bims-drucaf 2020-08-23 papers

Eur J Med Chem. 2020 Aug 01. pii: S0223-5234(20)30649-8. [Epub ahead of print]206 112677

Design and synthesis of novel Flavone-based histone deacetylase inhibitors antagonizing activation of STAT3 in breast cancer.

Mingming Wei, Maodun Xie, Zhen Zhang, Yujiao Wei, Juan Zhang, Hongli Pan, Benlong Li, Jingjing Wang, Yang Song, Chuangke Chong, Rui Zhao, Jiefu Wang, Li Yu, Guang Yang, Cheng Yang.

Histone deacetylases (HDACs) inhibitors have demonstrated a great clinical achievement in hematological malignancies. However, the efficacy of HDACs inhibitors in treating solid tumors remains limited due to the complicated tumor microenvironment. In this study, we designed and synthesized a class of novel HDACs inhibitors based on the structure of flavones and isoflavones, followed by biological evaluation. To be specific, a lead compound 15a was discovered with strong anti-proliferative effects on a variety of solid tumor cells, especially for breast cancer cells with resistance to SAHA. Studies demonstrated that 15a could significantly inhibit the activity of HDAC 1, 2, 3 (class I) and 6 (class IIB), leading to a dose-dependent accumulation of acetylated histones and α-Tubulin, cell cycle arrest (G1/S phase) and apoptosis in breast cancer cells. Furthermore, the lead compound 15a could also antagonize the activation of STAT3 induced by HDACs inhibition in some breast cancer cells, which further reduced the level of pro-survive proteins in tumor cells and enhanced anti-tumor activity regulated by STAT3 signaling in vivo. Overall, our findings demonstrated that the novel compound 15a might be a HDACs inhibitor candidate, which could be used as promising chemotherapeutic agent for breast cancer.

Keywords: Flavones; HDAC; Hybrid; STAT3 signaling pathway; Solid malignancies

DOI: https://doi.org/10.1016/j.ejmech.2020.112677

Semin Cancer Biol. 2020 Aug 16. pii: S1044-579X(20)30176-0. [Epub ahead of print]

Histone modifications in epigenetic regulation of cancer: perspectives and achieved progress.

Margarita E Neganova, Sergey G Klochkov, Yulia R Aleksandrova, Gjumrakch Aliev.

Epigenetic changes associated with histone modifications play an important role in the emergence and maintenance of the phenotype of various cancer types. In contrast to direct mutations in the main DNA sequence, these changes are reversible, which makes the development of inhibitors of enzymes of post-translational histone modifications one of the most promising strategies for the creation of anticancer drugs. To date, a wide variety of histone modifications have been found that play an important role in the regulation of chromatin state, gene expression, and other nuclear events. This review examines the main features of the most common and studied epigenetic histone modifications with a proven role in the pathogenesis of a wide range of malignant neoplasms: acetylation / deacetylation and methylation / demethylation of histone proteins, as well as the role of enzymes of the HAT / HDAC and HMT / HDMT families in the development of oncological pathologies. The data on the relationship between histone modifications and certain types of cancer are presented and discussed. Special attention is devoted to the consideration of various strategies for the development of epigenetic inhibitors. The main directions of the development of inhibitors of histone modifications are analyzed and effective strategies for their creation are identified and discussed. The most promising strategy is the use of multitarget drugs, which will affect multiple molecular targets of cancer. A critical analysis of the current status of approved epigenetic anticancer drugs has also been performed.

Keywords: cancer; epigenetic; histone acetyltransferase; histone deacetylase; histone demethylase; histone methyltransferase; histone modifications; inhibitors

DOI: https://doi.org/10.1016/j.semcancer.2020.07.015

Biochem Pharmacol. 2020 Aug 14. pii: S0006-2952(20)30436-6. [Epub ahead of print] 114200

The mechanisms of action of chromatin remodelers and implications in development and disease.

Rakesh Kumar Sahu, Sakshi Singh, Raghuvir Singh Tomar.

