A systems view of type 2 diabetes-associated metabolic perturbations in saliva, blood and urine at different timescales of glycaemic control

AIMS/HYPOTHESIS

Metabolomics has opened new avenues for studying metabolic alterations in type 2 diabetes. While many urine and blood metabolites have been associated individually with diabetes, a complete systems view analysis of metabolic dysregulations across multiple biofluids and over varying timescales of glycaemic control is still lacking.

METHODS

Here we report a broad metabolomics study in a clinical setting, covering 2,178 metabolite measures in saliva, blood plasma and urine from 188 individuals with diabetes and 181 controls of Arab and Asian descent. Using multivariate linear regression we identified metabolites associated with diabetes and markers of acute, short-term and long-term glycaemic control.

RESULTS

Ninety-four metabolite associations with diabetes were identified at a Bonferroni level of significance (p < 2.3 × 10(-5)), 16 of which have never been reported. Sixty-five of these diabetes-associated metabolites were associated with at least one marker of glycaemic control in the diabetes group. Using Gaussian graphical modelling, we constructed a metabolic network that links diabetes-associated metabolites from three biofluids across three different timescales of glycaemic control.

CONCLUSIONS/INTERPRETATION

Our study reveals a complex network of biochemical dysregulation involving metabolites from different pathways of diabetes pathology, and provides a reference framework for future diabetes studies with metabolic endpoints.

1,5-Anhydroglucitol in saliva is a noninvasive marker of short-term glycemic control

CONTEXT

In most ethnicities at least a quarter of all cases with diabetes is assumed to be undiagnosed. Screening for diabetes using saliva has been suggested as an effective approach to identify affected individuals.

OBJECTIVE

The objective of the study was to identify a noninvasive metabolic marker of type 2 diabetes in saliva.

DESIGN AND SETTING

In a case-control study of type 2 diabetes, we used a clinical metabolomics discovery study to screen for diabetes-relevant metabolic readouts in saliva, using blood and urine as a reference. With a combination of three metabolomics platforms based on nontargeted mass spectrometry, we examined 2178 metabolites in saliva, blood plasma, and urine samples from 188 subjects with type 2 diabetes and 181 controls of Arab and Asian ethnicities.

RESULTS

We found a strong association of type 2 diabetes with 1,5-anhydroglucitol (1,5-AG) in saliva (P = 3.6 × 10(-13)). Levels of 1,5-AG in saliva highly correlated with 1,5-AG levels in blood and inversely correlated with blood glucose and glycosylated hemoglobin levels. These findings were robust across three different non-Caucasian ethnicities (Arabs, South Asians, and Filipinos), irrespective of body mass index, age, and gender.

CONCLUSIONS

Clinical studies have already established 1,5-AG in blood as a reliable marker of short-term glycemic control. Our study suggests that 1,5-AG in saliva can be used in national screening programs for undiagnosed diabetes, which are of particular interest for Middle Eastern countries with young populations and exceptionally high diabetes rates.

Elevated HbA1c levels in individuals not diagnosed with type 2 diabetes in Qatar: a pilot study

BACKGROUND

The prevalence of type 2 diabetes (T2D) in Qatar and the Middle East is one of the highest in the world. It is estimated that about one quarter of the individuals with tbl2D are undiagnosed. Elevated HbA1c levels are an indicator of tbl2D or a pre-diabetic state. In this study we set out to examine which factors, such as anthropometric and socio-demographic risk factors, are associated with elevated HbA1c levels in a population without tbl2D.

METHODS

We examined 191 subjects with no record of tbl2D. Anthropometrics and HbA1c were measured. Socio-demographic (age, gender, ethnicity and educational level) and health information were assessed through questionnaires. Elevated HbA1c levels were defined as >6.0% (>42 mmol/mol). Individual risk factors were examined in relationship to having elevated HbA1c levels using logistic regression.

RESULTS

Thirty-eight (20%) study participants had elevated HbA1c levels. Participants from South Asian and Filipino descent were more likely to present with elevated HbA1c levels than Arab participants (adjusted odds ratios (OR): 13.30 (95% confidence interval (CI): 4.24, 41.79), p < 0.001 for South Asian and 4.54 (95% CI: 1.04, 19.83), p = 0.04 for Filipinos). A body mass index of above 30 kg/m(2) was associated with elevated HbA1c levels (adjusted OR: 2.90 (95% CI: 1.29, 6.51), p = 0.01). Neither gender nor educational level was associated with elevated HbA1c levels.

