Protocol to purify the histone deacetylase SIRT6 and assess its activity in vitro.

The histone deacetylase known as sirtuin 6 (SIRT6) deacetylates both histone and non-histone proteins but has low deacetylase activity in vitro. Here, we present a protocol to monitor SIRT6-mediated deacetylation of long-chain acyl-CoA synthase 5 in the presence of palmitic acid. We describe the purification of His-SIRT6 and a Flag-tagged substrate. We then detail a deacetylation assay protocol that can be widely applied to study other SIRT6-mediated deacetylation events and the effect of SIRT6 mutations on its activity. For complete details on the use and execution of this protocol, please refer to Hou et al. (2022).1.

Cytoplasmic SIRT6-mediated ACSL5 deacetylation impedes nonalcoholic fatty liver disease by facilitating hepatic fatty acid oxidation.

Nonalcoholic fatty liver disease (NAFLD) is characterized by excessive hepatic lipid accumulation, which can progress to nonalcoholic steatohepatitis (NASH). Histone deacetylase Sirtuin 6 (SIRT6) regulates NAFLD by regulating metabolism-related gene expression, but an extrachromosomal role for SIRT6 in NAFLD development remains elusive. We investigated whether SIRT6 functions on NAFLD in the cytoplasm. We found that SIRT6 binds saturated fatty acids, especially palmitic acid. This binding leads to its nuclear export, where it deacetylates long-chain acyl-CoA synthase 5 (ACSL5), thereby facilitating fatty acid oxidation. High-fat diet-induced NAFLD is suppressed by ACSL5 hepatic overexpression but is exacerbated by its depletion. As confirmation, overexpression of a deacetylated ACSL5 mimic attenuated NAFLD in Sirt6 liver-specific knockout mice. Moreover, NASH-hepatic tissues from both patients and diet-fed mice exhibited significantly reduced cytoplasmic SIRT6 levels and increased ACSL5 acetylation. The SIRT6/ACSL5 signaling pathway has a critical role in NAFLD progression and might constitute an avenue for therapeutic intervention.

WDFY2 Potentiates Hepatic Insulin Sensitivity and Controls Endosomal Localization of the Insulin Receptor and IRS1/2.

Endosomes help activate the hepatic insulin-evoked Akt signaling pathway, but the underlying regulatory mechanisms are unclear. Previous studies have suggested that the endosome-located protein WD repeat and FYVE domain-containing 2 (WDFY2) might be involved in metabolic disorders, such as diabetes. Here, we generated Wdfy2 knockout (KO) mice and assessed the metabolic consequences. These KO mice exhibited systemic insulin resistance, with increased gluconeogenesis and suppressed glycogen accumulation in the liver. Mechanistically, we found that the insulin-stimulated activation of Akt2 and its substrates FoxO1 and GSK-3ß is attenuated in the Wdfy2 KO liver and H2.35 hepatocytes, suggesting that WDFY2 acts as an important regulator of hepatic Akt2 signaling. We further found that WDFY2 interacts with the insulin receptor (INSR) via its WD1-4 domain and localizes the INSR to endosomes after insulin stimulation. This process ensures that the downstream insulin receptor substrates 1 and 2 (IRS1/2) can be recruited to the endosomal INSR. IRS1/2-INSR binding promotes IRS1/2 phosphorylation and subsequent activation, initiating downstream Akt2 signaling in the liver. Interestingly, adeno-associated viral WDFY2 delivery ameliorated metabolic defects in db/db mice. These findings demonstrate that WDFY2 activates insulin-evoked Akt2 signaling by controlling endosomal localization of the INSR and IRS1/2 in hepatocytes. This pathway might constitute a new potential target for diabetes prevention or treatment.

CBP mediated DOT1L acetylation confers DOT1L stability and promotes cancer metastasis.

