Epigenetic aberrations of gene expression in a rat model of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is mostly triggered by environmental and life-style factors and may involve epigenetic aberrations. However, a comprehensive documentation of the link between the dysregulated epigenome, transcriptome, and liver carcinogenesis is lacking. In the present study, Fischer-344 rats were fed a choline-deficient (CDAA, cancer group) or choline-sufficient (CSAA, healthy group) L-amino acid-defined diet. At the end of 52 weeks, transcriptomic alterations in livers of rats with HCC tumours and healthy livers were investigated by RNA sequencing. DNA methylation and gene expression were assessed by pyrosequencing and quantitative reverse-transcription PCR (qRT-PCR), respectively. We discovered 1,848 genes that were significantly differentially expressed in livers of rats with HCC tumours (CDAA) as compared with healthy livers (CSAA). Upregulated genes in the CDAA group were associated with cancer-related functions, whereas macronutrient metabolic processes were enriched by downregulated genes. Changes of highest magnitude were detected in numerous upregulated genes that govern key oncogenic signalling pathways, including Notch, Wnt, Hedgehog, and extracellular matrix degradation. We further detected perturbations in DNA methylating and demethylating enzymes, which was reflected in decreased global DNA methylation and increased global DNA hydroxymethylation. Four selected upregulated candidates, Mmp12, Jag1, Wnt4, and Smo, demonstrated promoter hypomethylation with the most profound decrease in Mmp12. MMP12 was also strongly overexpressed and hypomethylated in human HCC HepG2 cells as compared with primary hepatocytes, which coincided with binding of Ten-eleven translocation 1 (TET1). Our findings provide comprehensive evidence for gene expression changes and dysregulated epigenome in HCC pathogenesis, potentially revealing novel targets for HCC prevention/treatment.

Parallel metabolomics and lipidomics enables the comprehensive study of mouse brain regional metabolite and lipid patterns

Global profiling of the metabolome and lipidome of specific brain regions is essential to understanding the cellular and molecular mechanisms regulating brain activity. Given the limited amount of starting material, conventional mouse studies comparing brain regions have mainly targeted a set of known metabolites in large brain regions (e.g., cerebrum, cortex). In this work, we developed a multimodal analytical pipeline enabling parallel analyses of metabolomic and lipidomic profiles from anatomically distinct mouse brain regions starting with less than 0.2 mg of protein content. This analytical pipeline is composed of (1) sonication-based tissue homogenization, (2) parallel metabolite and lipid extraction, (3) BCA-based sample normalization, (4) ultrahigh performance liquid chromatography-mass spectrometry-based multimodal metabolome and lipidome profiling, (5) streamlined data processing, and (6) chord plot-based data visualization. We applied this pipeline to the study of four brain regions in males including the amygdala, dorsal hippocampus, nucleus accumbens and ventral tegmental area. With this novel approach, we detected over 5000 metabolic and 6000 lipid features, among which 134 metabolites and 479 lipids were directly confirmed via automated MS² spectral matching. Interestingly, our analysis identified unique metabolic and lipid profiles in each brain regions. Furthermore, we identified functional relationships amongst metabolic and lipid subclasses, potentially underlying cellular and functional differences across all four brain regions. Overall, our novel workflow generates comprehensive region-specific metabolomic and lipidomic profiles using very low amount of brain sub-regional tissue sample, which could be readily integrated with region-specific genomic, transcriptomic, and proteomic data to reveal novel insights into the molecular mechanisms underlying the activity of distinct brain regions.

