, while signatures of deficiencies in DNA repair tend to predict sensitivity towards particular therapeutics. Replication analyses across independent drug and CRISPR genetic screening data sets reveal hundreds of robust associations, which are provided as a resource for drug repurposing guided by mutational signature markers.

DOI: https://doi.org/10.1038/s41467-022-30582-3
Bioengineered. 2022 May;13(5): 12583-12597

EZH2 enhances proliferation and migration of trophoblast cell lines by blocking GADD45A-mediated p38/MAPK signaling pathway.

Xuefang Qian, Yuying Zhang.

  Impaired activity of the trophoblasts is a major contributor to the progression of pregnancy pathologies including preeclampsia (PE). This research probed the function of enhancer of zeste homolog 2 (EZH2) in activity of trophoblast cells and its correlation with growth arrest and DNA damage inducible alpha (GADD45A). EZH2 was predicted to be downregulated in placental tissues in PE according to a gene chip analysis, and reduced expression of EZH2 was detected in the placental tissues of patients with PE. Overexpression of EZH2 augmented proliferation and invasiveness of two trophoblast cell lines HTR-8/SVneo and JEG3 cells. EZH2 catalyzed trimethylation of lysine 27 on histone 3 (H3K27me3) in GADD45A promoter to suppress its transcription. GADD45A silencing increased the activity of the trophoblast cell lines and inactivated the p38/mitogen-activated protein kinase (MAPK) signaling pathway. Rescue experiments confirmed that either inhibition of GADD45A or p38 restored the proliferation, migration, and invasiveness of the trophoblast cell lines suppressed by EZH2 silencing. In conclusion, this work suggests that EZH2 enhances activity of trophoblast cell lines by suppressing GADD45A-mediated p38/MAPK signaling pathway.

Keywords:  EZH2; GADD45A; Preeclampsia; p38/MAPK; trophoblast

DOI:  https://doi.org/10.1080/21655979.2022.2074620
Biomark Res. 2022 May 23. 10(1): 34

The biology of YAP in programmed cell death.

Yifan Cheng, Misha Mao, Yong Lu.

  In the last few decades, YAP has been shown to be critical in regulating tumor progression. YAP activity can be regulated by many kinase cascade pathways and proteins through phosphorylation and promotion of cytoplasmic localization. Other factors can also affect YAP activity by modulating its binding to different transcription factors (TFs). Programmed cell death (PCD) is a genetically controlled suicide process present with the scope of eliminating cells unnecessary or detrimental for the proper development of the organism. In some specific states, PCD is activated and facilitates the selective elimination of certain types of tumor cells. As a candidate oncogene correlates with many regulatory factors, YAP can inhibit or induce different forms of PCD, including apoptosis, autophagy, ferroptosis and pyroptosis. Furthermore, YAP may act as a bridge between different forms of PCD, eventually leading to different outcomes regarding tumor development. Researches on YAP and PCD may benefit the future development of novel treatment strategies for some diseases. Therefore, in this review, we provide a general overview of the cellular functions of YAP and the relationship between YAP and PCD.

Keywords:  Apoptosis; Autophagy; Ferroptosis; Programmed cell death; Pyroptosis; YAP

DOI:  https://doi.org/10.1186/s40364-022-00365-5
Biomolecules. 2022 Apr 27. pii: 641. [Epub ahead of print]12(5):

Insights into a Cancer-Target Demethylase: Substrate Prediction through Systematic Specificity Analysis for KDM3A.

Anand Chopra, William G Willmore, Kyle K Biggar.

  Jumonji C (JmjC) lysine demethylases (KDMs) catalyze the removal of methyl (-CH3) groups from modified lysyl residues. Several JmjC KDMs promote cancerous properties and these findings have primarily been in relation to histone demethylation. However, the biological roles of these enzymes are increasingly being shown to also be attributed to non-histone demethylation. Notably, KDM3A has become relevant to tumour progression due to recent findings of this enzyme's role in promoting cancerous phenotypes, such as enhanced glucose consumption and upregulated mechanisms of chemoresistance. To aid in uncovering the mechanism(s) by which KDM3A imparts its oncogenic function(s), this study aimed to unravel KDM3A substrate specificity to predict high-confidence substrates. Firstly, substrate specificity was assessed by monitoring activity towards a peptide permutation library of histone H3 di-methylated at lysine-9 (i.e., H3K9me2). From this, the KDM3A recognition motif was established and used to define a set of high-confidence predictions of demethylation sites from within the KDM3A interactome. Notably, this led to the identification of three in vitro substrates (MLL1, p300, and KDM6B), which are relevant to the field of cancer progression. This preliminary data may be exploited in further tissue culture experiments to decipher the avenues by which KDM3A imparts cancerous phenotypes.

Keywords:  KDM3A; lysine demethylase; motif; non-histone; substrate prediction; substrate specificity

DOI:  https://doi.org/10.3390/biom12050641
Clin Epigenetics. 2022 May 23. 14(1): 70

Cross talk between acetylation and methylation regulators reveals histone modifier expression patterns posing prognostic and therapeutic implications on patients with colon cancer.