CONCLUSIONS

Elevated HbA1c levels in individuals not diagnosed with diabetes were most frequently found in the South Asian and Filipino immigrant population. Special attention should therefore be given to the early identification of tbl2D in these subjects.

Ethnic and gender differences in advanced glycation end products measured by skin auto-fluorescence

Background

Advanced glycation end products (AGEs) have been shown to be a predictor of cardiovascular risk in Caucasian subjects. In this study we examine whether the existing reference values are useable for non-Caucasian ethnicities. Furthermore, we assessed whether gender and smoking affect AGEs.

Methods

AGEs were determined by a non-invasive method of skin auto-fluorescence (AF). AF was measured in 200 Arabs, 99 South Asians, 35 Filipinos and 14 subjects of other/mixed ethnicity in the Qatar Metabolomics Study on Diabetes (QMDiab). Using multivariate linear regression analysis and adjusting for age and type 2 diabetes, we assessed whether ethnicity, gender and smoking were associated with AF.

Results

The mean AF was 2.27 arbitrary units (AU) (SD: 0.63). Arabs and Filipinos had a significant higher AF than the South Asian population (0.25 arbitrary units (AU) (95% CI: 0.11‒0.39), p = 0.001 and 0.34 (95% CI: 0.13‒0.55), p = 0.001 respectively). Also, AF was significantly higher in females (0.41 AU (95% CI: 0.29‒0.53), p < 0.001). AF associated with smoking (0.21 AU (95% CI: 0.01‒0.41), p = 0.04) and increased with the number of pack-years smoked (p = 0.02).

Conclusions

This study suggests that the existing reference values should take ethnicity, gender and smoking into account. Larger studies in specific ethnicities are necessary to create ethnic- and gender-specific reference values.

Structural and functional studies on the interstitial collagen genes

An understanding of the molecular mechanisms which control expression of the type I and III collagen genes may provide a rational basis for the design of more effective therapeutic approaches to fibrotic diseases. The structure of the interstitial collagen genes is reviewed and potential sites which could control their expression are examined. One approach to the study of the regulation of these genes consists in DNA-mediated gene transfection experiments and is discussed in this paper.

Michigan versus Kevorkian

Our personal reflections on the Michigan versus Kevorkian trial highlight the following issues: 1) the switch from physician-assisted suicide to euthanasia, 2) the television showing of the death, 3) the dropping of the prosecution of the charge of physician-assisted suicide, 4) Kevorkian serving as his own defense attorney, trying to argue that ALS was a secondary cause of Thomas Youk's death, 5) Kevorkian's attempt to employ a logical syllogism to demonstrate that euthanasia need not be murder, 6) Kevorkian's initial reference to the civil rights tradition but sudden change to the medical analogy of Nazi medicine: a final solution, 7) the insistence of Kevorkian on "all or nothing" sentencing, 8) the irony of Kevorkian being finally convicted by a prosecutor who was elected on a platform of not prosecuting Kevorkian, 9) Kevorkian hiring a lawyer after the verdict is in, and 10) Kevorkian's threat to starve himself to death if sent to prison.

Revegetation of an abandoned uranium millsite on the Colorado Plateau, Arizona

We attempted to restore native plants on disturbed sites at a former uranium mill on the Colorado Plateau near Tuba City, AZ. Four-wing saltbush [Atriplex canescens (Pursh) Nutt.] was successfully established in compacted caliche soil and in unconsolidated dune soil when transplants were irrigated through the first summer with 20 L/plant/wk. The caliche soil was ripped before planting to improve water-holding capacity. The diploid saltbush variety, angustifolia, had higher survival and growth than the common tetraploid variety, occidentalis, especially on dune soil. The angustifolia variety grew to 0.3 to 0.4 m3 per plant over 3 yr even though irrigation was provided only during the establishment year. By contrast, direct seeding of a variety of native forbs, grasses, and shrubs yielded poor results, despite supplemental irrigation throughout the first summer. In this arid environment (precipitation = 100 to 200 mm/yr), the most effective revegetation strategy is to establish keystone native shrubs, such as four-wing saltbush, using transplants and irrigation during the establishment year, rather than attempting to establish a diverse plant community all at once.