Metabolomics-Based Discovery of Molecular Signatures for Triple Negative Breast Cancer in Asian Female Population

Triple negative breast cancer (TNBC) is a devastating cancer disease characterized by its poor prognosis, distinct metastatic patterns, and aggressive biological behavior. Research indicates that the prevalence and presentation of TNBC varies among races, with Asian TNBC patients more commonly presenting with large invasive tumors, high node positivity, and high histologic grade. In this work, we applied ultra-high performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS)-based metabolomics to discover metabolic signatures in Asian female TNBC patients. Serum samples from 31 TNBC patients and 31 healthy controls (CN) were involved in this study. A total of 2860 metabolic features were detected in the serum samples. Among them, 77 metabolites, whose levels were significantly different between TNBC with CN, were confirmed. Using multivariate statistical analysis, literature mining, metabolic network and pathway analysis, we performed an in-depth study of the metabolic alterations in the Asian TNBC population. In addition, we discovered a panel of metabolic signatures that are highly correlated with the 5-year survival rate of the TNBC patients. This metabolomic study provides a better understanding of the metabolic details of TNBC in the Asian population.

The orderly, in vitro emergence of DNA from bacteriophage phi29 particles

phi29 DNA-containing 12-13- particles (produced by infecting nonsuppressor hosts of Bacillus subtilis with phage containing suppressible mutations in cistrons 12 and 13) can be complemented with lysates containing proteins p12* and p13 to yield infectious phage. Complementation of these particles with lysates containing p12* but not p13 or complementation with purified p12* in the absence of p13 produces a structure (called complex) which has a markedly different organization. Electron microscopy and sedimentation analysis after digestion with DNase I or proteinase K indicate that complex is composed of an intact phage head with a genome-sized linear DNA molecule attached at the collar-tail region. EcoRI digestion establishes that the DNA molecule has a unique orientation. Gel electrophoresis indicates that p12*, the neck appendage protein, is transferred to the particles when complex is formed. Complex can also be produced by incubation of 12-13- particles at 42 degrees , by incubation at pH 6.0, or by incubation in the presence of 20 mM EDTA. Complex is also formed from DNA-containing 12- particles but to a lesser extent.

Cisplatin plus gemcitabine with or without vinorelbine as neo-adjuvant therapy for radically treatable stage III non-small cell lung cancer. Results of a randomised study of the Grupo Oncológico del Norte de España

7121

The combinations of cisplatin (C) with gemcitabine (G) and/or vinorelbine (V) have shown to be effective and safe regimens in the first line treatment of NSCLC. This study has been designed to detect a 25% increase in objective response measured by CT scan with the triplet combination (CGV) with respect to cisplatin/gemcitabine combination (CG) administered as neo-adjuvant therapy in patients with radically-treatable stage III NSCLC. With 80% of power and one-sided 5% significant level, the simple size required to confirm this hypothesis is 75 evaluable patients in each arm of treatment. Patients (pts) ≤ 75 years old, Karnofsky index ≥ 70% and adequate haematological, renal and hepatic function are stratified by stage (IIIA versus IIIB) and randomly assigned to: C 50 mg/m2 i.v. and G 1250 mg/m2 i.v. d1 and d8 alone (CG) or in combination with V 25 mg/m 2 i.v. d1 and d8 (CGV) both regimens every 3 weeks for 3 consecutive cycles followed by definitive local treatment (LT). From December 1999 to December 2005, a hundred and forty-nine pts have been randomised (CG/CGV); median age 58/58; median Karnofsky index 80/80; stage IIIA 24/26; stage IIIB 51/48; squamous 37/39; adenocarcinoma 31/32; anaplastic 7/3. Major haematological toxicities grade 3–4 were (CG/CGV; %); Anaemia (5/5) neutropenia (31/34); thrombocytopenia (4/5). Two pts in CG (2.7%) and 4 in CGV arm (5.5%) developed neutropenic fever. Major non-haematological toxicities grade 2–3 were: N/Vomiting (31/32) and fatigue (12/20). Global recurrences have been registered in 57% and 54% of pts treated with CG and CGV arm respectively. Exclusive local/ distant failure (%) has been 16/23 in CG and 23/18 in CGV arm. Preliminary results show similar high efficacy associated with moderate toxicity in both groups of treatment. The study is continuing.

[Table: see text]

No significant financial relationships to disclose.

