Molecular medicine: a primer for clinicians. Part XIII: The human genome project and the practice of medicine

Publication earlier this year of the sequence of the human genome marked the end of one era of modern biology and initiated the beginning of another. This paper in our ongoing Molecular Medicine series briefly summarizes the history of the Human Genome Project, describes some of the major features of the structure and organization of the human genome and discusses some of the ways knowledge of the complete human genome might be clinically applicable in the near future.

Increase in class 2 aldehyde dehydrogenase expression by arachidonic acid in rat hepatoma cells

Aldehyde dehydrogenase (ALDH) is a family of several isoenzymes important in cell defence against both exogenous and endogenous aldehydes. Compared with normal hepatocytes, in rat hepatoma cells the following changes in the expression of ALDH occur: cytosolic class 3 ALDH expression appears and mitochondrial class 2 ALDH decreases. In parallel with these changes, a decrease in the polyunsaturated fatty acid content in membrane phospholipids occurs. In the present study we demonstrated that restoring the levels of arachidonic acid in 7777 and JM2 rat hepatoma cell lines to those seen in hepatocytes decreases hepatoma cell growth, and increases class 2 ALDH activity. This latter effect appears to be due to an increased gene transcription of class 2 ALDH. To account for this increase, we examined whether peroxisome-proliferator-activated receptors (PPARs) or lipid peroxidation were involved. We demonstrated a stimulation of PPAR expression, which is different in the two hepatoma cell lines: in the 7777 cell line, there was an increase in PPAR alpha expression, whereas PPAR gamma expression increased in JM2 cells. We also found increased lipid peroxidation, but this increase became evident at a later stage when class 2 ALDH expression had already increased. In conclusion, arachidonic acid added to the culture medium of hepatoma cell lines is able to partially restore the normal phenotype of class 2 ALDH, in addition to a decrease in cell growth.

Characterization of chemical interferences in the determination of unsaturated aldehydes using aromatic hydrazine reagents and liquid chromatography

A systematic investigation on interferences in the determination of unsaturated aldehydes and ketones using the 2,4-dinitrophenylhydrazine (DNPH) method is described. Acrolein, crotonaldehyde, methacrolein and 1-buten-3-one are derivatized with DNPH in the presence of an acidic catalyst to form the respective hydrazones. The unstable hydrazones react with excess reagent to form adducts. These are identified by high-performance liquid chromatography (HPLC)-mass spectrometry and spectroscopic techniques after cryogenic fraction collection of the adducts. The quantification of the unsaturated carbonyls with the DNPH method remains difficult. N-Methyl-4-hydrazino-7-nitrobenzofurazan (MNBDH) was used as an alternative reagent for this purpose. As with DNPH, the formation of a side product is observed. In contrast to DNPH, the alteration of the pH immediately after sampling leads to only one reaction product, which is stable and storable in solution at 4 degrees C for 2 days.

Molecular medicine: a primer for clinicians. Part XII: DNA microarrays and their application to clinical medicine

Previous papers in our Molecular Medicine series have described how the many tools of the molecular biologist are being used to develop practical bedside applications of modern molecular biology. We have discussed molecular diagnostics, gene therapy, and applications in clinical genetics. In this paper we discuss DNA microarray technology which provides a genome-wide profile of gene expression. We then describe some current and potential clinical applications in the disease diagnosis, prognosis and treatment. Particularly exciting is the potential of DNA array technology to provide individualized treatment for a wide variety of clinical conditions.

Aldehyde dehydrogenase. Maintaining critical active site geometry at motif 8 in the class 3 enzyme

Alignment of all known, diverse members of the aldehyde dehydrogenase (ALDH) extended family revealed only two strictly conserved, nonglycine residues, a glutamate and a phenylalanine residue. Both occur in one of the highly conserved 'motif' segments and both occupy strategic locations in the tertiary structure at the bottom of the catalytic funnel. In class 3 ALDH, these are Glu333 and Phe335. In addition, Asp247, which is not highly conserved but is characteristic of class 3 ALDHs, hydrogen bonds the main chain between Glu333 and Phe335. These three residues were mutated conservatively. Michaelis constants determined for both NAD/propanal and NADP/benzaldehyde substrate pairs show all three residues to be crucial to effective catalysis, and suggest that the hydrogen bond to Asp247 is a key element in maintaining precise geometry of key elements at the active site.

Determination of morpholine in air by derivatisation with 1-naphthylisothiocyanate and HPLC analysis

A method for the determination of morpholine in air was developed. Samples were collected with adsorbent tubes containing XAD-2 resin coated with 1-naphthylisothiocyanate (NIT). The thiourea derivative formed was subsequently desorbed with acetonitrile and analysed by HPLC with UV detection. The recovery after gas phase spiking with morpholine (2.2-1570 micrograms) was 91% (86-100%) with a relative standard deviation of 5.5%. No effect on recovery from relative humidity or amount of morpholine was seen. The lowest level tested corresponded to 7 mg m-3 (1/10 threshold limit value) for a 15 min sampling period with a sampling rate of 20 ml min-1. Exposed NIT-coated XAD-2 tubes were stable at room temperature for at least 2 weeks.

