Chronic exposure to dexamethasone induces hypomethylation of ornithine decarboxylase genes in a human myeloma cell line

The contribution of polyamine pathway to determinations of diagnosis for treatment-resistant depression: A metabolomic analysis

OBJECTIVES

Approximately one-third of major depressive disorder (MDD) patients do not respond to standard antidepressants and develop treatment-resistant depression (TRD). We aimed to reveal metabolic differences and discover promising potential biomarkers in TRD.

METHODS

Our study recruited 108 participants including healthy controls (n = 40) and patients with TRD (n = 35) and first-episode drug-naive MDD (DN-MDD) (n = 33). Plasma samples were presented to ultra performance liquid chromatography-tandem mass spectrometry. Then, a machine-learning algorithm was conducted to facilitate the selection of potential biomarkers.

RESULTS

TRD appeared to be a distinct metabolic disorder from DN-MDD and healthy controls (HCs). Compared to HCs, 199 and 176 differentially expressed metabolites were identified in TRD and DN-MDD, respectively. Of all the metabolites that were identified, spermine, spermidine, and carnosine were considered the most promising biomarkers for diagnosing TRD and DN-MDD patients, with the resulting area under the ROC curve of 0.99, 0.99, and 0.93, respectively. Metabolic pathway analysis yielded compelling evidence of marked changes or imbalances in both polyamine metabolism and energy metabolism, which could potentially represent the primary altered pathways associated with MDD. Additionally, L-glutamine, Beta-alanine, and spermine were correlated with HAMD score.

CONCLUSIONS

A more disordered metabolism structure is found in TRD than in DN-MDD and HCs. Future investigations should prioritize the comprehensive analysis of potential roles played by these differential metabolites and disturbances in polyamine pathways in the pathophysiology of TRD and depression.

Automated fluorescent genomic sequencing as applied to the methylation analysis of the human ornithine decarboxylase gene

A genomic sequencing method for an automated DNA sequencer was developed. The method described here is an improved version of the previously published protocol, which utilizes bisulfite-induced modification of genomic DNA. In our method, the modified DNA is purified without a time-consuming dialysis, and the subsequent 2-step DNA amplification is carried out with one biotinylated primer in order to separate and isolate the strands of the product with the aid of streptavidin-coated magnetic beads. The strands are then sequenced with fluorescent primers and automated DNA sequencer. This provides means to determine reliably the methylation status of cytosines as well as the degree of methylation in a given CpG, site of the target sequence. The method was successfully applied to analyze the promoter region and the 11th exon of the human ornithine decarboxylase ODC gene in various human myeloma cell lines. The study revealed a totally unmethylated promoter region in every cell line studied, whereas the protein coding region appeared to be extensively methylated, although a dexamethasone resistant cell line displayed demethylation in certain CpG sequences. Also, a previously unknown ODC allele was detected.

Certain changes in ornithine decarboxylase gene methylation accompany gene amplification

The ornithine decarboxylase (ODC; EC 4.1.1.17) gene in parental, dexamethasone-resistant and 2-difluoromethylornithine (DFMO)-resistant human IgG-myeloma-cell lines was studied with the aid of methylation-sensitive restriction endonucleases and probes recognizing different parts of the gene. In all cell lines the promoter region of the ODC gene appeared to be heavily methylated, whereas the first long intron was unmethylated. Methylation analyses of several clones from the parental cell line revealed that these cells are heterogeneous with respect to the methylation status of the ODC gene, whereas all clones from DFMO-resistant cell lines displayed the same methylation pattern. Two of the parental clones represented a hypomethylated type very close to that exclusively found among the DFMO-resistant clones with ODC gene amplification. This typical methylation pattern was due to decreased methylation of a few CCGG sequences in the 3'-flanking region of the gene. It is possible that this kind of hypomethylation favours the initiation of the gene-amplification process in certain individual cells. This hypothesis was supported by the finding that no hypomethylation was present in the ODC gene of another human myeloma cell line that had acquired resistance to DFMO without gene amplification. In a dexamethasone-resistant cell line that overproduced ODC mRNA at normal gene dosage there were some minor differences between the methylation pattern of the ODC gene of different clones, but no such hypomethylation could be found in clones from the parental cell line. In dexamethasone-resistant cells the ODC gene was hypomethylated around the two HpaII sites and three CfoI sites in the coding region and also, as well as in cells with amplified ODC sequences, in the 3'-flanking region of the gene. Some hypomethylation in the distant 5'-flanking region was also observed.