Prospective randomised phase II study of gemcitabine and vinorelbine versus gemcitabine and docetaxel combination in patients with previously untreated advanced non-small cell lung cancer

17052

Background: Previous comparative studies have shown similar efficacy and less toxicity with either the Gemcitabine(G)/Vinorelbine(V) or Gemcitabine/Docetaxel(D) combination with respect to platinum-based chemotherapies in patients with advanced NSCLC. This trial was designed to test the efficacy and safety of both GV and GD combination in non-selected patients with advanced NSCLC. Methods: Patients (n = 39) with ≤75 years of age, KPS ≥ 60% and adequate haematological, renal and hepatic function were randomly assigned to: G 1250 mg/m2 i.v. d1 and d8 plus either V 25 mg/m2 i.v. d1 and d8 or D 35 mg/m2 i.v. d1 and d8 every 3 weeks. Prophylactic i.v. ranitidine (50 mg), diphenhydramine (25 mg) and dexamethasone (8 mg) were prescribed just prior to the administration of taxane that was given over 30 minutes immediately before gemcitabine. Results: Baseline characteristics were comparable in GV (n = 20) and GD (n = 19) arms: median age (67 years) and KPS (70%), most patients were male (79%), had metastatic disease (85%) and adenocarcinoma histology (55%). Treatment indicated objective response of 7 (35%) versus 6 (31%) patients, median time-to-treatment failure of 120 versus 90 days, and overall survival of 209 versus 177 days in GV and GD arms respectively. The most common non-haematological toxicities were (GV versus GD; No. of patients): grade 2–4 pulmonary toxicity in 1 versus 7 (37%); grade 2–3 diarrhoea in 0 versus 4 (21%) and oedemas 1 versus 3. Grade 2–4 haematological toxicities in 5 versus 2 patients. All side effects were reversible phenomena since resolution was achieved by suspending the treatment and in the case of the pulmonary toxicity, by the prescription of additional corticoids. Conclusion: The combination of Gemcitabine/Docetaxel does not have a favourable safety profile with this schedule of administration, particularly in terms of pulmonary toxicity. Further patients’ enrolment was stopped and the study has been terminated. This kind of toxicity and alternative schedules of GD combination warrant further investigation.

No significant financial relationships to disclose.

Structural phosphoprotein M2-1 of the human respiratory syncytial virus is an RNA binding protein

The structural phosphoprotein M2-1 of human respiratory syncytial virus (HRSV) Long strain shows RNA binding capacity in three different assays that detect RNA-protein complexes: cross-linking, gel retardation, and Northern-Western assays. It is able to bind HRSV leader RNA specifically with cooperative kinetics, with an apparent K(d) of at least 90 nM. It also binds to long RNAs with no sequence specificity. The RNA binding domain has been located between amino acid residues 59 and 85, at the NH(2) terminus of the protein. This region contains the phosphorylatable amino acid residues threonine 56 and serine 58, whose modification decreases the binding capacity of M2-1 protein to long RNAs.

Regulated but not constitutive human respiratory syncytial virus (HRSV) P protein phosphorylation is essential for oligomerization

Purified human respiratory syncytial virus (HRSV) P phosphoprotein from transfected HEp-2 cells is able to oligomerize forming tetramers. The bulk of constitutive P protein phosphorylation (99. 8%) (serine residues 116, 117, 119, 232 and 237) can be removed without affecting protein oligomerization. However, dephosphorylated P protein, produced in bacteria, is unable to oligomerize. This difference can be explained by a transient P protein phosphorylation, detected in HEp-2 cells, that could be essential for P protein oligomerization.

The bulk of the phosphorylation of human respiratory syncytial virus phosphoprotein is not essential but modulates viral RNA transcription and replication

The ability of variants of the human respiratory syncytial virus (HRSV) phosphoprotein (P protein) to support RNA transcription and replication has been studied by using HRSV-based subgenomic replicons. The serine residues normally phosphorylated in P during HRSV infection have been replaced by other residues. The results indicate that the bulk of phosphorylation of P (98%) is not essential for viral RNA transcription or replication but that phosphorylation can modulate these processes.