Beyond the catalytic core of ALDH: a web of important residues begins to emerge

Site-directed mutagenesis was performed in class 3 aldehyde dehydrogenase (ALDH) on both strictly conserved, non-glycine residues, Glu-333 and Phe-335. Both lie in Motif 8 and are indicated to be of central catalytic importance from their positions in the tertiary structure. In addition, a highly conserved residue at the end of Motif 8, Pro-337, and Asp-247, which interacts with the main chain of Motif 8, were also mutated. All substitutions were conservative. Kinetic values clearly show that Glu-333 and Phe-335 are crucial to efficient catalysis, along with Asp-247. Pro-337 appears to have a different role, most likely relating to folding.

Coenzyme specificity in aldehyde dehydrogenase

Influences on coenzyme preference are explored. Lysine 137 (192 in class 1/2 ALDH) lies close to the adenine ribose, directly interacting with the adenine ribose in NAD-specific ALDHs and the 2'-phosphate of NADP in NADP-specific ALDHs. Lys-137 in class 3 ALDH interacts with the adenine ribose indirectly through an intervening water molecule. However, this residue is present in all ALDHs and, as a result, is unlikely to directly influence coenzyme specificity. Glutamate 140 (195) coordinates the 2'- and 3'-hydroxyls of the adenine ribose of NAD in the class 3 tertiary structure. Thus, it appeared that this residue would influence coenzyme specificity. Mutation to aspartate, asparagine, glutamine or threonine shifts the coenzyme specificity towards NADP, but did not completely change the specificity. Still, the mutants show the 2'-phosphate of NADP is repelled by Glu-140 (195). Although Glu-140 (195) has a major influence on coenzyme specificity, it is not the only influence since class 3 ALDHs, can use both coenzymes, and class 2 ALDHs, which are NAD-specific, have a glutamate at this position. One explanation may be that the larger space between Lys-137 (192) and the adenine ribose hydroxyls in the class 3 ALDH:NAD binary structure may provide space to accommodate the 2'-phosphate of NADP. Also, a structural shift upon binding NADP may also occur in class 3 ALDHs to help accommodate the 2'-phosphate of NADP.

Aldehyde dehydrogenase 3 gene regulation: studies on constitutive and hypoxia-modulated expression

We have previously shown that expression of the Class 3 aldehyde dehydrogenase gene (ALDH3) is abrogated by hypoxia. This phenomenon occurs in rat hepatoma systems in which ALDH3 expression is xenobiotic-inducible as well as in rat primary corneal epithelial cells that exhibit high constitutive ALDH3 expression. We have begun to test various segments of the ALDH3 5' flanking region for elements that may mediate this effect using CAT reporter gene constructs. In addition, although the involvement of the Ah receptor nuclear translocator (ARNT) in xenobiotic induction of ALDH3 is well established, the role of ARNT in constitutive ALDH3 expression is not clear. Moreover, ARNT is also a component of the hypoxia inducible factor-1 (HIF-1) bipartite transcription factor complex that mediates hypoxic induction of a variety of genes. Concomitant activation of the xenobiotic and hypoxia pathways results in cross-talk and functional interference. It has been hypothesized that this interference is due to limiting levels of ARNT. To examine if ARNT levels are limiting during hypoxic and xenobiotic induction in the context of ALDH3 expression and to examine possible roles of ARNT in constitutive expression of ALDH3 in corneal epithelial cells we co-transfected rat corneal epithelial cells and H4-II-EC3 rat hepatoma cells with ALDH3 5' UTR-CAT reporter genes and expression vectors containing either wild type or dominant negative forms of ARNT. Our results indicate that during hypoxia and xenobiotic induction of ALDH3 in H4-II-EC3 cells ARNT is not the limiting transcription factor. Further, neither wild type nor dominant negative ARNT had effects on constitutive ALDH3 expression in corneal epithelial cells.

Shifting the NAD/NADP preference in class 3 aldehyde dehydrogenase

Among pyridine-nucleotide-dependent oxidoreductases, the class 3 family of aldehyde dehydrogenases (ALDHs) is unusual in its ability to function with either NAD or NADP. This is all the more surprising because an acidic residue, Glu140, coordinates the adenine ribose 2' hydroxyl. In many NAD-dependent dehydrogenases a similarly placed carboxylate is thought to be responsible for exclusion of NADP. The corresponding residue in most (approximately 71%) sequences in the ALDH extended family is also Glu, and most of these are NAD-specific enzymes. Site-directed mutagenesis was performed on this residue in rat class 3 ALDH. Our results indicate that this residue contributes to tighter binding of NAD in the native enzyme, but suggest that additional factors must contribute to the ability to utilize NADP. Mutagenesis of an adjacent basic residue (Lys137) indicates that it is even more essential for binding both coenzymes, consistent with its conservation in nearly all ALDHs (> 98%).