Cross-regulation of C/EBP alpha and PPAR gamma controls the transcriptional pathway of adipogenesis and insulin sensitivity

Mice deficient in C/EBP alpha have defective development of adipose tissue, but the precise role of C/EBP alpha has not been defined. Fibroblasts from C/EBP alpha(-/-) mice undergo adipose differentiation through expression and activation of PPAR gamma, though several clear defects are apparent. C/EBP alpha-deficient adipocytes accumulates less lipid, and they do not induce endogenous PPAR gamma, indicating that cross-regulation between C/EBP alpha and PPAR gamma is important in maintaining the differentiated state. The cells also show a complete absence of insulin-stimulated glucose transport, secondary to reduced gene expression and tyrosine phosphorylation for the insulin receptor and IRS-1. These results define multiple roles for C/EBP alpha in adipogenesis and show that cross-regulation between PPAR gamma and C/EBP alpha is a key component of the transcriptional control of this cell lineage.

A conserved region in the first intron of the insulin receptor gene binds nuclear proteins during adipocyte differentiation

The insulin receptor gene is induced 8 to 10-fold during adipocyte differentiation. Plasmids containing the promoter, exon 1 and a portion of the first intron from either the mouse or human gene are able to modulate the expression of an insulin receptor/CAT gene 3 to 7-fold during differentiation. We have shown that several nuclear proteins from both preadipocyte and adipocyte nuclear extracts bind to two discrete sites within a 278-bp region in the 5' end of the first intron. Sequence comparison between the first intron of the human gene and the mouse gene shows two regions of sequence identity which correspond to the protein binding regions detected by DNase footprinting. One of these sites binds proteins that are enriched in adipocyte nuclear extracts and can be competed by adipose regulatory element, ARE6.

A case-comparison of intermittent exotropia and quality of life measurements

A Vision Quality of Life Questionnaire that combines the SF-20 and a Vision Quality Scale developed by the authors was pilot tested in a case-comparison of extreme groups, patients with intermittent exotropia (IXT) and those with no vision problems (Non-IXT), at the University of Houston (UH) Optometry Clinic. The purposes of the study were to measure the internal consistency reliability and examine the validity-related evidence of vision function associated with the instrument. The pilot study involved mailing the instrument to 52 patients in each group (IXT and Non-IXT patients). IXT patients were then frequency-matched by age and separately by sex, to control for confounding variables, to Non-IXT group patients. The Cronbach's Alpha internal consistency reliability of both scales was acceptable at > 0.70 for both the IXT and Non-IXT groups. The Wilcoxon signed ranks test was used to determine validity-related evidence. The differences between groups on the SF-20 (p = 0.0276) and Vision Function Scale (VFS) (p = 0.0385) confirm that the scales discriminate between IXT and Non-IXT populations. Two conclusions can be drawn from the pretesting and pilot testing of the SF-20 and the VFS: (1) both have acceptable internal consistency reliability scores, and (2) both show validity-related evidence that they can discriminate vision function between IXT and Non-IXT patient populations.

Proximal enhancer of the human insulin receptor gene binds the transcription factor Sp1

The insulin receptor is a growth regulator present on the surface of most cells that transmits a mitogenic signal in response to insulin. Thus, the gene for the insulin receptor is constitutively expressed at low levels in all cells. We characterize a constitutive enhancer element that is present in the proximal promoter of the human insulin receptor gene. We have localized the enhancer to a 26-base-pair (26-bp) sequence from -528 to -503. When this sequence is inserted into the proximal promoter, a three- to fourfold increase in promoter activity is observed, and when two copies are inserted, a five- to sixfold increase is seen. Electrophoretic mobility shift analysis demonstrates that nuclear factors binding to this sequence are found in many different cell types. At least two proteins with different specificities bind within this 26-bp sequence. The identity of the predominant binding protein is Sp1, because an oligonucleotide composed of an Sp1 consensus binding sequence can compete for several of the DNA-protein complexes. In addition, we demonstrate that purified Sp1 can bind to the 26-bp oligonucleotide and that this complex comigrates with a DNA-protein complex formed with a HeLa nuclear extract. Finally, an antibody to human Sp1 protein is able to bind to the enhancer DNA/HeLa protein complex and supershift this complex. These findings suggest that this sequence corresponds to a general element that may contribute to the ubiquitous expression of the human insulin receptor gene.

