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In Escherichia coli, cytosine DNA methylation is catalyzed by the Dcm (DNA cytosine methyltransferase) protein and occurs at the second cytosine in the sequence 5′CCWGG3′. Although the presence of cytosine DNA methylation was reported over 35 years ago, the biological role of 5-methylcytosine in E. coli remains unclear. In order to gain insight into the role of cytosine DNA methylation in E. coli, we: (a) screened the 72 strains of the ECOR collection and 90 recently isolated environmental samples for the presence of the full-length dcm gene using the polymerase chain reaction; (b) examined the same strains for the presence of 5-methylcytosine at 5′CCWGG3′ sites using a restriction enzyme isoschizomer digestion assay; and (c) quantified the levels of 5-methyl-2′-deoxycytidine in selected strains using liquid chromatography tandem mass spectrometry. Dcm-mediated cytosine DNA methylation is conserved in all 162 strains examined, and the level of 5-methylcytosine ranges from 0.86% to 1.30% of the cytosines. We also demonstrate that Dcm reduces expression of ribosomal protein genes during stationary phase, and this may explain the highly conserved nature of this DNA modification pathway.

Context.-The highly invasive properties demonstrated by head and neck squamous cell carcinoma (HNSCC) are often associated with locoregional recurrence and lymph node metastasis in patients and is a key factor leading to an expected 5-year survival rate of approximately 50% for patients with advanced disease. It is important to understand the features and mediators of HNSCC invasion so that new treatment approaches can be developed.Objectives.-To provide an overview of the characteristics, mediators, and mechanisms of HNSCC invasion.Data Sources.-A literature review of peer-reviewed articles in PubMed on HNSCC invasion.Conclusions.-Histologic features of HNSCC tumors can help predict prognosis and influence clinical treatment decisions. Cell surface receptors, signaling pathways, proteases, invadopodia function, epithelial-mesenchymal transition, microRNAs, and tumor microenvironment are all involved in the regulation of the invasive behavior of HNSCC cells. Identifying effective HNSCC invasion inhibitors has the potential to improve outcomes for patients by reducing the rate of spread and increasing responsiveness to chemoradiation.

It is currently unclear if there are modified DNA bases in Trypanosoma brucei other than J-base. We identify herein a cytosine-5 DNA methyltransferase gene and report the presence and location of 5-methylcytosine in genomic DNA. Our data demonstrate that African trypanosomes contain a functional cytosine DNA methylation pathway.Experiments from the early 1980s demonstrated that inactive Trypanosoma brucei variant surface glycoprotein (VSG) genes were resistant to digestion by certain restriction enzymes, suggesting the presence of modified DNA bases (2, 18). Searches for the presence of modified DNA bases in T. brucei uncovered J-base and its precursor, 5-hydroxymethyluracil (11, 12). It generally has been assumed that no other modified DNA bases exist in T. brucei.Since the modified DNA base 5-methylcytosine (5MC) is widespread in prokaryotes and higher eukaryotes, we searched for genes capable of encoding a cytosine-5 DNA methyltransferase (C5-DNA MTase) in T. brucei. TBLASTN was used to search the T. brucei TREU927 nuclear genome sequence, using the Escherichia coli Dcm C5-DNA MTase protein as a query (4, 16). A significant match (E ϭ 1.2 ϫ 10 Ϫ20 ) was found on T. brucei chromosome 3, and we named the locus the Tb-DMT gene. The TbDMT gene codes for a protein with a predicted molecular mass of 69 kDa, and it is now listed as a putative C5-DNA MTase in GeneDB (www.genedb.org). No other T. brucei C5-DNA MTase homologs were identified by BLAST analyses with the Dcm protein or other queries, suggesting but not proving that T. brucei has a single C5-DNA MTase. The alignment of the predicted TbDMT protein sequence with experimentally validated prokaryotic C5-DNA MTases indicates that TbDMT contains the 10 conserved domains found in all C5-DNA MTases, including the catalytic cysteine residue of domain IV (Fig. 1) (19). The predicted TbDMT protein is more homologous to prokaryotic enzymes than to eukaryotic enzymes with respect to the 10 conserved domains (data not shown). However, TbDMT contains an Nterminal extension that is longer than that of most prokaryotic enzymes, which is a characteristic of the human DNMT1 and DNMT3A/B enzymes (10). Quantitative PCR analysis of RNA from T. brucei bloodstream-form (BF) and procyclic-form (PF) parasites indicates that the TbDMT gene is expressed in both stages. BF parasites have 2.3 (Ϯ0.3, which is one standard deviation) times more TbDMT RNA using ␤-tubulin as a loading control and 1.5 (Ϯ0.2) times more TbDMT RNA using 18S rRNA as a loading control, indicating that there is little stagespecific regulation.The expression of TbDMT in both PF and BF parasites warranted the examination of DNA from these stages for the presence of 5MC. We began by using a blotting assay with a monoclonal antibody against 5MC (Fig. 2) (9, 15, 17). DNAs from T. brucei and control organisms were treated with sodium hydroxide to remove RNA, spotted onto a nitrocellulose membrane, fixed via baking, and incubated overnight with a 1:5,000 dilution of anti-5MC antibody (Calbiochem). Antibody binding was...