Validation of a diffusive sampler for NO2

A diffusive sampler for NO2, Willems badge, was validated in laboratory experiments and field tests. The collecting reagent for NO2 in the sampler is triethanolamine, and the analysis is based on a modified colorimetric method, the Saltzman method. The analysis was performed by a flow injection analysis (FIA) technique. The sampling rate for the sampler was determined to be 40.0 ml min-1. There was no effect of NO2 concentration or relative humidity on sampling rate, and the influence of sampling time was found to be small. The detection limit was 4 micrograms m-3 for a 24 h sample. The capacity is high enough to allow sampling of 150 micrograms m-3 for 7 days, which is twice the recommended Swedish short-term (24 h) guideline value as a 98-percentile over 6 months. In field tests, the sampler performed well, even at wind speeds higher than 2 m s-1, and at low temperatures. The overall uncertainty of the method was 24%. The sensitivity and capacity of the method also make it suitable for personal sampling for 2-8 h in working environments.

Negative regulation of rat hepatic aldehyde dehydrogenase 3 by glucocorticoids

The expression of the aldehyde dehydrogenase 3 gene is known to be controlled by multiple regulatory processes. In liver, inducible expression appears to be mediated by two AhRE sequences which allow regulation of this gene by xenobiotic compounds which are ligands for the Ah receptor (Takimoto et al., 1994; this work). Constitutive expression of ALDH3 in tissues such as the cornea also involves the -3,500 region which contains an AhRE (Boesch et al., 1996; Boesch et al, 1998). However, the constellation of transcription factors which appear to interact with the AhRE in constitutively expressing corneal cells does not include either the Ah receptor nor the prototypical ARNT protein (Boesch et al., 1998). For both inducible and constitutive ALDH3 expression the more distal 5' flanking region sequences appear to interact with more proximal regulatory elements. Of particular interest is the region near -1 kb which includes the GC (-930 to -910) and cAMP (-1057 to -991) responsive elements as well as the 2 NF1 sites (-916 to -815), all of which appear to act as negative modulators of ALDH3 expression. A second putative ALDH3 negative regulatory region lies even more distal than -3,500 bp. To date, this region has been little studied, but appears to be involved in regulating both inducible and constitutive ALDH3 expression. This region may also be responsible for some of the tissue-specificity of ALDH3 expression. With respect to the work described here, in both isolated hepatocytes and HepG2 cells, no consistent negative regulation by glucocorticoids was observed in the basal expression of ALDH3. This indicates that the mechanism of GC-mediated negative regulation involves direct interference with ALDH3 gene activation mediated by the Ah receptor. Our results suggest a complex interplay between multiple transcription factors, including the GC and Ah receptors, regulates the hepatic expression of the ALDH3 gene. Active recruitment of transcription factors needed for gene transactivation, amelioration of the actions of negative regulatory trans-acting factors or cis-acting elements and/or chromatin remodeling may be required for achieve proper regulation of the aldehyde dehydrogenase 3 gene.

The negative regulation of the rat aldehyde dehydrogenase 3 gene by glucocorticoids: involvement of a single imperfect palindromic glucocorticoid responsive element

Glucocorticoids repressed the polycyclic aromatic hydrocarbon-dependent induction of Class 3 aldehyde dehydrogenase (ALDH3) enzyme activity and mRNA levels in isolated rat hepatocytes by more than 50 to 80%, with a concentration-dependence consistent with the involvement of the glucocorticoid receptor (GR). No consistent effect on the low basal transcription rate was observed. This effect of glucocorticoids (GC) on polycyclic aromatic hydrocarbon induction was effectively antagonized at the mRNA and protein level by the GR antagonist RU38486. The response was cycloheximide-sensitive, because the protein synthesis inhibitor caused a GC-dependent superinduction of ALDH3 mRNA levels. This suggests that the effects of GC on this gene are complex and both positive and negative gene regulation is possible. The GC-response was recapitulated in HepG2 cells using transient transfection experiments with CAT reporter constructs containing 3.5 kb of 5'-flanking region from ALDH3. This ligand-dependent response was also observed when a chimeric GR (GR DNA-binding domain and peroxisome proliferator-activated receptor ligand-binding domain) was used in place of GR in the presence of the peroxisome proliferator, nafenopin. A putative palindromic glucocorticoid-responsive element exists between -930 and -910 base pairs relative to the transcription start site. If this element was either deleted or mutated, the negative GC-response was completely lost, which suggests that this sequence is responsible, in part, for the negative regulation of the gene. Electrophoretic mobility shift analysis demonstrated that this palindromic glucocorticoid-responsive element is capable of forming a specific DNA-protein complex with human glucocorticoid receptor. In conclusion, the negative regulation of ALDH3 in rat liver is probably mediated through direct GR binding to its canonical responsive element.

Efficiency of automotive cabin air filters to reduce acute health effects of diesel exhaust in human subjects

OBJECTIVES

To evaluate the efficiency of different automotive cabin air filters to prevent penetration of components of diesel exhaust and thereby reduce biomedical effects in human subjects. Filtered air and unfiltered diluted diesel exhaust (DDE) were used as negative and positive controls, respectively, and were compared with exposure to DDE filtered with four different filter systems.

