Brown adipose tissue (BAT) has been suggested to play an important role in lipid and glucose metabolism in rodents and possibly also in humans. In the current study, we used genetic and correlation analyses in the BXH/HXB recombinant inbred (RI) strains, derived from Brown Norway (BN) and spontaneously hypertensive rats (SHR), to identify genetic determinants of BAT function. Linkage analyses revealed a quantitative trait locus (QTL) associated with interscapular BAT mass on chromosome 4 and two closely linked QTLs associated with glucose oxidation and glucose incorporation into BAT lipids on chromosome 2. Using weighted gene coexpression network analysis (WGCNA) we identified 1,147 gene coexpression modules in the BAT from BXH/HXB rats and mapped their module eigengene QTLs. Through an unsupervised analysis, we identified modules related to BAT relative mass and function. The Coral4.1 coexpression module is associated with BAT relative mass (includes Cd36 highly connected gene), and the Darkseagreen coexpression module is associated with glucose incorporation into BAT lipids (includes Hiat1, Fmo5, and Sort1 highly connected transcripts). Because multiple statistical criteria were used to identify candidate modules, significance thresholds for individual tests were not adjusted for multiple comparisons across modules. In summary, a systems genetic analysis using genomic and quantitative transcriptomic and physiological information has produced confirmation of several known genetic factors and significant insight into novel genetic components functioning in BAT and possibly contributing to traits characteristic of the metabolic syndrome.

• MeSH
• Genetic Predisposition to Disease genetics   MeSH
• Glucose metabolism   MeSH
• Adipose Tissue, Brown metabolism   MeSH
• Rats MeSH
• Quantitative Trait Loci genetics   MeSH
• Metabolic Syndrome genetics   metabolism   MeSH
• Rats, Inbred BN MeSH
• Rats, Inbred SHR MeSH
• Animals MeSH
• Check Tag
• Rats MeSH
• Male MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH

BACKGROUND: A statistical pipeline was developed and used for determining candidate genes and candidate gene coexpression networks involved in 2 alcohol (i.e., ethanol [EtOH]) metabolism phenotypes, namely alcohol clearance and acetate area under the curve in a recombinant inbred (RI) (HXB/BXH) rat panel. The approach was also used to provide an indication of how EtOH metabolism can impact the normal function of the identified networks. METHODS: RNA was extracted from alcohol-naïve liver tissue of 30 strains of HXB/BXH RI rats. The reconstructed transcripts were quantitated, and data were used to construct gene coexpression modules and networks. A separate group of rats, comprising the same 30 strains, were injected with EtOH (2 g/kg) for measurement of blood EtOH and acetate levels. These data were used for quantitative trait loci (QTL) analysis of the rate of EtOH disappearance and circulating acetate levels. The analysis pipeline required calculation of the module eigengene values, the correction of these values with EtOH metabolism rates and acetate levels across the rat strains, and the determination of the eigengene QTLs. For a module to be considered a candidate for determining phenotype, the module eigengene values had to have significant correlation with the strain phenotypic values and the module eigengene QTLs had to overlap the phenotypic QTLs. RESULTS: Of the 658 transcript coexpression modules generated from liver RNA sequencing data, a single module satisfied all criteria for being a candidate for determining the alcohol clearance trait. This module contained 2 alcohol dehydrogenase genes, including the gene whose product was previously shown to be responsible for the majority of alcohol elimination in the rat. This module was also the only module identified as a candidate for influencing circulating acetate levels. This module was also linked to the process of generation and utilization of retinoic acid as related to the autonomous immune response. CONCLUSIONS: We propose that our analytical pipeline can successfully identify genetic regions and transcripts which predispose a particular phenotype and our analysis provides functional context for coexpression module components.

• MeSH
• Ethanol administration & dosage   metabolism   MeSH
• Liver drug effects   metabolism   MeSH
• Rats MeSH
• Metabolic Clearance Rate drug effects   physiology   MeSH
• Multifactorial Inheritance drug effects   physiology   MeSH
• Alcohol Drinking genetics   metabolism   MeSH
• Rats, Inbred BN MeSH
• Rats, Inbred SHR MeSH
• Rats, Transgenic MeSH
• Unsupervised Machine Learning * MeSH
• Systems Biology methods   MeSH
• Animals MeSH
• Check Tag
• Rats MeSH
• Male MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH

The Bcl-2 protein family comprises both pro- and antiapoptotic members that control the permeabilization of the mitochondrial outer membrane, a crucial step in the modulation of apoptosis. Recent research has demonstrated that the carboxyl-terminal transmembrane domain (TMD) of some Bcl-2 protein family members can modulate apoptosis; however, the transmembrane interactome of the antiapoptotic protein Mcl-1 remains largely unexplored. Here, we demonstrate that the Mcl-1 TMD forms homooligomers in the mitochondrial membrane, competes with full-length Mcl-1 protein with regards to its antiapoptotic function, and induces cell death in a Bok-dependent manner. While the Bok TMD oligomers locate preferentially to the endoplasmic reticulum (ER), heterooligomerization between the TMDs of Mcl-1 and Bok predominantly takes place at the mitochondrial membrane. Strikingly, the coexpression of Mcl-1 and Bok TMDs produces an increase in ER mitochondrial-associated membranes, suggesting an active role of Mcl-1 in the induced mitochondrial targeting of Bok. Finally, the introduction of Mcl-1 TMD somatic mutations detected in cancer patients alters the TMD interaction pattern to provide the Mcl-1 protein with enhanced antiapoptotic activity, thereby highlighting the clinical relevance of Mcl-1 TMD interactions.