Background and Aim: DOT1L regulates various genes involved in cancer onset and progression by catalyzing H3K79 methylation, but how DOT1L activity itself is regulated is unclear. Here, we aimed to identify specific DOT1L post-translational modifications that might regulate DOT1L activity and thus impact on colorectal cancer (CRC) progression. Methods: We conducted affinity purification and mass spectrometry to explore DOT1L post-translational modifications. We then established transwell migration and invasion assays to specifically investigate the role of DOT1L(K358) acetylation on CRC cellular behavior in vitro and a bioluminescence imaging approach to determine the role of DOT1L(K358) acetylation in CRC metastasis in vivo. We performed chromatin immunoprecipitation to identify DOT1L acetylation-controlled target genes. Finally, we used immunohistochemical staining of human tissue arrays to examine the relevance of DOT1L(K358) acetylation in CRC progression and metastasis and the correlation between DOT1L acetylation and CBP. Results: We found that CBP mediates DOT1L K358 acetylation in human colon cancer cells and positively correlates with CRC stages. Mechanistically, DOT1L acetylation confers DOT1L stability by preventing the binding of RNF8 to DOT1L and subsequent proteasomal degradation, but does not affect its enzyme activity. Once stabilized, DOT1L can catalyze the H3K79 methylation of genes involved in epithelial-mesenchymal transition, including SNAIL and ZEB1. An acetylation mimic DOT1L mutant (Q358) could induce a cancer-like phenotype in vitro, characterized by metastasis and invasion. Finally, DOT1L(K358) acetylation correlated with CRC progression and a poor survival rate as well as with high CBP expression. Conclusions: DOT1L acetylation by CBP drives CRC progression and metastasis. Targeting DOT1L deacetylation signaling is a potential therapeutic strategy for DOT1L-driven cancers.

SIRT6 coordinates with CHD4 to promote chromatin relaxation and DNA repair.

Genomic instability is an underlying hallmark of cancer and is closely associated with defects in DNA damage repair (DDR). Chromatin relaxation is a prerequisite for DDR, but how chromatin accessibility is regulated remains elusive. Here we report that the histone deacetylase SIRT6 coordinates with the chromatin remodeler CHD4 to promote chromatin relaxation in response to DNA damage. Upon DNA damage, SIRT6 rapidly translocates to DNA damage sites, where it interacts with and recruits CHD4. Once at the damage sites, CHD4 displaces heterochromatin protein 1 (HP1) from histone H3 lysine 9 trimethylation (H3K9me3). Notably, loss of SIRT6 or CHD4 leads to impaired chromatin relaxation and disrupted DNA repair protein recruitment. These molecular changes, in-turn, lead to defective homologous recombination (HR) and cancer cell hypersensitivity to DNA damaging agents. Furthermore, we show that SIRT6-mediated CHD4 recruitment has a specific role in DDR within compacted chromatin by HR in G2 phase, which is an ataxia telangiectasia mutated (ATM)-dependent process. Taken together, our results identify a novel function for SIRT6 in recruiting CHD4 onto DNA double-strand breaks. This newly identified novel molecular mechanism involves CHD4-dependent chromatin relaxation and competitive release of HP1 from H3K9me3 within the damaged chromatin, which are both essential for accurate HR.

GLP-catalyzed H4K16me1 promotes 53BP1 recruitment to permit DNA damage repair and cell survival.

The binding of p53-binding protein 1 (53BP1) to damaged chromatin is a critical event in non-homologous DNA end joining (NHEJ)-mediated DNA damage repair. Although several molecular pathways explaining how 53BP1 binds damaged chromatin have been described, the precise underlying mechanisms are still unclear. Here we report that a newly identified H4K16 monomethylation (H4K16me1) mark is involved in 53BP1 binding activity in the DNA damage response (DDR). During the DDR, H4K16me1 rapidly increases as a result of catalyzation by the histone methyltransferase G9a-like protein (GLP). H4K16me1 shows an increased interaction level with 53BP1, which is important for the timely recruitment of 53BP1 to DNA double-strand breaks. Differing from H4K16 acetylation, H4K16me1 enhances the 53BP1-H4K20me2 interaction at damaged chromatin. Consistently, GLP knockdown markedly attenuates 53BP1 foci formation, leading to impaired NHEJ-mediated repair and decreased cell survival. Together, these data support a novel axis of the DNA damage repair pathway based on H4K16me1 catalysis by GLP, which promotes 53BP1 recruitment to permit NHEJ-mediated DNA damage repair.

PKCζ Phosphorylates SIRT6 to Mediate Fatty Acid ß-Oxidation in Colon Cancer Cells.