The eukaryotic genetic material is packaged in the form of chromatin by wrapping DNA around nucleosomes. Cells maintain chromatin in a dynamic state by utilising various ATP-dependent chromatin remodelling complexes which can induce structural transformations in chromatin. All chromatin remodelers contain an ATP hydrolysing-DNA translocase motor which facilitates nucleosomal DNA translocation. By DNA translocation ISWI and CHD subfamily remodelers slide nucleosomes and arrange them in a regularly spaced array. While SWI/SNF subfamily remodelers evict or displace nucleosomes from chromatin which promotes accessibility recruitment of transcription machinery and DNA repair factors on the DNA. Beside DNA translocation, ISWI, CHD and INO80 subfamily remodelers escort nucleosome organisation and editing. In this review; we discuss different mechanisms by which chromatin remodelers regulate chromatin accessibility, nucleosome assembly and nucleosome editing. We attempt to elucidate how their action mediates various cellular and developmental processes, and their deregulation leads to disease pathogenesis. We emphasised on their role in cancer progression and potential therapeutic implications of these complexes. We also described the drugs and strategies which are being developed to target different subunits remodelling complexes, histone modifying enzymes and polycomb repressive complex to cure various cancer types. This includes ATPase inhibitors, EZH2 (enhancer of zeste homolog 2) inhibitors, BET (bromodomain and extra terminal) inhibitors, PROTAC (proteolysis targeting chimaera) and inhibitors of protein-protein interaction.

Keywords: ATP-dependent chromatin remodelers; CHD; Chromatin remodelling; INO80; ISWI; SWI/SNF

DOI: https://doi.org/10.1016/j.bcp.2020.114200

Gastroenterology. 2020 Aug 16. pii: S0016-5085(20)35055-1. [Epub ahead of print]

In Colorectal Cancer Cells With Mutant KRAS, SLC25A22-Mediated Glutaminolysis Reduces DNA Demethylation to Increase WNT Signaling, Stemness, and Drug Resistance.

Chi Chun Wong, Jiaying Xu, Xiqing Bian, Jian-Lin Wu, Wei Kang, Yun Qian, Weilin Li, Huarong Chen, Hongyan Gou, Dabin Liu, Simson Tsz Yat Luk, Qiming Zhou, Fenfen Ji, Lam-Shing Chan, Senji Shirasawa, Joseph Jy Sung, Jun Yu.

BACKGROUND & AIMS: Mutant KRAS promotes glutaminolysis, a process that uses steps from the tricarboxylic cycle to convert glutamine to α-ketoglutarate and other molecules, via glutaminase and solute carrier family 25 member 22 (SLC25A22). This results in inhibition of demethylases and epigenetic alterations in cells that increase proliferation and stem cell features. We investigated whether mutant KRAS-mediated glutaminolysis affects the epigenomes and activities of colorectal cancer (CRC) cells.
METHODS: We created ApcminKrasG12D mice with intestine-specific knockout of SLC25A22 (ApcminKrasG12DSLC25A22fl/fl mice). Intestine tissues were collected and analyzed by histology, immunohistochemistry, and DNA methylation assays; organoids were derived and studied for stem cell features, along with organoids derived from 2 human colorectal tumor specimens. Colon epithelial cells (1CT) and CRC cells (DLD1, DKS8, HKE3, and HCT116) that expressed mutant KRAS, with or without knockdown of SLC25A22 or other proteins, were deprived of glutamine or glucose and assayed for proliferation, colony formation, glucose or glutamine consumption, and apoptosis; gene expression patterns were analyzed by RNA sequencing, proteins by immunoblots, and metabolites by liquid chromatography-mass spectrometry, with [U-13C5]-glutamine as a tracer. Cells and organoids with knocked down, knocked out, or overexpressed proteins were analyzed for DNA methylation at CpG sites using arrays. We performed immunohistochemical analyses of colorectal tumor samples from 130 patients in Hong Kong (57 with KRAS mutations) and Kaplan-Meier analyses of survival. We analyzed gene expression levels of colorectal tumor samples in the Cancer Genome Atlas.
RESULTS: CRC cells that express activated KRAS required glutamine for survival, and rapidly incorporated it into the tricarboxylic cycle (glutaminolysis); this process required SLC25A22. Cells incubated with succinate could proliferate under glutamine-free conditions. Mutant KRAS cells maintained a low ratio of α-ketoglutarate:succinate, resulting in reduced 5-hydroxymethylcytosine-a marker of DNA demethylation, and hypermethylation at CpG sites. Many of the hypermethylated genes were in the WNT signaling pathway and at the protocadherin gene cluster on chromosome 5q31. CRC cells without mutant KRAS, or with mutant KRAS and knockout of SLC25A22, expressed protocadherin genes (PCDHAC2, PCDHB7, PCDHB15, PCDHGA1, and PCDHGA6)-DNA was not methylated at these loci. Expression of the protocadherin genes reduced WNT signaling to β-catenin and expression of the stem-cell marker LGR5. ApcminKrasG12DSLC25A22fl/fl mice developed fewer colon tumors than ApcminKrasG12D mice (P<.01). Organoids from ApcminKrasG12DSLC25A22fl/fl mice had reduced expression of LGR5 and other markers of stemness compared with organoids derived from ApcminKrasG12D mice. Knockdown of SLC25A22 in human colorectal tumor organoids reduced clonogenicity. Knockdown of lysine demethylases, or succinate supplementation, restored expression of LGR5 to SLC25A22-knockout CRC cells. Knockout of SLC25A22 in CRC cells that express mutant KRAS increased their sensitivity to 5-fluorouacil. Level of SLC25A22 correlated with levels of LGR5, nuclear β-catenin, and a stem cell-associated gene expression pattern in human colorectal tumors with mutations in KRAS and reduced survival times of patients.
CONCLUSIONS: In CRC cells that express activated KRAS, SLC25A22 promotes accumulation of succinate, resulting in increased DNA methylation, activation of WNT signaling to β-catenin, increased expression of LGR5, proliferation, stem cell features, and resistance to 5-fluorouacil. Strategies to disrupt this pathway might be developed for treatment of CRC.