Interactions between cellular actin and human respiratory syncytial virus (HRSV)

Actin the main component of the cellular microfilament network, is present in human respiratory syncytial virus (HRSV) purified virions, as an internal component. This fact and the results of immunoprecipitation studies indicate that during HRSV infection in HEp-2 cells there are interactions between cellular actin and viral components, that can promote a transitory increase in the polymerization of synthetized actin, mainly of the beta isotype. This increased actin polymerization can be related with the formation of cytoplasmic extensions, that contain beta actin and viral particles observed in the HRSV infected HEp-2 cells. The formation of these structures may indicate that HRSV has developed an actin-based motility system similar to that described for other viral and bacterial systems.

C-terminal phosphorylation of human respiratory syncytial virus P protein occurs mainly at serine residue 232

To determine which human respiratory syncytial virus (HRSV) P protein serine residues are modified by cellular protein kinase(s), several mutated versions of P protein were expressed in the absence of other viral proteins. Mutations at serines 232 or 232 and 237 drastically reduced the extent of phosphorylation P protein in vivo. Serine 232 is the main site of modification and is also essential for in vitro phosphorylation by casein kinase II. Additional in vivo phosphorylation was also detected in the region containing serines 116, 117 and 119.

Identification of a protein kinase involved in the phosphorylation of the C-terminal region of human respiratory syncytial virus P protein

P protein, the structural phosphoprotein of the Long strain of respiratory syncytial (RS) virus, is phosphorylated at serine residues. Some of these residues are candidates for modification by casein kinase II, as they are contained in consensus sequences. A cellular protein kinase, able to phosphorylate the P protein in vitro and apparently associated with purified RS virions, has been partially purified from HEp-2 cells. It shows several characteristics similar to those of casein kinase II. The P protein is modified in vitro by this activity mainly at serine residues located near the C terminus, which are also modified during virus infection. Thus, the P protein is phosphorylated in vivo in two regions, a central region as previously described, and another located in the C-terminal part of the molecule. The protein kinase involved in the phosphorylation of the C-terminal domain is similar to a cellular casein kinase II.

Location of phosphorylated residues in human respiratory syncytial virus phosphoprotein

The phosphoprotein (P protein) from human respiratory syncytial virus Long strain, labelled in vivo with [32P]orthophosphate, was purified from virions or virus-infected human epithelial (Hep-2) cells. The main phosphorylated amino acid found was serine. The determination of the N-terminal sequence of unphosphorylated and phosphorylated fragments of P protein obtained after chemical or enzymic treatments suggested that some or all of the six serines present at positions 116, 117, 119, 143, 156 and 161 are the major phosphorylated residues, although a modification in serine residues at positions 86, 94 and 99 can not be ruled out.

Antiviral effects of xanthate D609 on the human respiratory syncytial virus growth cycle

The antiviral compound tricyclo-decan-9-yl-xanthogenate (D609) inhibits respiratory syncytial (RS) virus growth in human epithelial (Hep 2) cells. D609 treatment resulted in a decrease in the accumulation of viral proteins, in the phosphorylation of the viral phosphoprotein, and in the amount of extracellular antigens and infectious particles. The relative accumulation of viral proteins was also unbalanced, however no differences were found in the amount of viral RNA with plus or minus polarity. In addition nucleocapsids formation was not inhibited. These observations suggested that this antiviral compound affects the relative proportion of viral proteins and the phosphorylation of P protein. Both features appear to be important in RS virus morphogenesis.

Nucleotide sequence of the fusion and phosphoprotein genes of human respiratory syncytial (RS) virus Long strain: evidence of subtype genetic heterogeneity

The nucleotide and deduced amino acid sequences of the fusion (F) and phosphoprotein (P) genes of the Long strain of human respiratory syncytial (RS) virus have been determined from cDNA copies cloned into pBSV9 shuttle vector. Comparison of these sequences with their counterparts of other strains reveals genetic heterogeneity within the same subtype. The percentage of nucleotide and amino acid changes occurring in both proteins is similar. Thus, the Long F and P proteins share 97.9% and 98.3% amino acid identity, respectively, with their homologs of the A2 strain. Nevertheless the F2 subunit of the fusion protein accumulates 3.1 times more amino acid changes than the F1 subunit. In addition, the percentage of nucleotide changes in the 3' extracistronic sequences is 6 times higher in the P than in the F gene. These results are discussed in terms of selective pressures operating in the evolution of RS virus in nature.