Protein kinase C (PKC) has critical roles in regulating lipid anabolism and catabolism. PKCζ, a member of atypical PKC family, has been reported to mediate glucose metabolism. However, whether and how PKCζ regulates tumor cells fatty acid ß-oxidation are unknown. Here, we report that the phosphorylation of SIRT6 is significantly increased after palmitic acid (PA) treatment in colon cancer cells. PKCζ can physically interact with SIRT6 in vitro and in vivo, and this interaction enhances following PA treatment. Further experiments show that PKCζ is the phosphorylase of SIRT6 and phosphorylates SIRT6 at threonine 294 residue to promote SIRT6 enrichment on chromatin. In the functional study, we find that the expression of ACSL1, CPT1, CACT, and HADHB, the genes related to fatty acid ß-oxidation, increases after PA stimulation. We further confirm that PKCζ mediates the binding of SIRT6 specifically to the promoters of fatty acid ß-oxidation-related genes and elicits the expression of these genes through SIRT6 phosphorylation. Our findings demonstrate the mechanism of PKCζ as a new phosphorylase of SIRT6 on maintaining tumor fatty acid ß-oxidation and define the new role of PKCζ in lipid homeostasis.

p53 cooperates with SIRT6 to regulate cardiolipin de novo biosynthesis.

The tumor suppressor p53 has critical roles in regulating lipid metabolism, but whether and how p53 regulates cardiolipin (CL) de novo biosynthesis is unknown. Here, we report that p53 physically interacts with histone deacetylase SIRT6 in vitro and in vivo, and this interaction increases following palmitic acid (PA) treatment. In response to PA, p53 and SIRT6 localize to chromatin in a p53-dependent manner. Chromatin p53 and SIRT6 bind the promoters of CDP-diacylglycerol synthase 1 and 2 (CDS1 and CDS2), two enzymes required to catalyze CL de novo biosynthesis. Here, SIRT6 serves as a co-activator of p53 and effectively recruits RNA polymerase II to the CDS1 and CDS2 promoters to enhance CL de novo biosynthesis. Our findings reveal a novel, cooperative model executed by p53 and SIRT6 to maintain lipid homeostasis.

Destabilization of linker histone H1.2 is essential for ATM activation and DNA damage repair.

Linker histone H1 is a master regulator of higher order chromatin structure, but its involvement in the DNA damage response and repair is unclear. Here, we report that linker histone H1.2 is an essential regulator of ataxia telangiectasia mutated (ATM) activation. We show that H1.2 protects chromatin from aberrant ATM activation through direct interaction with the ATM HEAT repeat domain and inhibition of MRE11-RAD50-NBS1 (MRN) complex-dependent ATM recruitment. Upon DNA damage, H1.2 undergoes rapid PARP1-dependent chromatin dissociation through poly-ADP-ribosylation (PARylation) of its C terminus and further proteasomal degradation. Inhibition of H1.2 displacement by PARP1 depletion or an H1.2 PARylation-dead mutation compromises ATM activation and DNA damage repair, thus leading to impaired cell survival. Taken together, our findings suggest that linker histone H1.2 functions as a physiological barrier for ATM to target the chromatin, and PARylation-mediated active H1.2 turnover is required for robust ATM activation and DNA damage repair.

Mechanisms controlling the anti-neoplastic functions of FoxO proteins.

The Forkhead box O (FoxO) proteins comprise a family of evolutionarily conserved transcription factors that predominantly function as tumor suppressors. These proteins assume diverse roles in the cellular anti-neoplastic response, including regulation of apoptosis and autophagy, cancer metabolism, cell-cycle arrest, oxidative stress and the DNA damage response. More recently, FoxO proteins have been implicated in cancer immunity and cancer stem-cell (CSC) homeostasis. Interestingly, in some sporadic sub-populations, FoxO protein function may also be manipulated by factors such as ß-catenin whereby they instead can facilitate cancer progression via maintenance of CSC properties or promoting drug resistance or metastasis and invasion. This review highlights the essential biological functions of FoxOs and explores the areas that may be exploited in FoxO protein signaling pathways in the development of novel cancer therapeutic agents.

G9a coordinates with the RPA complex to promote DNA damage repair and cell survival.