Polyamines: from molecular biology to clinical applications

The polyamines putrescine, spermidine and spermine represent a group of naturally occurring compounds exerting a bewildering number of biological effects, yet despite several decades of intensive research work, their exact physiological function remains obscure. Chemically these compounds are organic aliphatic cations with two (putrescine), three (spermidine) or four (spermine) amino or amino groups that are fully protonated at physiological pH values. Early studies showed that the polyamines are closely connected to the proliferation of animal cells. Their biosynthesis is accomplished by a concerted action of four different enzymes: ornithine decarboxylase, adenosylmethionine decarboxylase, spermidine synthase and spermine synthase. Out of these four enzyme, the two decarboxylases represent unique mammalian enzymes with an extremely short half life and dramatic inducibility in response to growth promoting stimuli. The regulation of ornithine decarboxylase, and to some extent also that of adenosylmethionine decarboxylase, is complex, showing features that do not always fit into the generally accepted rules of molecular biology. The development and introduction of specific inhibitors to the biosynthetic enzymes of the polyamines have revealed that an undisturbed synthesis of the polyamines is a prerequisite for animal cell proliferation to occur. The biosynthesis of the polyamines thus offers a meaningful target for the treatment of certain hyperproliferative diseases, most notably cancer. Although most experimental cancer models responds strikingly to treatment with polyamine antimetabolites--namely, inhibitors of various polyamine synthesizing enzymes--a real breakthrough in the treatment of human cancer has not yet occurred. It is, however, highly likely that the concept is viable. An especially interesting approach is the chemoprevention of cancer with polyamine antimetabolites, a process that appears to work in many experimental animal models. Meanwhile, the inhibition of polyamine accumulation has shown great promise in the treatment of human parasitic diseases, such as African trypanosomiasis.

Methylation of human ornithine decarboxylase gene before transfection abolishes its transient expression in Chinese hamster ovary cells

Different methylations of cloned human ornithine decarboxylase gene with restriction methylases in vitro before transfection greatly reduced the transient expression of ODC in Chinese hamster ovary cells. Single methylation of the gene with Hpa II (CCGG) methylase decreased the transiently expressed peak activity by about 50%, single methylation with Hha I (CCGG) methylase by about 80% whilst a double methylation at both Hpa II and Hha I restriction sites virtually abolished any transiently expressed ornithine decarboxylase activity. These results together with our earlier circumventing evidence indicate that the expression of mammalian ornithine decarboxylase is critically influenced by the methylation state of the gene.

Molecular genetics of ornithine decarboxylase in human tumor cells

As the molecular biology of mammalian ornithine decarboxylase is coming of age, more and more interesting features of this unique protein are being uncovered. Ornithine decarboxylase belongs to those 20 or so enzymes or binding proteins, the genes for which are easily amplified under suitable selection pressure. This also applies to the human enzyme. Gene amplification of ornithine decarboxylase is not the only means to acquire resistance to inhibitors of the enzyme, as its overproduction can occur through an enhanced transcription or even through a more efficient translation of normal mRNA amounts. The resistance in human tumors can likewise be acquired by activating other enzymes, such as arginase. In contrast to the multigene family in mouse, it appears that in the human genome only two ornithine decarboxylase genes are present mapping to the chromosomes 2 and 7. Out of these, at least the sequences in the short arm of chromosome 2 are transcriptionally active and amplifiable. Human ornithine decarboxylase also belongs to those proteins which show a positive correlation between gene hypomethylation and expression. The genes of human ornithine decarboxylase are methylated to varying extents and distinct hypomethylation is seen in certain malignant cells, most notably human lymphatic leukemia cells. The human ornithine decarboxylase gene is easily transferrable into other mammalian cells in which it is efficiently expressed. Some indirect evidence seems to indicate that overproduction of ornithine decarboxylase may confer a growth advantage to mammalian cells. A further piece of information suggesting an important role for the enzyme is the fact that the structure of the ornithine decarboxylase gene is extremely well conserved during evolution. This does not apply only to the coding region but also to the overall organization of the gene itself.

Effect of dexamethasone on the activity and expression of ornithine decarboxylase in rat liver and thymus

A single intraperitoneal injection of the synthetic glucocorticoid dexamethasone into rats resulted in a marked stimulation (more than 60-fold) of hepatic ornithine decarboxylase (ODC) at 4 h after the injection, whereas the enzyme activity in thymus was almost totally (about 95%) depressed at the same time. The stimulation of ODC activity in liver was in all likelihood attributable to a greatly enhanced accumulation of mRNA species for the enzyme as revealed by Northern blot and dot-blot hybridization analyses. ODC activity in thymus, in response to dexamethasone, was only 5% of that found in control animals, but this decrease was apparently not accompanied by similar reductions of the levels of ODC message, which was in fact decreased only by 50% at the maximum. In addition to two mRNA species (2.1 and 2.6 kilobases; kb), typical to mouse cells, rat tissues seemed to contain a third hybridizable message for ODC, smaller (1.6 kb) than the above-mentioned species and not seen in samples obtained from mouse or human cells. Interestingly, these smaller poly(A)+ RNA sequences, hybridizable with cDNA complementary to mouse ODC mRNA, were apparently constitutively expressed, as the treatment with glucocorticoid altered the amount of these sequences only slightly.