Isolation of cross-reactive, subtype-specific monoclonal antibodies against influenza virus HA1 and HA2 hemagglutinin subunits

The large (HA1) and small (HA2) subunits of influenza virus A/Vict/3/75 hemagglutinin were purified in denatured form by preparative electrophoresis. Both polypeptides were used to immunize mice from which monoclonal antibodies were obtained. These antibodies reacted not only with the corresponding hemagglutinin subunit but also with purified virions. When tested by radioimmunoassay against a panel of human viruses, most anti-HA1 and -HA2 antibodies behaved as subtype-specific, whereas anti-HA antibodies, raised against purified virus, were more restricted. The anti-subunit antibodies were negative in hemagglutination-inhibition and neutralization tests. The interest of these antibodies as reagents for research and diagnosis is discussed.

Fixation of mutations in the viral genome during an outbreak of foot-and-mouth disease: heterogeneity and rate variations

Rates of fixation of mutations during the evolution of the foot-and-mouth disease virus (FMDV) C1 in nature have been estimated by hybridization of viral RNA to cloned cDNAs representing defined FMDV genome segments, and comparison of the selected RNAs by T1 RNase oligonucleotide fingerprinting. Values ranged from less than 0.04 X 10(-2) to 4.5 X 10(-2) substitutions per nucleotide per year (s/nt/yr), depending on the time period and the genomic segment considered. Rates for viral structural protein genes were up to sixfold higher than for nonstructural protein genes. Values in excess of 10(-2) s/nt/yr have been measured for the RNA region that encodes VP1-VP3. The nucleotide sequences of the major immunogenic region of capsid protein VP1 have been determined for six new FMDV C1 isolates, and they are compared with the two previously known sequences of FMDV C1 (C-S8 and C1-O). Both oligonucleotide fingerprinting of selected RNA fragments and direct nucleotide sequencing demonstrate that genetic heterogeneity exists among three viruses isolated on the same day, introducing a significant indetermination in the evaluation of fixation rates of mutations. During the FMDV C1 outbreak, amino acid substitutions did occur that are known to affect the immunological properties of the virus. The proportion of mutations between two viral RNAs does not increase significantly with the time elapsed between the two isolations, suggesting a cocirculation of multiple, related, nonidentical FMDVs ('evolving quasispecies') as the mode of evolution of this agent.

Analysis of drug-tubulin interaction by trypsin cleavage: comparison for colchicine, podophyllotoxin, griseofulvin, vinblastine and taxol

Trypsin preferentially cleaves the alpha subunit of depolymerized tubulin or vinblastine induced aggregates (in which longitudinal interactions between tubulin molecules could take place). No cleavage was found for tubulin polymerized into microtubules (containing lateral and longitudinal tubulin interactions), in the presence of taxol. In the presence of colchicine or podophyllotoxin the alpha subunit was partially protected from proteolytic digestion. Trypsin digestion pattern varied upon the addition of different concentrations of griseofulvin. At the higher concentration used, in which microtubules assembly was inhibited, both tubulin subunits were cleaved.

The quasispecies (extremely heterogeneous) nature of viral RNA genome populations: biological relevance--a review

We review evidence that cloned (or uncloned) populations of most RNA viruses do not consist of a single genome species of defined sequence, but rather of heterogeneous mixtures of related genomes (quasispecies). Due to very high mutation rates, genomes of a quasispecies virus population share a consensus sequence but differ from each other and from the consensus sequence by one, several, or many mutations. Viral genome analyses by sequencing, fingerprinting, cDNA cloning etc. indicate that most viral RNA populations (quasispecies) contain all possible single and double genomic site mutations and varying proportions of triple, quadruple, etc. site mutations. This quasispecies structure of RNA virus populations has many important theoretical and practical implications because mutations at only one or a few sites may alter the phenotype of an RNA virus.