METHODS

32 Healthy non-smoking subjects (age 21-53) participated in the study. Each subject was exposed six times for 1 hour in a specially designed exposure chamber: once to air, once to unfiltered DDE, and once to DDE filtered with the four different cabin air filters. Particle concentrations during exposure to unfiltered DDE were kept at 300 micrograms/m3. Two of the filters were particle filters. The other two were particle filters combined with active charcoal filters that might reduce certain gaseous components. Subjective symptoms were recorded and nasal airway lavage (NAL), acoustic rhinometry, and lung function measurements were performed.

RESULTS

The two particle filters decreased the concentrations of diesel exhaust particles by about half, but did not reduce the intensity of symptoms induced by exhaust. The combination of active charcoal filters and a particle filter significantly reduced the symptoms and discomfort caused by the diesel exhaust. The most noticable differences in efficacy between the filters were found in the reduction of detection of an unpleasant smell from the diesel exhaust. In this respect even the two charcoal filter combinations differed significantly. The efficacy to reduce symptoms may depend on the abilities of the filters investigated to reduce certain hydrocarbons. No acute effects on NAL, rhinometry, and lung function variables were found.

CONCLUSIONS

This study has shown that the use of active charcoal filters, and a particle filter, clearly reduced the intensity of symptoms induced by diesel exhaust. Complementary studies on vehicle cabin air filters may result in further diminishing the biomedical effects of diesel exhaust in subjects exposed in traffic and workplaces.

Inhibition of class-3 aldehyde dehydrogenase and cell growth by restored lipid peroxidation in hepatoma cell lines

Hepatoma cells have a below-normal content of polyunsaturated fatty acids; this reduces lipid peroxidation and the production of cytotoxic and cytostatic aldehydes within the cells. In proportion to the degree of deviation, hepatoma cells also show an increase in the activity of Class-3 aldehyde dehydrogenase, an enzyme important in the metabolism of lipid peroxidation products and also in that of several drugs. When hepatoma cells with different degrees of deviation were enriched with arachidonic acid and stimulated to peroxidize by ascorbate/iron sulphate, their growth rate was reduced in proportion to the quantity of aldehydes produced and to the activity of aldehyde dehydrogenase. Therefore, 7777 cells, less deviated and with low Class-3 aldehyde dehydrogenase activity, were more susceptible to lipid peroxidation products than JM2 cells. It is noteworthy that repeated treatments with prooxidant also caused a decrease in mRNA and activity of Class-3 aldehyde dehydrogenase, contributing to the decreased growth and viability. Thus, Class-3 aldehyde dehydrogenase could be considered relevant for the growth of hepatoma cells, since it defends them against cell growth inhibiting aldehydes derived from lipid peroxidation.

A diffusive sampling device for the determination of formaldehyde in air using N-methyl-4-hydrazino-7-nitrobenzofurazan (MNBDH) as reagent

A new method utilizing the diffusive sampling of formaldehyde in air has been developed. Formaldehyde is sampled with the use of a glass fiber filter impregnated with N-methyl-4-hydrazino-7-nitrobenzofurazan (MNBDH) and phosphoric acid. The formaldehyde hydrazone formed is desorbed from the filter with acetonitrile and determined by high-performance liquid chromatography (HPLC) with UV/visible detection at 474 nm. The sampling rate was determined to be 24.7 mL min-1 with a relative standard deviation of 7% for 48 experiments. The measured sampling rates were not dependent on the formaldehyde concentration (0.1-1.0 mg m-3), sampling time (15-482 min) or relative humidity (20-85%). The detection limit was 70 micrograms m-3 for a 15 min sampling period and 2 micrograms m-3 for an 8 h sampling period.

The same xenobiotic response element is required for constitutive and inducible expression of the mammalian aldehyde dehydrogenase-3 gene

The mammalian aldehyde dehydrogenase-3 gene (ALDH3) exhibits several aspects of tissue-specific expression. Certain normal tissues, such as the cornea, constitutively express ALDH3 at very high levels. Other tissues, such as normal liver, do not express ALDH3. In liver, ALDH3 is inducible by polycyclic aromatic hydrocarbon xenobiotics by an Ah-receptor (AhR)-mediated pathway in which a liganded AhR complexes with nuclear ARNT protein, and the complex binds to a xenobiotic response element (XRE) sequence located near -3.0 kb in the ALDH3 5' flanking region and initiates transcription. We used our recently developed rat corneal epithelium culture model (Boesch et al., J. Biol. Chem. 271, 5150-5157, 1996) to study the molecular basis of constitutive ALDH3 expression. Transient transfection assays of corneal epithelium using a battery of ALDH3 5' flanking region-CAT reporter gene constructs indicate that high constitutive ALDH3 expression involves the same cis-acting elements as xenobiotic-induced ALDH3 expression in liver. These elements include a strong basal promoter region and the XRE located near -3.0 kb. Western analysis confirms the presence of AhR and ARNT proteins in 3-methylcholanthrene-treated rat liver, as well as ARNT protein in rat corneal epithelium. No AhR protein is found in rat cornea. The -3.0-kb ALDH3 XRE region contains multiple overlapping transcription factor binding sequences, including consensus sites for AhR, ARNT, HNF1, HNF4, and C/ebp. Electrophoretic mobility shift assays (EMSAs) indicate that constitutive expression of ALDH3 in cornea involves binding of ARNT, HNF1, and HNF4 to the ALDH3-XRE in an Ah-receptor-independent, ARNT-requiring manner. Transient transfection of ALDH3-CAT reporter gene constructs possessing a mutation in either the ARNT- or HNF4-DNA binding sites of the XRE confirms the functional importance of these sequence motifs in constitutive ALDH3 expression.