• MeSH
• Apoptosis physiology   MeSH
• Cell Death physiology   MeSH
• Endoplasmic Reticulum metabolism   MeSH
• HeLa Cells MeSH
• Humans MeSH
• Mitochondrial Membranes metabolism   MeSH
• Mitochondria metabolism   MeSH
• Myeloid Cell Leukemia Sequence 1 Protein metabolism   MeSH
• Protein Domains MeSH
• Proto-Oncogene Proteins c-bcl-2 metabolism   MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

The "pocket proteins" pRb (retinoblastoma tumor suppressor protein), p107, and p130 regulate cell proliferation via phosphorylation-sensitive interactions with E2F transcription factors and other proteins. We previously identified 22 in vivo phosphorylation sites in human p130, including three sites selectively targeted by cyclin D-Cdk4(6) kinases. Here we assessed the effects of alanine substitution at the individual or combined Cdk4(6)-specific sites in p130, compared with homologous sites in p107 (Thr(369)/Ser(650)/Ser(964)). In U-2-OS cells, the triple p107(DeltaCdk4)* mutant strongly inhibited E2F-4 activity and imposed a G(1) arrest resistant to cyclin D1 coexpression. In contrast, the p130(DeltaCdk4) mutant still responded to cyclin D1, suggesting the existence of additional phosphorylation sites critical for E2F-4 regulation. Extensive mutagenesis, sensitive E2F reporter assays, and cell cycle analyses allowed the identification of six such residues (serines 413, 639, 662, 1044, 1080, and 1112) that, in addition to the Cdk4-specific sites, are necessary and sufficient for the regulation of E2F-4 and the cell cycle by p130. Surprisingly, 12 of the in vivo phosphorylation sites seem dispensable for E2F regulation and probably modulate other functions of p130. These results further elucidate the complex regulation of p130 and provide a molecular mechanism to explain the differential control of p107 and p130 by cyclin-dependent kinases.

• MeSH
• Models, Biological MeSH
• Cell Division MeSH
• Cell Line MeSH
• Cell Cycle MeSH
• Cyclin D1 metabolism   MeSH
• DNA-Binding Proteins * metabolism   MeSH
• Phosphoproteins * metabolism   MeSH
• Phosphorylation MeSH
• G1 Phase MeSH
• Glutathione Transferase metabolism   MeSH
• Immunohistochemistry MeSH
• Nuclear Proteins * metabolism   MeSH
• Humans MeSH
• Mutation MeSH
• Peptide Mapping MeSH
• Peptides chemistry   MeSH
• Plasmids metabolism   MeSH
• Retinoblastoma-Like Protein p107 MeSH
• Retinoblastoma-Like Protein p130 MeSH
• Proteins * MeSH
• Flow Cytometry MeSH
• Recombinant Fusion Proteins metabolism   MeSH
• Protein Structure, Tertiary MeSH
• E2F4 Transcription Factor MeSH
• Transcription Factors * metabolism   MeSH
• Binding Sites MeSH
• Check Tag
• Humans MeSH

Dipeptidyl peptidase-IV (DPP-IV) represents a unique proteolytic activity cleaving N-terminal X-Pro dipeptides. In addition to canonical DPP-IV/CD26, a number of other molecules have been discovered which exhibit DPP-IV-like enzymatic activity and various degree of structural similarity. These comprise enzymatically active fibroblast activation protein-alpha, DPP-II, DPP8, DPP9 and enzymatically inactive DPP6 and DPP10 that have been grouped as "DPP-IV activity and/or structure homologues" (DASH). Because the enzymatically active DASH can share similar sets of biologically active substrates and are frequently coexpressed within single cell or on tissue level, it is tempting to consider their participation on biological function(s) previously attributed to DPP-IV/CD26. It is speculated that disrupted expression and enzymatic activity of some DASH might corrupt the message carried by their substrates, with consequent promotion of abnormal cell behavior. Thus, modulation of activity of a particular enzyme using e.g. inhibitors, specific antibodies or modifying its expression may be an attractive therapeutic concept in cancer treatment. This review summarizes current knowledge of the expression and possible function of DPP-IV enzymatic activity bearing molecules in human brain tumors.

• MeSH
• Models, Biological MeSH
• Cell Differentiation MeSH
• Chemokine CXCL12 metabolism   MeSH
• Chemokines metabolism   MeSH
• Dipeptidyl Peptidase 4 metabolism   MeSH
• Financing, Organized MeSH
• Glioblastoma metabolism   MeSH
• Glioma enzymology   metabolism   MeSH
• Humans MeSH
• Brain metabolism   MeSH
• Brain Neoplasms enzymology   metabolism   MeSH
• Peptide Hydrolases metabolism   MeSH
• Receptors, CXCR4 metabolism   MeSH
• Gene Expression Regulation, Enzymologic MeSH
• Gene Expression Regulation, Neoplastic MeSH
• Check Tag
• Humans MeSH
• Publication type
• Review MeSH