Histone methyltransferase G9a has critical roles in promoting cancer-cell growth and gene suppression, but whether it is also associated with the DNA damage response is rarely studied. Here, we report that loss of G9a impairs DNA damage repair and enhances the sensitivity of cancer cells to radiation and chemotherapeutics. In response to DNA double-strand breaks (DSBs), G9a is phosphorylated at serine 211 by casein kinase 2 (CK2) and recruited to chromatin. The chromatin-enriched G9a can then directly interact with replication protein A (RPA) and promote loading of the RPA and Rad51 recombinase to DSBs. This mechanism facilitates homologous recombination (HR) and cell survival. We confirmed the interaction between RPA and G9a to be critical for RPA foci formation and HR upon DNA damage. Collectively, our findings demonstrate a regulatory pathway based on CK2-G9a-RPA that permits HR in cancer cells and provide further rationale for the use of G9a inhibitors as a cancer therapeutic.

Downregulation of SIRT7 by 5-fluorouracil induces radiosensitivity in human colorectal cancer.

5-Fluorouracil (5-FU) combined with radiotherapy is a common treatment strategy to treat human cancers, but the underlying mechanisms of this combination treatment remain unclear. Here, we report that NAD+-dependent deacetylase sirtuin-7 (SIRT7) protein levels were decreased due to 5-FU exposure rendering colorectal cancer cells sensitive to radiation. We found that SIRT7 downregulation was mediated via a Tat-binding Protein 1 (TBP1) proteasome-dependent pathway. Specifically, TBP1 was dephosphorylated at tyrosine 381 upon 5-FU treatment, which enhanced its direct interaction with SIRT7 and targeted it for degradation. Depletion of SIRT7 in cultured colorectal cancer cells induced radiosensitivity triggering cell death. Interestingly, decreased levels of SIRT7 mediated by 5-FU correlated well with improved therapeutic effect in patients with rectal cancer and with inhibited tumor growth in immune-compromised mice post-irradiation. Taken together, these data suggest that 5-FU induces radiosensitivity via SIRT7 degradation to favor a cell death pathway in targeted cancer cells. Thus, downregulation of SIRT7 could be a promising pharmacologic strategy to increase the effectiveness of chemoradiation therapy in cancer patients.

PTK2-mediated degradation of ATG3 impedes cancer cells susceptible to DNA damage treatment.

ATG3 (autophagy-related 3) is an E2-like enzyme essential for autophagy; however, it is unknown whether it has an autophagy-independent function. Here, we report that ATG3 is a relatively stable protein in unstressed cells, but it is degraded in response to DNA-damaging agents such as etoposide or cisplatin. With mass spectrometry and a mutagenesis assay, phosphorylation of tyrosine 203 of ATG3 was identified to be a critical modification for its degradation, which was further confirmed by manipulating ATG3Y203E (phosphorylation mimic) or ATG3Y203F (phosphorylation-incompetent) in Atg3 knockout MEFs. In addition, by using a generated phospho-specific antibody we showed that phosphorylation of Y203 significantly increased upon etoposide treatment. With a specific inhibitor or siRNA, PTK2 (protein tyrosine kinase 2) was confirmed to catalyze the phosphorylation of ATG3 at Y203. Furthermore, a newly identified function of ATG3 was recognized to be associated with the promotion of DNA damage-induced mitotic catastrophe, in which ATG3 interferes with the function of BAG3, a crucial protein in the mitotic process, by binding. Finally, PTK2 inhibition-induced sustained levels of ATG3 were able to sensitize cancer cells to DNA-damaging agents. Our findings strengthen the notion that targeting PTK2 in combination with DNA-damaging agents is a novel strategy for cancer therapy.

Characterization of degradation products of midazolam maleate by UHPLC-HR-IT-MSn and NMR.

Forced degradation studies on midazolam maleate were carried out according to ICH guidelines. Midazolam maleate was subjected to acidic and basic hydrolysis, oxidation, photolysis, high humidity and thermal stress conditions, and the resulting degradation products were investigated by HPLC. Significant degradation of the drug was observed under acidic/basic hydrolysis and thermal stress conditions. The thermal degradation product (Impurity I) was isolated using column chromatography and its structure was elucidated by UHPLC-HRIT-MSn and extensive NMR studies, which was not reported in previous literatures. The acidic/basic hydrolytic degradation product (Impurity II) was characterized by UHPLC-HR-IT-MSn technique and previous literature. The fragmentation pathways of these two degradation products are also described in the paper.

