Nicotinamide <i>N</i>‑Methyltransferase Interacts with Enzymes of the Methionine Cycle and Regulates Methyl Donor Metabolism

Methyl donor balance is critical for epigenetic regulation in cells and is maintained by the so-called methionine cycle proteins that regenerate S-adenosylmethionine (SAM), the universal methyl donor, from homocysteine formed by the activity of methyltransferases. Nnmt is a liver enzyme that methylates nicotinamide, but its role in regulating methyl donor balance in the liver is unclear. In this study, we assessed the effect of altered Nnmt expression on various aspects of methyl donor metabolism in the liver. We found that Nnmt overexpression decreased SAM levels and the SAM/ S-adenosylhomocysteine (SAH) ratio both in vivo and in vitro. Nnmt knockdown did not change methyl donor balance in mouse primary hepatocytes but increased SAM levels and the SAM/SAH ratio when Gnmt, the dominantly expressed methyltransferase in liver, was simultaneously knocked down. Paradoxically, expression of enzymatically deficient Nnmt increased the SAM/SAH ratio, suggesting that Nnmt can regulate methyl donor balance independent of its methyltransferase activity. Proteomics analysis of Nnmt-interacting proteins in the liver identified Bhmt, Mat1a, and Ahcy, all components of the methionine cycle, and functional experiments showed that mutant Nnmt increased the level of remethylation of homocysteine to SAM. In summary, we show that the function of Nnmt in hepatic methyl donor balance is multifactorial. On one hand, Nnmt decreases methyl donor balance, consistent with its activity as a methyltransferase consuming methyl donors. On the other hand, by co-opting the enzymes of the methionine cycle, Nnmt aids the recycling of homocysteine to SAM for another round of methylation

Supplemental_PDF - Laparoscopic Microwave Ablation of Hepatocellular Carcinoma at Liver Surface: Technique Effectiveness and Long-Term Outcomes

Supplemental_PDF for Laparoscopic Microwave Ablation of Hepatocellular Carcinoma at Liver Surface: Technique Effectiveness and Long-Term Outcomes by Tao Wang, Xiao-Yu Zhang, Xiaojie Lu, and Bo Zhai in Technology in Cancer Research & Treatment</p

Phosphoproteome Analysis of <i>Drosophila melanogaster</i> Embryos

Protein phosphorylation is a key regulatory event in most cellular processes and development. Mass spectrometry-based proteomics provides a framework for the large-scale identification and characterization of phosphorylation sites. Here, we used a well-established phosphopeptide enrichment and identification strategy including the combination of strong cation exchange chromatography, immobilized metal affinity chromatography, and high-accuracy mass spectrometry instrumentation to study phosphorylation in developing Drosophila embryos. In total, 13 720 different phosphorylation sites were discovered from 2702 proteins with an estimated false-discovery rate (FDR) of 0.63% at the peptide level. Because of the large size of the data set, both novel and known phosphorylation motifs were extracted using the Motif-X algorithm, including those representative of potential ordered phosphorylation events

Phosphoproteome Analysis of <i>Drosophila melanogaster</i> Embryos

Protein phosphorylation is a key regulatory event in most cellular processes and development. Mass spectrometry-based proteomics provides a framework for the large-scale identification and characterization of phosphorylation sites. Here, we used a well-established phosphopeptide enrichment and identification strategy including the combination of strong cation exchange chromatography, immobilized metal affinity chromatography, and high-accuracy mass spectrometry instrumentation to study phosphorylation in developing Drosophila embryos. In total, 13 720 different phosphorylation sites were discovered from 2702 proteins with an estimated false-discovery rate (FDR) of 0.63% at the peptide level. Because of the large size of the data set, both novel and known phosphorylation motifs were extracted using the Motif-X algorithm, including those representative of potential ordered phosphorylation events

Kaplan-Meier curve comparing disease free survival of patients with positive YKL-40 intratumoral staining versus those with negative YKL-40 intratumoral staining.

<p>Log-rank test determined that the disease-free survival in YKL-40 positive tumor group was 36 months (95%CI.: 28.95 to 43.05 months)), which was significantly shorter than those in the YKL-40 negative tumor group (49 months (95%CI: 38.23 to 59.77 months) (P = 0.001).</p

Phosphoproteome Analysis of <i>Drosophila melanogaster</i> Embryos

Protein phosphorylation is a key regulatory event in most cellular processes and development. Mass spectrometry-based proteomics provides a framework for the large-scale identification and characterization of phosphorylation sites. Here, we used a well-established phosphopeptide enrichment and identification strategy including the combination of strong cation exchange chromatography, immobilized metal affinity chromatography, and high-accuracy mass spectrometry instrumentation to study phosphorylation in developing Drosophila embryos. In total, 13 720 different phosphorylation sites were discovered from 2702 proteins with an estimated false-discovery rate (FDR) of 0.63% at the peptide level. Because of the large size of the data set, both novel and known phosphorylation motifs were extracted using the Motif-X algorithm, including those representative of potential ordered phosphorylation events

Association of patients’ characteristics with rate of positive YKL-40 intratumoral staining and YKL-40 serum levels.

<p>YKL-40 intratumoral staining of each breast cancer patient were compiled as n (%) and differences in YKL-40 intratumoral staining between specific patients’ characteristics were compared using Pearson Chi-square test.</p><p>YKL-40 serum concentrations for each characteristic were presented as mean±SD. Differences in serum YKL-40 levels between specific patients’ characteristics were compared by using one-way ANOVA with post-hoc Bonferroni comparison or two-sample t-test.</p>*<p>P<0.05, indicated a significance.</p>a,b<p>P<0.0167 (0.05/3), indicated a significant difference compared with the ^afirst category and ^bsecond category of the specific variable.</p

Kaplan-Meier survival curves of breast cancer patients with positive YKL-40 intratumoral staining versus those with negative YKL-40 intratumoral staining.

<p>The Log-rank test showed that the survival times were significantly shorter in patients with positive YKL-40 intratumoral staining (55.13 months.95%CI.: 49.69 to 60.58 months) than those with negative YKL-40 intratumoral staining (65.78 months, 95%CI: 60.17 to 71.40 months) (P = 0.014).</p

Additional file 1 of Integration of ATAC-Seq and RNA-Seq reveals FOSL2 drives human liver progenitor-like cell aging by regulating inflammatory factors

Additional file 1: Figure S1. Functional analysis of DEGs between different cell states, related to Figure 2. Figure S2. Quality assessment of ATAC-Seq data, related to Figure 3. Figure S3. Association of expression levels and chromatin accessibility, related to Figure 3. Figure S4. GO-BP analysis of genes with significantly differential distal accessibility among different cell states, related to Figure 4-5. Figure S5. Protein-protein interaction networks of TFs. Figure S6. Functional analysis of DEGs between sh-FOSL2 affected HepLPC-P10 and ctrl HepLPC-P10, related to Figure 6. Table S1. Primer sequences used for RT-qPCR

Representative photographs of YKL-40 immunohistochemical staining for positive cell and intensity scoring.

<p>A) Noninvasive ductal carcinoma staining at positive score 1 and intensity score 2, B) Noninvasive ductal carcinoma staining at positive score 3 and intensity score 2. C) Invasive ductal carcinoma staining positive score 2 and intensity score 2. D) Invasive ductal carcinoma staining positive score 3 and intensity score 2. All photos had x100 magnification.</p