Transcriptional regulation of the insulin receptor gene promoter

The insulin receptor is a highly regulated promoter. A schematic of several of the elements so far identified is shown in Figure 4. The gene has a basic "housekeeping" promoter which controls low level expression in all cells. This promoter seems to be regulated by the transcription factor, Sp1 at several locations upstream. There are in addition several potential Sp1 binding sites in the first intron. Specific enhancers are present to allow increased expression in certain cell types or in response to hormones. Several potential enhancers have been identified including a potential GRE binding site, muscle specific binding protein, and adipocyte binding protein. Clearly additional elements need to be identified in order to elucidate the complexed interactions which are required for appropriate regulation of the insulin receptor.

Structural and functional analysis of the insulin receptor promoter

The insulin receptor plays a critical role in the maintenance of glucose homeostasis. Regulation of this key function must be under stringent controls. In order to study the regulation of insulin receptor gene expression, we have cloned, sequenced and characterized its promoter. The first exon of the insulin receptor gene is embedded in an unusual segment of DNA composed of Alu repeats. The promoter has the characteristics typical of a housekeeping gene. It is GC-rich and has multiple start sites of transcription. A 574 base pair fragment immediately upstream of the translation initiation site contains promoter activity when transfected into eukaryotic cell lines. Deletion analysis was performed to study promoter function. These studies showed that only 150 base pairs of promoter sequence were necessary for promoter function. This region contains three potential binding sites for the transcription factor, Sp1 and a TC box sequence. Furthermore, the fragment functions equally well in either orientation. We have defined an element in this region with enhancer function for both its homologous and a heterologous promoter. In addition, this region seems to contribute some degree of tissue specificity to insulin receptor gene expression.

Mutations in insulin-receptor gene in insulin-resistant patients

Defects in insulin-receptor function have been associated with insulin-resistant states such as obesity and non-insulin-dependent diabetes mellitus (NIDDM). Several types of mutations in the insulin-receptor gene have been identified in patients with genetic syndromes of extreme insulin resistance. In some patients, insulin resistance results from a decrease in the number of insulin receptors on the cell surface. In one patient with leprechaunism (leprechaun/Minn-1), there is greater than 90% decrease in the levels of insulin-receptor mRNA. This patient is a compound heterozygote for two mutations in the insulin-receptor gene, both of which act in a cis-dominant fashion to decrease levels of mRNA transcribed from that allele. In one allele, there is a nonsense mutation at codon 897. All 22 exons of the other allele have a normal sequence, so that the mutation in this allele appears to map outside the coding sequence of the gene. Impaired insertion in the plasma membrane also causes insulin resistance. In two sisters (patients A-5 and A-8) with type A extreme insulin resistance, there is an 80-90% decrease in the number of insulin receptors expressed on the surface of their cells. Both sisters, whose parents are first cousins, are homozygous for a point mutation in which valine is substituted for phenylalanine at position 382 in the alpha-subunit of the insulin receptor. This mutation retards the posttranslational processing of the receptor and impairs the transport of receptors to the cell surface. Another patient with leprechaunism (leprechaun/Ark-1) is a compound heterozygote with two different mutant alleles of the insulin-receptor gene. In the allele derived from the father, there is a nonsense mutation at codon 672 that truncates the insulin receptor by deleting the COOH-terminal of the alpha-subunit and the entire beta-subunit. This truncated receptor, lacking a transmembrane domain, appears not to be expressed at the plasma membrane. In leprechaun/Ark-1, there is a missense mutation in the allele of the insulin-receptor gene derived from the mother. This point mutation results in substitution of glutamic acid for lysine at position 460 in the COOH-terminal half of the alpha-subunit. This mutation increases receptor affinity and impairs the ability of acid pH to dissociate insulin from the receptor within the endosome. There is a defect in recycling the receptor back to the plasma membrane associated with this defect. This results in an accelerated rate of receptor degradation and a consequent decrease in the number of receptors on the cell surface in vivo.(ABSTRACT TRUNCATED AT 400 WORDS)