Molecular cloning of cDNA from foot-and-mouth disease virus C1-Santa Pau (C-S8). Sequence of protein-VP1-coding segment

cDNA segments copied from the RNA of foot-and-mouth disease virus (FMDV) C1-Santa Pau (isolate C-S8) have been cloned in plasmid pBR322. A 998-bp DNA fragment, that includes the region coding for capsid protein VP1, the carboxy terminus of VP3, and the amino terminus of precursor protein p52 has been sequenced. Comparison of the nucleotide sequence with those from FMDV O1K, A(10)61, A12 and C3 Indaial (Kurz et al., Nucl. Acids Res. 9 (1981) 1919-1931; Kleid et al., Science 214 (1981) 1125-1129; Boothroyd et al., Gene 17 (1982) 153-161; Makoff et al., Nucl. Acids Res. 10 (1982) 8285-8295) indicates extensive variability between the corresponding gene segments, including short insertions and deletions. Base transversions are more frequent than transitions within the VP1 coding segment, but not in the sequence coding for the amino-terminal end of p52. The nucleotide sequence divergence is reflected in variability in both the primary and the predicted higher-order structures of the encoded VP1s.

Evolution of the nucleotide sequence of influenza virus RNA segment 7 during drift of the H3N2 subtype

The complete genetic information contained in the influenza virus RNA segment 7 of the A/Bangkok/1/79 (H3N2) strain has been cloned by in vitro synthesis of the complementary dsDNA and its insertion into plasmid pBR322. The nucleotide sequence of the viral RNA segment has been determined from the cDNA insert. It is 1027 nucleotides long, and contains two open reading frames, as shown for other influenza virus strains. When compared with the previously published sequence for the A/Udorn/72 (H3N2) strain, 15 nucleotide exchanges are observed, most of them silent mutations, and only two causing amino acid changes in each of the M1 and M2 protein sequences.

Microtubule-associated protein MAP2 preferentially binds to a dA/dT sequence present in mouse satellite DNA

Microtubule-associated protein MAP2 binds to the Sau96.1 restriction monomer fragment of mouse satellite DNA. This fragment is also present in a lower proportion in bulk DNA. The digestion of MAP2-Sau96.1 fragment complex by DNase results in the protection of certain nucleotide sequences. The sequence poly(dA)4/poly(dT)4 is mainly protected against DNase digestion.

Purification, properties and assembly of the neck-appendage protein of the Bacillus subtilis phage phi 29

The purification of the neck appendage protein of phi 29, p12*, which is involved in the adsorption of the phage to Bacillus subtilis, is described. The purified native protein is in a dimeric form and can be assembled, in vitro, onto purified 12- particles that lack the neck appendages, suggesting that the incorporation of p12* to the rest of the phage structure is a self-assembly process. The assembly of protein p12* in vitro follows cooperative kinetics and it occurs with an efficiency of about 4%.

Adsorption of bacteriophage phi 29 to Bacillus subtilis through the neck appendages of the viral particle

Phage phi 29 particles produced under restrictive conditions by mutants in gene 12 have normal amounts of all of the structural proteins except the appendage protein, p12*, which is missing. These particles are not infective and do not adsorb to Bacillus subtilis cells. By in vitro complementation of 12- particles with extracts containing protein p12* or with purified protein p12*, the defective particles could bind the appendage protein and become infective and able to adsorb to bacteria. Therefore, the neck appendages of phage phi 29, formed by protein p12*, are involved in the interaction of the phage with the cell wall receptors. Protein p12*, purified in its native state, competed with wild-type phage for adsorption to bacteria. Also, protein p12* could displace adsorbed phage from bacteria. Since the displaced phage was infective, protein p12* does not seem to be modified after phage adsorption.