Rui Zhou, Fuli Xie, Kuncai Liu, Xuee Zhou, Xuemei Chen, Jinzhang Chen, Shaoyan Xi, Zhenhua Huang, Xiaoxiang Rong.

  BACKGROUND: Alterations in histone modifications have been reported to be related to tumorigenicity and tumor progression. However, whether histone modification can aid the classification of patients or influence clinical behavior in patients with colon cancer remains unclear. Therefore, this study aimed to evaluate histone modifier expression patterns using the unsupervised clustering of the transcriptomic expressions of 88 histone acetylation and methylation regulators.RESULTS: In this study, by consensus clustering analysis based on the transcriptome data of 88 histone modification regulators, we identified four distinct expression patterns of histone modifiers associated with different prognoses, intrinsic fluorouracil sensitivities, biological pathways, and tumor microenvironment characteristics among 1372 colon cancer samples. In these four clusters, the HMC4 cluster represented a stroma activation phenotype characterized by both the worst prognosis and lowest response rates to fluorouracil treatment. Then, we established a scoring scheme comprising 155 genes designated as "HM_score" by using the Boruta algorithm to distinguish colon cancer patients within the HMC4 cluster. Patients with a high HM_score were considered to have high stromal pathway activation, high stromal fraction, and an unfavorable prognosis. Further analyses indicated that a high HM_score also correlated with reduced therapeutic benefits from fluorouracil chemotherapy. Moreover, through CRISPR library screening, ZEB2 was found to be a critical driver gene that mediates fluorouracil resistance, which is associated with histone modifier expression patterns.
CONCLUSIONS: This study highlights that characterizing histone modifier expression patterns may help better understand the epigenetic mechanisms underlying tumor heterogeneity in patients with colon cancer and provide more personalized therapeutic strategies.

Keywords:  CRISPR library screen; Chemotherapy; Colon cancer; Fluorouracil; Histone modifications; Prognosis; ZEB2

DOI:  https://doi.org/10.1186/s13148-022-01290-y
Proc Natl Acad Sci U S A. 2022 May 31. 119(22): e2201883119

Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation.

Katerina Kraft, Kathryn E Yost, Sedona E Murphy, Andreas Magg, Yicheng Long, M Ryan Corces, Jeffrey M Granja, Lars Wittler, Stefan Mundlos, Thomas R Cech, Alistair N Boettiger, Howard Y Chang.

  SignificanceThe relationship between long-range Polycomb-associated chromatin contacts and the linear propagation of histone H3 lysine 27 trimethylation (H3K27me3) by Polycomb repressive complex 2 (PRC2) is not well-characterized. Here, we nominate a role for developmental loci as genomic architectural elements that enable long-range spreading of H3K27me3. Polycomb-associated loops are disrupted upon loss of PRC2 binding and deletion of loop anchors results in alterations of H3K27me3 deposition and ectopic gene expression. These results suggest that Polycomb-mediated genome architecture is important for gene repression during embryonic development.

Keywords:  3D genome; Polycomb-group proteins; RNA-mediated Polycomb loops; epigenetic silencing; heterochromatin

DOI:  https://doi.org/10.1073/pnas.2201883119
Biology (Basel). 2022 May 01. pii: 698. [Epub ahead of print]11(5):

Osteosarcoma-Specific Genes as a Diagnostic Tool and Clinical Predictor of Tumor Progression.

Pattaralawan Sittiju, Parunya Chaiyawat, Dumnoensun Pruksakorn, Jeerawan Klangjorhor, Weerinrada Wongrin, Phichayut Phinyo, Rawikant Kamolphiwong, Areerak Phanphaisarn, Pimpisa Teeyakasem, Prachya Kongtawelert, Peraphan Pothacharoen.

  A liquid biopsy is currently an interesting tool for measuring tumor material with the advantage of being non-invasive. The overexpression of vimentin and ezrin genes was associated with epithelial-mesenchymal transition (EMT), a key process in metastasis and progression in osteosarcoma (OS). In this study, we identified other OS-specific genes by calculating differential gene expression using the Gene Expression Omnibus (GEO) database, confirmed by using quantitative reverse transcription-PCR (qRT-PCR) to detect OS-specific genes, including VIM and ezrin in the buffy coat, which were obtained from the whole blood of OS patients and healthy donors. Furthermore, the diagnostic model for OS detection was generated by utilizing binary logistic regression with a multivariable fractional polynomial (MFP) algorithm. The model incorporating VIM, ezrin, and COL5A2 genes exhibited outstanding discriminative ability, as determined by the receiver operating characteristic curve (AUC = 0.9805, 95% CI 0.9603, 1.000). At the probability cut-off value of 0.3366, the sensitivity and the specificity of the model for detecting OS were 98.63% (95% CI 90.5, 99.7) and 94.94% (95% CI 87.5, 98.6), respectively. Bioinformatic analysis and qRT-PCR, in our study, identified three candidate genes that are potential diagnostic and prognostic genes for OS.

Keywords:  biomarker; mRNA expression; osteosarcoma; qRT-PCR

DOI:  https://doi.org/10.3390/biology11050698
Autophagy. 2022 May 23.