Regulatory T cells (Treg) are immunosuppressive and negatively impact response to cancer immunotherapies. CREBbinding protein (CBP) and p300 are closely related acetyltransferases and transcriptional coactivators. Here, we evaluate the mechanisms by which CBP/p300 regulate Treg differentiation and the consequences of CBP/p300 loss-of-function mutations in follicular lymphoma. Transcriptional and epigenetic profiling identified a cascade of transcription factors essential for Treg differentiation. Mass spectrometry analysis showed that CBP/p300 acetylates prostacyclin synthase, which regulates Treg differentiation by altering proinflammatory cytokine secretion by T and B cells. Reduced Treg presence in tissues harboring CBP/p300 loss-of-function mutations was observed in follicular lymphoma. Our findings provide novel insights into the regulation of Treg differentiation by CBP/ p300, with potential clinical implications on alteration of the immune landscape. Significance: This study provides insights into the dynamic role of CBP/p300 in the differentiation of Tregs, with potential clinical implications in the alteration of the immune landscape in follicular lymphoma.

The discovery of covalent inhibitors binding the switch II (SWII) pocket has enabled therapeutic intervention in KRAS G12C driven tumors and represents a milestone in targeting KRAS-driven cancers. However, the transient nature and high energetic barrier required for binding this pocket has been an obstacle in successfully targeting other KRAS mutant oncoproteins. We report the discovery of KRAS Conformation Locking Antibodies for Molecular Probe discovery (CLAMP)s that specifically recognize the unique conformation of KRAS G12C induced 5 by covalent inhibitors. KRAS CLAMPs enable single cell resolution of covalent inhibitor-bound KRAS G12C in cells and in vivo tumor models, providing a biomarker for direct target engagement of KRAS G12C inhibition. KRAS CLAMPs bind multiple KRAS mutants and stabilize an open conformation of the SWII pocket increasing the affinity of weak non-covalent SWII pocket ligands. This work provides new insights into KRAS G12C upon treatment with covalent inhibitors and offers a path towards targeting the SWII pocket in other RAS mutants. 10 3 Main: RAS proteins are small, membrane-bound guanine nucleotide-binding proteins encoded by three genes (HRAS, NRAS and KRAS). RAS proteins act as molecular switches by cycling between active GTP-bound and inactive GDP-bound conformations 1 . The active GTP-bound conformation allows RAS to signal to a diverse set of downstream effectors including RAF, PI3K, and RAL GDS 2-11 and oncogenic mutations in RAS, frequently at position 12, reduce GTP hydrolysis resulting in constitutively active RAS signaling [12][13][14][15] . The picomolar affinity for GTP or GDP, in addition to the lack of obvious pockets for small molecule binding in RAS have hampered drug discovery efforts against oncogenic mutant RAS for several decades.The landmark discovery of KRAS G12C inhibitors that covalently modify the mutant Cys12 residue has provided a novel and promising opportunity for drugging KRAS G12C mutant tumors 16 . Compound 12, ARS-853, ARS-1620, AIM-4, and clinical molecules AMG 510 and MRTX849 bind and stabilize an "open" conformation in the switch II (SWII) region not previously observed in KRAS-GDP or KRAS-GTP [16][17][18][19][20][21][22][23] . The mechanism of action of such SWII pocket covalent binders is through stabilization of this transient pocket via initial binding to the pocket followed by chemical reaction with Cys12 17 . This modification irreversibly locks KRAS G12C in a GDP-bound inactive state by preventing intrinsic or SOS-mediated exchange, causes tumor growth inhibition in pre-clinical models, and is showing promising clinical activity 17,18 . Discovery of these KRAS G12C inhibitors relied heavily on the covalent reactivity with Cys12 to inhibit KRAS G12C protein 24 . Thus, the viability of strategies targeting this pocket in other KRAS mutants lacking this critical mutant cysteine residue remains to be determined.

Oral squamous cell carcinoma (OSCC) patients generally have a poor prognosis, because of the invasive nature of these tumors. In comparing transcription profiles between OSCC tumors with a more invasive (worst pattern of tumor invasion 5) versus a less invasive (worst pattern of tumor invasion 3) pattern of invasion, we identified a total of 97 genes that were overexpressed at least 1.5-fold in the more invasive tumor subtype. The most functionally relevant genes were assessed using in vitro invasion assays with an OSCC cell line (UM-SCC-1). Individual siRNA knockdown of 15 of these 45 genes resulted in significant reductions in tumor cell invasion compared to a nontargeting siRNA control. One gene whose knockdown had a strong effect on invasion corresponded to apolipoprotein E (APOE). Both matrix degradation and the number of mature invadopodia were significantly decreased with APOE knockdown. APOE knockdown also resulted in increased cellular cholesterol, consistent with APOE's role in regulating cholesterol efflux. APOE knockdown resulted in decreased levels of phospho-extracellular signal-regulated kinase 1/2, phospho-c-Jun N-terminal kinase, and phospho-cJun, as well as decreased activator protein 1 (AP-1) activity. Expression of matrix metalloproteinase 7 (MMP7), an AP-1 target, was also significantly decreased. Our findings suggest that APOE protein plays a significant role in OSCC tumor invasion because of its effects on cellular cholesterol and subsequent effects on cell signaling and AP-1 activity, leading to changes in the expression of invasion-related proteins, including MMP7.

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