Keywords: Cancer stemness; DNA methylation; H3K4me3; WNT/β-catenin pathway

DOI: https://doi.org/10.1053/j.gastro.2020.08.016

Molecules. 2020 Aug 18. pii: E3754. [Epub ahead of print]25(16):

IDH1 Targeting as a New Potential Option for Intrahepatic Cholangiocarcinoma Treatment-Current State and Future Perspectives.

Fabiana Crispo, Michele Pietrafesa, Valentina Condelli, Francesca Maddalena, Giuseppina Bruno, Annamaria Piscazzi, Alessandro Sgambato, Franca Esposito, Matteo Landriscina.

Cholangiocarcinoma is a primary malignancy of the biliary tract characterized by late and unspecific symptoms, unfavorable prognosis, and few treatment options. The advent of next-generation sequencing has revealed potential targetable or actionable molecular alterations in biliary tumors. Among several identified genetic alterations, the IDH1 mutation is arousing interest due to its role in epigenetic and metabolic remodeling. Indeed, some IDH1 point mutations induce widespread epigenetic alterations by means of a gain-of-function of the enzyme, which becomes able to produce the oncometabolite 2-hydroxyglutarate, with inhibitory activity on α-ketoglutarate-dependent enzymes, such as DNA and histone demethylases. Thus, its accumulation produces changes in the expression of several key genes involved in cell differentiation and survival. At present, small-molecule inhibitors of IDH1 mutated enzyme are under investigation in preclinical and clinical phases as promising innovative treatments for IDH1-mutated intrahepatic cholangiocarcinomas. This review examines the molecular rationale and the results of preclinical and early-phase studies on novel pharmacological agents targeting mutant IDH1 in cholangiocarcinoma patients. Contextually, it will offer a starting point for discussion on combined therapies with metabolic and epigenetic drugs, to provide molecular support to target the interplay between metabolism and epigenetics, two hallmarks of cancer onset and progression.

Keywords: 2-hydroxyglutarate; IDH1 inhibitors; intrahepatic cholangiocarcinoma; isocitrate dehydrogenase

DOI: https://doi.org/10.3390/molecules25163754

Cancer Discov. 2020 Aug 21. pii: CD-19-0970. [Epub ahead of print]

The Folate Cycle Enzyme MTHFR is a Critical Regulator of Cell Response to MYC-Targeting Therapies.