Relationships within the aldehyde dehydrogenase extended family

One hundred-forty-five full-length aldehyde dehydrogenase-related sequences were aligned to determine relationships within the aldehyde dehydrogenase (ALDH) extended family. The alignment reveals only four invariant residues: two glycines, a phenylalanine involved in NAD binding, and a glutamic acid that coordinates the nicotinamide ribose in certain E-NAD binary complex crystal structures, but which may also serve as a general base for the catalytic reaction. The cysteine that provides the catalytic thiol and its closest neighbor in space, an asparagine residue, are conserved in all ALDHs with demonstrated dehydrogenase activity. Sixteen residues are conserved in at least 95% of the sequences; 12 of these cluster into seven sequence motifs conserved in almost all ALDHs. These motifs cluster around the active site of the enzyme. Phylogenetic analysis of these ALDHs indicates at least 13 ALDH families, most of which have previously been identified but not grouped separately by alignment. ALDHs cluster into two main trunks of the phylogenetic tree. The largest, the "Class 3" trunk, contains mostly substrate-specific ALDH families, as well as the class 3 ALDH family itself. The other trunk, the "Class 1/2" trunk, contains mostly variable substrate ALDH families, including the class 1 and 2 ALDH families. Divergence of the substrate-specific ALDHs occurred earlier than the division between ALDHs with broad substrate specificities. A site on the World Wide Web has also been devoted to this alignment project.

Hypoxia exerts cell-type-specific effects on expression of the class 3 aldehyde dehydrogenase gene

The Class 3 aldehyde dehydrogenase gene (ALDH3) is expressed differentially in a tissue-specific manner, occurring constitutively in some tissues and in others as a result of xenobiotic induction via the Ah receptor/ARNT pathway. ARNT is also involved in regulating gene expression in response to hypoxia. It dimerizes with hypoxia-inducible factor 1 alpha (HIF-1 alpha) and enhances expression of hypoxia-responsive genes. To determine if ARNT plays a role in regulating ALDH3 in response to low oxygen tension, we studied the effects of 1% oxygen and the hypoxia mimic cobalt chloride on constitutive and inducible ALDH3 expression in rat hepatoma cells and rat corneal epithelial cells. Hypoxia sharply down-regulates constitutive ALDH3 expression in corneal epithelial cells. Likewise, aromatic hydrocarbon-induced ALDH3 expression in H4-II-EC3 cells is significantly reduced by hypoxia. In contrast, hypoxia has no effect on constitutive or aromatic hydrocarbon-inducible ALDH3 expression in HTC cells. Our data indicate that hypoxia exerts cell type-specific effects on both constitutive and induced ALDH3 expression.

The first structure of an aldehyde dehydrogenase reveals novel interactions between NAD and the Rossmann fold

The first structure of an aldehyde dehydrogenase (ALDH) is described at 2.6 A resolution. Each subunit of the dimeric enzyme contains an NAD-binding domain, a catalytic domain and a bridging domain. At the interface of these domains is a 15 A long funnel-shaped passage with a 6 x 12 A opening leading to a putative catalytic pocket. A new mode of NAD binding, which differs substantially from the classic beta-alpha-beta binding mode associated with the 'Rossmann fold', is observed which we term the beta-alpha,beta mode. Sequence comparisons of the class 3 ALDH with other ALDHs indicate a similar polypeptide fold, novel NAD-binding mode and catalytic site for this family. A mechanism for enzymatic specificity and activity is postulated.

Characterization of the rat Class 3 aldehyde dehydrogenase gene promoter

The Class 3 aldehyde dehydrogenase gene (ALDH-3) is differentially expressed. Expression is either constitutive or xenobiotic inducible via an aromatic hydrocarbon (Ah) receptor-mediated pathway, depending upon the tissue. A series of studies were performed to examine the regulation of rat ALDH-3 basal expression. DNase I footprint analysis identified four DNA regions within the proximal 1 kb of the 5' flanking region of rat ALDH-3 which interact with regulatory proteins. Reporter gene and gel mobility shift assays indicate that Sp1-like proteins interact with two proximal DNase I footprinted sites to confer strong promoter activity. Two distal DNase I footprinted sites are found within a region that inhibits rat ALDH-3 promoter activity. This negative region is bound by NF1-like proteins and/or unique proteins. This 1 kb 5' flanking region of rat ALDH-3 may act constitutively in many cell types. In contrast with other Ah receptor regulated genes, no DNA elements or transcription factors acting within this region appear to be involved in regulating xenobiotic-inducible expression of rat ALDH-3.