A novel crosstalk between autophagosomes and phagosomes that facilitates the clearance of apoptotic cells.

Zheng Zhou, Omar Peña-Ramos.

  During an animal's life, many cells undergo apoptosis, a form of genetically programmed cell death. These cells are swiftly engulfed by other cells through phagocytosis and subsequently degraded inside phagosomes. Phagocytosis and macroautophagy/autophagy are two different cellular events: whereas phagocytosis is a cell-eat-cell event, autophagy, or "self-eating", occurs within one cell, resulting in the enveloping of protein aggregates or damaged organelles within double-membrane autophagosomes. Despite this critical difference, these two events share common features: (1) both are means of safe garbage disposal; (2) both phagosomes and autophagosomes fuse to lysosomes, which drive the degradation of their contents; and (3) both events facilitate the recycling of biological materials. Previously, whether autophagosomes per se directly participate in the degradation of apoptotic cells was unknown, although autophagy proteins were implicated in apoptotic cell clearance. We recently discovered that autophagosomes fuse with phagosomes and contribute to the degradation of apoptotic cells.

Keywords:  Autophagosomes, C. elegans; CED-1; LGG-1/LGG-2; crosstalk; degradation of apoptotic cells; membrane fusion; membrane signaling; phagocytosis; phagosomes

DOI:  https://doi.org/10.1080/15548627.2022.2080384
Trends Cell Biol. 2022 May 20. pii: S0962-8924(22)00116-7. [Epub ahead of print]

The heterogeneity of cellular senescence: insights at the single-cell level.

Rachel L Cohn, Nathan S Gasek, George A Kuchel, Ming Xu.

  Senescent cells are highly associated with aging and pathological conditions and could be targeted to slow the aging process. One commonly used marker to examine senescent cells in vivo is p16, which has led to important discoveries. Recent studies have also described new senescence markers beyond p16 and have highlighted the importance of investigating senescence heterogeneity in cell types and tissues. With the development of high-throughput technologies, such as single-cell RNA-seq and single-nucleus RNA-seq, we can examine senescent cells at the single-cell level and potentially uncover new markers. This review emphasizes that there is an urgent need to investigate senescence heterogeneity and discuss how this could be accomplished by using advanced technologies and sequencing datasets.

Keywords:  RNA-sequencing; aging; p16; p21; senolytics

DOI:  https://doi.org/10.1016/j.tcb.2022.04.011
Curr Res Pharmacol Drug Discov. 2022 ;3 100110

Evaluation of synergism in drug combinations and reference models for future orientations in oncology.

Diana Duarte, Nuno Vale.

  Current cancer therapy includes a variety of strategies that can comprise only one type of treatment or a combination of multiple treatments. Chemotherapy is still the gold standard for cancer therapy, though sometimes associated with undesired side effects and the development of drug resistance. For this reason, drug combination is an approach that has been proposed to overcome the problems related to monotherapy and several studies have already demonstrated the superiority of combined therapies compared to monotherapy. The main goal when designing and evaluating drug combinations is to achieve synergistic effects by demonstrating that the combined effects are greatly superior to the expected from the additive effects of the single drugs, allowing for dosage reduction and therefore decreasing toxicity. Nevertheless, synergism quantification is not a simple task due to the different definitions of additivity and over the years several reference models have been proposed based on different assumptions and with different mathematical frameworks. In this review, we begin to cover the available treatment options for cancer therapy, with emphasis on the importance of drug combinations in cancer therapy. We next describe the classical reference models that have been proposed for synergism evaluation, usually classified as effect-based and dose-effect based methods, with a brief analysis of the current limitations of these models. We also describe here the novel methods for the accurate quantification of drug interactions in combined treatments. At the end of this manuscript, we covered some of the most recent preclinical and clinical combination studies that reflect the importance of the appropriate, accurate and precise application of the concepts and methodologies here described for the evaluation of synergism.

Keywords:  Bliss; Combination index; Drug combination; Loewe; Oncology; Synergy

DOI:  https://doi.org/10.1016/j.crphar.2022.100110
Stem Cells Int. 2022 ;2022 9179111

Mechanical Cues Regulate Histone Modifications and Cell Behavior.

Buwei Hu, Dandan Zhou, Haoming Wang, Ning Hu, Weikang Zhao.

Change of biophysical factors in tissue microenvironment is an important step in a chronic disease development process. A mechanical and biochemical factor from cell living microniche can regulate cell epigenetic decoration and, therefore, further induce change of gene expression. In this review, we will emphasize the mechanism that biophysical microenvironment manipulates cell behavior including gene expression and protein decoration, through modifying histone amino acid residue modification. The influence given by different mechanical forces, including mechanical stretch, substrate surface stiffness, and shear stress, on cell fate and behavior during chronic disease development including tumorigenesis will also be teased out. Overall, the recent work summarized in this review culminates on the hypothesis that a mechanical factor stimulates the modification on histone which could facilitate disease detection and potential therapeutic target.

DOI: https://doi.org/10.1155/2022/9179111