A mutation in the insulin receptor gene that impairs transport of the receptor to the plasma membrane and causes insulin-resistant diabetes

Insulin binds to a receptor on the cell surface, thereby triggering a biological response within the target cell. Mutations in the insulin receptor gene can render the cell resistant to the biological action of insulin. We have studied a family in which two sisters have a genetic form of insulin-resistant diabetes mellitus. The technique of homozygosity mapping has been used to demonstrate that the mutation causing diabetes in this consanguineous family is genetically linked to the insulin receptor gene. The two insulin-resistant sisters are homozygous for a mutation encoding substitution of valine for phenylalanine at position 382 in the alpha-subunit of the insulin receptor. Transfection of mutant insulin receptor cDNA into NIH3T3 cells demonstrated that the Val382 mutation impaired post-translational processing and retarded transport of the insulin receptor to the plasma membrane. Thus, the mutation causes insulin resistance by decreasing the number of insulin receptors on the surface of the patients' cells.

A new EcoRI polymorphism for the insulin receptor gene

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Hormonal regulation of insulin receptor gene expression. Hydrocortisone and insulin act by different mechanisms

Incubation of cultured human (IM-9) lymphocytes with glucocorticoids increases the number of insulin receptors on the cell surface. Recently it has been shown that this results from a 3-fold increase in the rate of proreceptor synthesis. In the case of homologous insulin receptor down-regulation, a moderate rise in proreceptor biosynthesis has also been demonstrated. To further delineate the mechanisms of insulin receptor regulation, we have measured insulin receptor mRNA levels in hydrocortisone-treated and insulin-treated IM-9 lymphocytes. An increase in insulin receptor mRNA could be detected after 2 h of incubation with hydrocortisone and a plateau was reached by 4-6 h. The response was dose-dependent, being detectable with 50 nM hydrocortisone and reaching a maximal 3.7-fold increase at 200 nM. Actinomycin D completely suppressed the effect, whereas cycloheximide inhibited the effect by no more than 50%. These findings were extended by performing in vitro nuclear transcription assays which revealed that the 3-4-fold increase in insulin receptor mRNA could be attributed to increases in transcription. In contrast, homologous down-regulation was not associated with any change in total insulin receptor mRNA levels. The present study demonstrates that hydrocortisone, but not insulin, stimulates insulin receptor biosynthesis by increasing the rate of transcription and that de novo protein synthesis is probably required for a maximal effect.

Indistinguishable patterns of protooncogene expression in two distinct but closely related tumors: Ewing's sarcoma and neuroepithelioma

Genetic characterization of human tumors promises new insights of biological importance and clinical relevance. We have found that two solid tumors, peripheral neuroepithelioma and Ewing's sarcoma of bone, which share a common cytogenetic rearrangement, are characterized by an indistinguishable and highly reproducible pattern of protooncogene expression. c-myc, N-myc, c-myb, and c-mil/raf-1 are all expressed at similar levels in these tumors. c-fes and c-sis expression was not detected in any specimens of either tumor. In contrast, the protooncogene c-ets-1, located near the breakpoint of the chromosomal translocation in these tumors, is variable in its expression. We also detected high levels of choline acetyltransferase in these tumors, which suggests a common neural origin. Since it is likely that the clinical behavior and therapeutic responsiveness of tumors relate closely to their biological and genetic features, the pattern of protooncogene expression of individual tumors may provide a novel basis for their characterization.

Vasoactive intestinal polypeptide and the innervation of the human lacrimal gland

Vasoactive intestinal polypeptide (VIP) is a biologically active neuropeptide found in both the peripheral and the central nervous systems. Previous studies have shown that VIP-like immunoreactive nerves are present in the uveal tissues of the human eye. The distribution of VIP-like immunoreactivity of the human lacrimal gland and sphenopalatine ganglion was studied. A lacy network of VIP-like immunoreactive nerve fibers was found in the lacrimal gland and was predominantly located along the basilar surface of the acinar epithelium and in the interstitial connective tissue of the gland. This pattern of innervation was nearly identical to the distribution of cholinesterase-positive fibers in human lacrimal glands. The VIP-like immunoreactive cell bodies were found throughout the sphenopalatine ganglion obtained at autopsy. The distribution of VIP-like immunoreactive nerves in the human lacrimal gland and sphenopalatine ganglion was generally similar to that described in mammalian and avian systems, although some differences were noted. Vasoactive intestinal polypeptide may represent an important cotransmitter or neuromodulator for the facial parasympathetic nerves that supply the eye and the lacrimal gland.