Mouse microsomal Class 3 aldehyde dehydrogenase: AHD3 cDNA sequence, inducibility by dioxin and clofibrate, and genetic mapping

We have cloned and sequenced the mouse AHD3 cDNA, which codes for the Class 3 microsomal aldehyde dehydrogenase (ALDH3m). The cDNA is 2,997 bp in length excluding the poly(A)+ tail, and has 5' and 3' non-translated regions of 113 bp and 1,429 bp, respectively. The deduced amino acid sequence consists of 484 amino acids, including the first methionine (Mr = 53,942), and contains a hydrophobic segment at the carboxyl terminus which is the putative membrane anchor. The mouse AHD3 protein was found to be: 95% similar to the rat microsomal ALDH3m protein, 65% identical to the mouse, rat and human cytosolic ALDH3c protein, and <28% similar to the rat Class 1 and Class 2 ALDH and methylmalonate-semialdehyde dehydrogenase proteins. Southern hybridization analysis of mouse cDNA probed with the full-length AHD3 cDNA revealed that the Ahd3 gene likely spans less than a total of 25 kb. The mouse Ahd3 gene is very tightly linked to the Ahd4 gene on chromosome 11. Mouse AHD3 mRNA levels are increased by dioxin in mouse Hepa-1c1c7 hepatoma wild-type (wt) cells but not in the Ah receptor nuclear translocator (ARNT)-defective (c4) mutant line, indicating that the induction process is mediated by the Ah (aromatic hydrocarbon) dioxin-binding receptor. AHD3 mRNA levels are also inducible by clofibrate in both the wt and c4 lines. AHD3 mRNA levels are not elevated in the CYP1A1 metabolism-deficient c37 mutant line or as part of the oxidative stress response found in the untreated 14CoS/14CoS mouse cell line. These data indicate that, although inducible by dioxin, the Ahd3 gene does not qualify as a member of the aromatic hydrocarbon [Ah] gene battery.

Molecular medicine: a primer for clinicians--part IX human gene therapy

Previous papers in our Molecular Medicine series have described how many tools of the molecular biologist are being used to develop practical bedside applications of modern molecular biology. We have discussed the development of molecular diagnostics and their emerging use in clinical settings. In this paper we discuss how the tools of the molecular biologist are being used to develop "gene therapy", genetic treatments or cures for a wide variety of medical conditions. Recent results suggest that effective gene-based treatments or cures for many human diseases may soon be practical.

Relative potencies of induction of hepatic drug-metabolizing enzyme genes by individual PCB congeners

The induction of a variety of drug-metabolizing enzymes by polychlorinated biphenyl (PCB) congeners that elicit a 2,3,7,8,-tetrachlorodibenzo-p-dioxin (TCDD)-type hepatic pleiotropic response, including 2,3,3',4,4'-pentachlorobiphenyl (BZ 105), 2,3',4,4',5-pentachlorobiphenyl (BZ 118), 2,3,3',4,4',5-hexachlorobiphenyl (BZ 156), and 3,3',4,4',5,5'-hexachlorobiphenyl (BZ 169) was examined. Following dietary exposure to the individual congeners for 5 days, livers were removed and catalytic assays for cytochrome P450 (CYP) isozymes 1A1 and 1A2 were performed. Additionally, total cellular RNA coding for hepatic drug-metabolizing genes (CYP 1A1, CYP 1A2, microsomal epoxide hydrolase, glutathione S-transferase [GST] Ya/Yc, and the TCDD-inducible isozyme of aldehyde dehydrogenase [ALDH] was quantified. 3-Methylcholanthrene (MC), TCDD, or BZ 156 (32 ppm) caused nearly maximal induction of the CYP 1A proteins but lower induction of the other genes. When the dose-response curves for induction of various drug-metabolizing genes (CYP 1A1 and 1A2, microsomal epoxide hydrolase, the GST Ya/Yc subfamily and ALDH) were examined, a spectrum of ED50s (half-maximal inductions) was observed. While CYP 1A2 exhibited an ED50 of 1.7 ppm, the induction of ALDH was shifted far to the right (ED50 > 11 ppm). Thus, different genes in a single tissue may display different dose-response characteristics. The potency (extent of induction of CYP 1A1 activity resulting from a given dietary dose) was BZ 169 >> BZ 156 > BZ 118 > BZ 105. In contrast, the potencies of the four congeners for CYP 1A1 induction were nearly equivalent when related to hepatic PCB burden, apparently due to the preferential accumulation in the liver of BZs 169 and 156 following low-level administration in the diet.