Deciphering the impact of metabolic intervention on response to anticancer therapy may elucidate a path toward improved clinical responses. Here, we identify amino acid-related pathways connected to the folate cycle whose activation predicts sensitivity to MYC-targeting therapies in acute myeloid leukemia (AML). We establish that folate restriction and deficiency of the rate-limiting folate cycle enzyme, MTHFR - which exhibits reduced-function polymorphisms in about 10% of Caucasians - induce resistance to MYC targeting by BET and CDK7 inhibitors in cell lines, primary patient samples, and syngeneic mouse models of AML. Further, this effect is abrogated by supplementation with the MTHFR enzymatic product, CH3-THF. Mechanistically, folate cycle disturbance reduces H3K27/K9 histone methylation and activates a SPI1 transcriptional program counteracting the effect of BET inhibition. Our data provide a rationale for screening MTHFR polymorphisms and the folate cycle status to nominate patients most likely to benefit from MYC-targeting therapies.

DOI: https://doi.org/10.1158/2159-8290.CD-19-0970

Sci Adv. 2020 Aug;6(32): eabb2745

The Polycomb-associated factor PHF19 controls hematopoietic stem cell state and differentiation.

Pedro Vizán, Arantxa Gutiérrez, Isabel Espejo, Marc García-Montolio, Martin Lange, Ana Carretero, Atefeh Lafzi, Luisa de Andrés-Aguayo, Enrique Blanco, Roshana Thambyrajah, Thomas Graf, Holger Heyn, Anna Bigas, Luciano Di Croce.

Adult hematopoietic stem cells (HSCs) are rare multipotent cells in bone marrow that are responsible for generating all blood cell types. HSCs are a heterogeneous group of cells with high plasticity, in part, conferred by epigenetic mechanisms. PHF19, a subunit of the Polycomb repressive complex 2 (PRC2), is preferentially expressed in mouse hematopoietic precursors. Here, we now show that, in stark contrast to results published for other PRC2 subunits, genetic depletion of Phf19 increases HSC identity and quiescence. While proliferation of HSCs is normally triggered by forced mobilization, defects in differentiation impede long-term correct blood production, eventually leading to aberrant hematopoiesis. At molecular level, PHF19 deletion triggers a redistribution of the histone repressive mark H3K27me3, which notably accumulates at blood lineage-specific genes. Our results provide novel insights into how epigenetic mechanisms determine HSC identity, control differentiation, and are key for proper hematopoiesis.

DOI: https://doi.org/10.1126/sciadv.abb2745

Sci Signal. 2020 Aug 18. pii: eaba8091. [Epub ahead of print]13(645):

Degradation of 5hmC-marked stalled replication forks by APE1 causes genomic instability.

Suhas S Kharat, Xia Ding, Divya Swaminathan, Akshey Suresh, Manish Singh, Satheesh K Sengodan, Sandra Burkett, Hanna Marks, Chinmayi Pamala, Yafeng He, Stephen D Fox, Eugen C Buehler, Kathrin Muegge, Scott E Martin, Shyam K Sharan.

Synthetic lethality between poly(ADP-ribose) polymerase (PARP) inhibition and BRCA deficiency is exploited to treat breast and ovarian tumors. However, resistance to PARP inhibitors (PARPis) is common. To identify potential resistance mechanisms, we performed a genome-wide RNAi screen in BRCA2-deficient mouse embryonic stem cells and validation in KB2P1.21 mouse mammary tumor cells. We found that resistance to multiple PARPi emerged with reduced expression of TET2 (ten-eleven translocation), which promotes DNA demethylation by oxidizing 5-methylcytosine (5mC) to 5-hydroxymethycytosine (5hmC) and other products. TET2 knockdown in BRCA2-deficient cells protected stalled replication forks (RFs). Increasing 5hmC abundance induced the degradation of stalled RFs in KB2P1.21 and human cancer cells by recruiting the base excision repair-associated apurinic/apyrimidinic endonuclease APE1, independent of the BRCA2 status. TET2 loss did not affect the recruitment of the repair protein RAD51 to sites of double-strand breaks (DSBs) or the abundance of proteins associated with RF integrity. The loss of TET2, of its product 5hmC, and of APE1 recruitment to stalled RFs promoted resistance to the chemotherapeutic cisplatin. Our findings reveal a previously unknown role for the epigenetic mark 5hmC in maintaining the integrity of stalled RFs and a potential resistance mechanism to PARPi and cisplatin.

DOI: https://doi.org/10.1126/scisignal.aba8091