Two mutant alleles of the insulin receptor gene in a patient with extreme insulin resistance

Insulin receptor complementary DNA has been cloned from an insulin-resistant patient with leprechaunism whose receptors exhibited multiple abnormalities in insulin binding. The patient is a compound heterozygote, having inherited two different mutant alleles of the insulin receptor gene. One allele contains a missense mutation encoding the substitution of glutamic acid for lysine at position 460 in the alpha subunit of the receptor. The second allele has a nonsense mutation causing premature chain termination after amino acid 671 in the alpha subunit, thereby deleting both the transmembrane and tyrosine kinase domains of the receptor. Interestingly, the father is heterozygous for this nonsense mutation and exhibits a moderate degree of insulin resistance. This raises the possibility that mutations in the insulin receptor gene may account for the insulin resistance in some patients with non-insulin-dependent diabetes mellitus.

Differential protooncogene expression characterizes histopathologically indistinguishable tumors of the peripheral nervous system

We have found highly predictable patterns of protooncogene expression in cell lines and tumor tissue of neuroblastoma (NB), a tumor of the peripheral nervous system (PNS). These patterns make it possible to recognize two different genetically definable subgroups among histopathologically indistinguishable tumors. Additionally, we have identified a difference in neurotransmitter biosynthetic enzyme activity in these two subgroups of NB. The patterns of protooncogene expression and neurotransmitter biosynthetic enzymes suggests that these tumors arise in different cells of the PNS.

Comparison of constitutional and tumor-associated 11;22 translocations: nonidentical breakpoints on chromosomes 11 and 22

Recurring, site-specific chromosomal rearrangements are associated with several human syndromes and malignant disorders. Such nonrandom translocations involving chromosome 22 in band q11 are numerous and found to be associated with a diversity of neoplasms as well as constitutional disorders. Chromosome 11 in bands q23-q24 is similarly involved in several types of tumors as well as in a recurring constitutional reciprocal translocation with chromosome 22. Here we report the use of chromosomal in situ hybridization to compare the translocation breakpoints in the cytologically indistinguishable constitutional t(11;22) and the tumor-related t(11;22) associated with Ewing sarcoma and peripheral neuroepithelioma. We have shown that the breakpoints can be distinguished from each other with respect to the locus encoding the constant region of the Ig lambda light chain (C lambda) at 22q11 and the ETS1 locus at 11q23----q24; ETS1 has been called hu-ets-1 or human c-ets-1. The tumor-associated chromosome 11 breakpoint is also different from those of leukemias with t(9;11) and t(4;11) translocations. Southern-blot analysis showed no rearrangement of ETS1 in these disorders in the region detected by our probe. ETS1 has also been mapped more precisely to 11q23.3----q24 by in situ hybridization to cells from an individual with an 11q23.3----qter deletion.

Translocation breakpoint mapping: molecular and cytogenetic studies of chromosome 22

A number of clinically significant human diseases are associated with rearrangements of chromosome #22. These include the t(9;22) of chronic myelogenous leukemia (CML), the t(8;22) of Burkitt's lymphoma (BL), the t(11;22)(q23;q11) constitutional rearrangement and the t(11;22) of Ewing's sarcoma (ES) and neuroepithelioma (NE). All of these translocations have breakpoints in 22q11. Using a molecular cytogenetic approach and various cloned portions of the lambda light chain gene as probe, we have assigned a linear order within 22q11 to these breakpoints. Using chromosomal in situ hybridization we have determined that the 22q11 breakpoint in BL2, a t(8;22) Burkitt's lymphoma is proximal to the breakpoint of the t(9;22) of CML. We have demonstrated that the 22q11 breakpoint of PA682, another t(8;22) BL cell line, interrupts the lambda light chain locus. Using a combination of variable and constant region probes and PA682 cells, we have shown that the lambda light chain locus is oriented such that V lambda is proximal to C lambda in 22q11. Our results for the constitutional t(11;22) indicate that the 22q11 breakpoint is distal to that of BL, proximal both to that of CML and ES and, in addition, it interrupts the C lambda gene cluster. Our studies of the 22q11 breakpoint of the t(11;22) of ES and NE suggest that they are the most distal of the breakpoints we studied on chromosome #22.