Enrichment with arachidonic acid increases the sensitivity of hepatoma cells to the cytotoxic effects of oxidative stress

Hepatoma cells are, at most, moderately sensitive to oxidative stress. An important cause of this lack of sensitivity is the decreased content of polyunsaturated fatty acids in comparison with normal cells. These fatty acids are one cellular target of oxygen radicals, by which they are broken down into several toxic carbonyl compounds. If the membrane phospholipids of tumor cells are enriched with polyunsaturated fatty acids, such as arachidonic acid, they become able to undergo lipid peroxidation in the presence of prooxidants. This effect is studied in the highly deviated Yoshida AH-130 ascites hepatoma and in two rat hepatoma cell lines. In parallel to their increased lipid peroxidation, cells enriched with arachidonic acid and exposed to ascorbic acid/FeSO4 showed lower viability and growth than unenriched ones.

Molecular medicine: a primer for clinicians--Part VII: Ethical issues associated with genetic testing

Previously, we described the concepts and methods of DNA-based or genetic testing. The unlimited diagnostic power of genetic testing, coupled with the reality that effective treatments for many conditions are not available, raises many ethical and legal issues. These issues are discussed as they relate to the bed-side practice of molecular medicine.

Molecular medicine: a primer for clinicians--Part VI: Introduction to genetic testing

Application of the tools of molecular biology to clinical medicine is most apparent than in the development of DNA-based diagnostic and predictive tests. Such tests allow direct examination of the DNA of individuals for the presence or absence of the causative or predisposing molecular defect for a disease or condition. In this and the next two papers, in our series, we will discuss various aspects of genetic testing. We will consider the different types of testing, their current and potential clinical applications and discuss some of the major ethical and legal issues that genetic testing poses.

Oxazaphosphorine-specific resistance in human MCF-7 breast carcinoma cell lines expressing transfected rat class 3 aldehyde dehydrogenase

Overexpression of either class 1 or class 3 aldehyde dehydrogenase (ALDH) has been found in cell lines selected for resistance to the oxazaphosphorine (OAP) alkylating anticancer agent cyclophosphamide (CPA). Direct oxidation of the CPA metabolic intermediate aldophosphamide (ALDO) is catalyzed efficiently in vitro by the class 1 ALDH isozyme, but the involvement of the class 3 isozyme in OAP resistance is problematic since in vitro studies do not show efficient oxidation of ALDO. Cell lines were established that express stably transfected rat class 3 ALDH to model the potential role of this isozyme in OAP resistance. Clonogenic survival assay data indicated that even modest expression of rat class 3 ALDH was associated with resistance (2-4-fold) to the CPA analog mafosfamide and that the fold resistance was directly proportional to the class 3 ALDH activity expressed in clonal transfectants. Pretreatment of the highest activity cell line (3A1-31A) with 75 microM diethylaminobenzaldehyde, an ALDH substrate and inhibitor of benzaldehyde oxidation, effectively reversed the 3.8-fold resistance in this line; drug sensitivity was unaffected by diethylaminobenzaldehyde in the control transfected cell line. The resistance conferred by ALDH to mafosfamide is OAP-specific since the 3A1-31A line is also resistant to 4-hydroperoxycyclophosphamide (2.9-fold) and 4-hydroperoxyifosfamide (3.2-fold) but not to the non-oxazaphosphorine drugs phosphoramide mustard and melphalan, which cannot be detoxified by aldehyde dehydrogenase enzymes.

Structure of the 5' flanking region of class 3 aldehyde dehydrogenase in the rat

Class 3 aldehyde dehydrogenase (ALDH-3) is induced by exposure to the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and during chemical carcinogenesis. These inductions as well as the basal expression of ALDH-3 vary significantly in different organs. In order to identify DNA elements controlling ALDH-3 expression, we have cloned and analyzed approximately 5.5 kb of the 5' flanking region of the ALDH-3 gene. Deletion analysis showed that the 5' flanking region contains at least three functional domains: a strong promoter proximal to the transcription start site, inhibitory regions upstream of the promoter, and TCDD-responsive enhancers. The TCDD-responsive enhancers in the ALDH-3 gene were functionally similar to xenobiotic responsive elements in the cytochrome P450IA1 gene. These results indicate that transcription of the ALDH-3 gene is controlled by cooperation of at least three functional domains.

Role of aldehyde metabolizing enzymes in mediating effects of aldehyde products of lipid peroxidation in liver cells