Sirtuins in glucose and lipid metabolism.

Sirtuins are evolutionarily conserved protein, serving as nicotinamide adenine dinucleotide-dependent deacetylases or adenosine diphosphate-ribosyltransferases. The mammalian sirtuins family, including SIRT1~7, is involved in many biological processes such as cell survival, proliferation, senescence, stress response, genome stability and metabolism. Evidence accumulated over the past two decades has indicated that sirtuins not only serve as important energy status sensors but also protect cells against metabolic stresses. In this review, we summarize the background of glucose and lipid metabolism concerning sirtuins and discuss the functions of sirtuins in glucose and lipid metabolism. We also seek to highlight the biological roles of certain sirtuins members in cancer metabolism.

[The Roles of Sirtuins in DNA Damage and Repair].

Sirtuins, class III HDAC, has originally been defined as a family of nicotinamide adenine dinucleotide-dependent enzymes. There are seven mammalian sirtuins (SIRTI07), which mainly deaceylate lysine residue on various proteins as a deacetylase. Sirtuins regulate a diverse array of biological processes, including DNA damage and repair, gene transcription regulation, apoptosis, metabolism and aging. In this research perspective we review the role and molecular mechanism of Sirtuin in DNA damage and repair.

The transcription factor c-Fos coordinates with histone lysine-specific demethylase 2A to activate the expression of cyclooxygenase-2.

Cyclooxygenase-2 (COX-2) is overexpressed in a variety of human epithelial cancers, including lung cancer, and is highly associated with a poor prognosis and a low survival rate. Understanding how COX-2 is regulated in response to carcinogens will offer insight into designing anti-cancer strategies and preventing cancer development. Here, we analyzed COX-2 expression in several human lung cancer cell lines and found that COX-2 expression was absent in the H719 and H460 cell lines by a DNA methylation-independent mechanism. The re-expression of COX-2 was observed after 12-O-tetradecanoylphorbol-13-acetate (TPA) treatment in both cell lines. Further investigation found that H3K36 dimethylation was significantly reduced near the COX-2 promoter because histone demethylase 2A (KDM2A) was recruited to the COX-2 promoter after TPA treatment. In addition, the transcription factor c-Fos was found to be required to recruit KDM2A to the COX-2 promoter for reactivation of COX-2 in response to TPA treatment in both the H719 and H460 cell lines. Together, our data reveal a novel mechanism by which the carcinogen TPA activates COX-2 expression by regulating H3K36 dimethylation near the COX-2 promoter.

SET7/9 regulates cancer cell proliferation by influencing ß-catenin stability.

ß-Catenin, which is a key mediator of the wingless-integration site (Wnt)/ß-catenin signaling pathway, plays an important role in cell proliferation, cell fate determination, and tumorigenesis, by regulating the expression of a wide range of target genes. Although a variety of posttranslational modifications are involved in ß-catenin activity, the role of lysine methylation in ß-catenin activity is largely unknown. In this study, su(var)3-9, enhancer-of-zeste, trithorax (SET) domain-containing protein 7 (SET7/9), a lysine methyltransferase, interacted with and methylated ß-catenin, as demonstrated both in vitro and in vivo. The interaction and methylation were significantly enhanced in response to H2O2 stimulation. A mutagenesis assay and mass spectrometric analyses revealed that ß-catenin was monomethylated by SET7/9 at lysine residue 180. Methylated ß-catenin was easily recognized by phosphokinase glycogen synthase kinase (GSK)-3ß for degradation. Consistent with this finding, the mutated ß-catenin (K180R) that cannot be methylated exhibited a longer half-life than did the methylated ß-catenin. The consequent depletion of SET7/9 by shRNA or the mutation of the ß-catenin (K180R) significantly enhanced the expression of Wnt/ß-catenin target genes such as c-myc and cyclin D1 and promoted the growth of cancer cells. Together, these results provide a novel mechanism by which Wnt/ß-catenin signaling is regulated in response to oxidative stress.