It is well established that many types of tumor cells have reduced lipid peroxidation capacity compared to their normal counterparts. Changes in the activity of enzymes metabolizing aldehydes produced by lipid peroxidation have also been reported in a variety of tumor cells. We have investigated the relationship between changes in lipid peroxidation and changes in aldehyde-metabolizing enzymes in normal hepatocytes and two representative rat hepatoma cell lines, McA-RH-7777 and JM2. Compared to hepatocytes, both 7777 and JM2 cells have significantly lower basal and prooxidant-induced levels of lipid peroxidation than normal hepatocytes. Using 4-hydroxynonenal (4-HNE) as substrate, both cell lines also have significantly reduced activities of alcohol dehydrogenase (ADH) and glutathione S-transferase (GST) compared to hepatocytes. JM2 cells have significantly increased aldehyde dehydrogenase (ALDH) and aldehyde reductase (ALRD) activities with 4-HNE. In 7777 cells the ALDH and ALRD activities are not different from hepatocytes. The changes in enzyme activity are inversely correlated with the sensitivity of cells to 4-HNE. JM2 cells, with increased ALDH and ALRD and decreased ADH and GST, are much more resistant to the toxic effects of 4-HNE than 7777 cells. Normal hepatocytes and JM2 cells are approximately equally resistant to 4-HNE even though hepatocytes rely primarily on GST-mediated aldehyde conjugation to metabolize 4-HNE. Coupled with previous results from our laboratories, the overall increased sensitivity of certain hepatoma cells to lipid aldehydes appears due to decreased ability of these hepatoma cells to remove toxic products of lipid peroxidation. Moreover, hepatoma cells with increased levels of aldehyde dehydrogenase and aldehyde reductase appear most like hepatocytes in their ability to metabolize lipid aldehydes.

Molecular medicine: a primer for clinicians. Part IV: Cystic fibrosis and the power and limitations of molecular medicine

Cystic fibrosis (CF) is among the most common genetic diseases in caucasians of Northern European ancestry. The cloning of the gene responsible for cystic fibrosis, the characterization of the product of the gene and identification of mutations occurring in CF patients are excellent examples of the potential clinical utility of molecular medicine. The ethical issues associated with the ability to identify carriers of CF mutations highlight the magnitude of the questions molecular medicine raises.

Aldehyde dehydrogenases: widespread structural and functional diversity within a shared framework

Sequences of 16 NAD and/or NADP-linked aldehyde oxidoreductases are aligned, including representative examples of all aldehyde dehydrogenase forms with wide substrate preferences as well as additional types with distinct specificities for certain metabolic aldehyde intermediates, particularly semialdehydes, yielding pairwise identities from 15 to 83%. Eleven of 23 invariant residues are glycine and three are proline, indicating evolutionary restraint against alteration of peptide chain-bending points. Additionally, another 66 positions show high conservation of residue type, mostly hydrophobic residues. Ten of these occur in predicted beta-strands, suggesting important interior-packing interactions. A single invariant cysteine residue is found, further supporting its catalytic role. A previously identified essential glutamic acid residue is conserved in all but methyl malonyl semialdehyde dehydrogenase, which may relate to formation by that enzyme of a CoA ester as a product rather than a free carboxylate species. Earlier, similarity to a GXGXXG segment expected in the NAD-binding site was noted from alignments with fewer sequences. The same region continues to be indicated, although now only the first glycine residue is strictly conserved and the second (usually threonine) is not present at all, suggesting greater variance in coenzyme-binding interactions.

Organization and characterization of the rat class 3 aldehyde dehydrogenase gene

Expression of class 3 aldehyde dehydrogenase (ALDH-3) is constitutive or inducible, depending on the tissue. ALDH-3 induction occurs both during neoplastic development and after exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). In order to study the regulation of ALDH-3 gene expression, ALDH-3 genomic sequences have been obtained from normal rat genomic DNA. Two overlapping genomic fragments (ALDH-UTR-1 and ALDH-NL2) contain the entire ALDH-3 gene along with considerable 5'- and 3'-flanking sequences. The rat ALDH-3 gene spans approximately 9 kilobases in length and consists of eleven exons; ten coding and one 5'-noncoding. The region 5' to exon one contains several putative transcription factor binding elements which may be important in the TCDD inducibility of this gene. These include a xenobiotic response element (XRE), a drug response element (DRE), LAP and Ap1 binding sites, and one Sp1 site. There are considerable differences in organization between the rat and human class 3 ALDH genes. Primer extension and RNase protection analysis indicate that both basal and TCDD-inducible expression of the ALDH-3 gene utilize the same multiple transcription start sites.

Molecular medicine: a primer for clinicians. Part III: Molecular tools for analyzing human genes

This is the third paper in our series on how today's practicing clinician is affected by the concepts of molecular medicine. Described are the major tools of molecular biologist, previously used primarily in basic research, that are finding widespread application in the day-to-day practice of medicine. Discussed are Southern and Northern analyses, restriction fragment length polymorphisms, the polymerase chain reaction and in situ hybridization as applied to clinical problems.

Molecular medicine: a primer for clinicians. Part I. Essential concepts of human gene expression

Molecular medicine refers to the application of the tools of modern molecular biology to the practice of medicine. The impact of molecular medicine will be increasingly felt by the practicing clinician as increased understanding of disease etiology, significantly improved diagnostic methods and patient care techniques designed to affect a cure rather than treat symptoms. This first paper in an on-going series provides a basic review of human gene expression as a framework for understanding how molecular medicine is irreversibly altering how clinicians will practice medicine. Subsequent papers will detail the application of molecular biology's tools to the practice of medicine.