A sequence conserved in both the chicken and mouse alpha 2(I) collagen promoter contains sites sensitive to S1 nuclease

We have examined the S1 nuclease sensitivity in the promoter of both the chicken and mouse alpha 2(I) collagen genes. When these DNAs are introduced into supercoiled plasmids and digested with S1 nuclease, a discrete region containing one or more cleavages is found in each promoter. These S1 cleavage sites were mapped by the distance of the S1 site from known restriction enzyme cleavage sites. In the chicken gene, the S1-sensitive segment is located 180 to 200 base pairs preceding the start site of transcription, whereas in the mouse promoter it is between -145 to -165 base pairs. This site in the chicken promoter maps to the segment that has previously been shown to be S1 and DNase I hypersensitive in chromatin. Although these S1 sites are found at different distances from the start site of transcription in the two promoters, the sequences at these sites are strongly conserved between the two species. Each sequence consists of an identical tandem repeat containing a short palindrome within each repeat. Since the DNA sequence does not exhibit the features that would favor either a left-handed Z-DNA configuration or a cruciform structure, an alternative model is discussed that could account for the S1 sensitivity of these sequences. The conservation of these sequences and their S1 sensitivity suggests they play a role in the activation or regulation of the alpha 2(I) collagen gene promoters.

DNase I sensitivity of the alpha 2(I) collagen gene: correlation with its expression but not with its methylation pattern

The chromatin structure of the chick alpha 2(I) collagen gene was probed with DNase I. Because our previous work strongly suggested that the 5' end of this gene is not methylated whereas the rest of the gene is methylated whether or not the gene is expressed, we compared the relative DNase I sensitivity of the methylated and unmethylated segments. Both regions demonstrate similar relative DNase I sensitivities within a given tissue. In chromatin of chick embryo fibroblasts, we find a DNase I hypersensitive site which maps between 100 and 300 bp preceding the start of transcription. This site is not found in brain chromatin but is present in chick embryo fibroblasts transformed by Rous Sarcoma virus although the rate of transcription of the alpha 2(I) collagen gene is greatly reduced in these cells. Hence, the mechanism responsible for the large decrease in alpha 2(I) collagen gene expression in RSV transformed cells is different from the mechanism that is responsible for the presence of a DNase I hypersensitive site in the promoter. Furthermore, changes in the DNase I sensitivity of the chromatin of the alpha 2(I) collagen promoter occur without changes in the methylation pattern of the gene.

Regulation of the expression of genes encoding types I, II, and III collagen during chick embryonic development

During the embryonic development of the chicken, stimulation of production of collagen-enriched tissue such as bone matrix, cartilage matrix, and skin dermis occurs between day 7 and day 15. We have examined the levels of the RNAs encoding the interstitial collagens (types I, II, and III) to determine if this developmental progress is associated with increased accumulation of collagen RNA. Using cell-free translation and DNA:RNA hybridization techniques, we have detected a coordinate enhancement of approximately 10-fold in the steady state levels of whole embryo RNAs encoding the alpha 1(I), alpha 2(I), alpha 1(II), and alpha 1(III) collagens between 5 and 10 days of chick embryonic development. The developmental pattern of expression of these collagen genes in whole embryos is in marked contrast to that of two noncollagenous proteins, cellular fibronectin and beta-actin, whose RNA levels were not found to change dramatically during early chicken development. In addition, we have observed that at least 3 of the 4 collagen genes examined were expressed at low levels beginning between 1-2 days. Both 5'- and 3'-specific alpha 2(I) collagen gene DNA probes hybridized to early stage and late stage chick embryo RNAs of identical sizes. DNase I-hypersensitive sites have been detected near the 5' end of the alpha 2(I) collagen gene in chromatin isolated from both 2-day and 5-day embryos, representing developmental time points well before and at the threshold of the onset of enhanced collagen RNA synthesis, respectively. These results suggest that the same gene is expressed in early and late chick embryos to yield alpha 2(I) collagen RNAs of similar structure.

Unusual methylation pattern of the alpha 2 (l) collagen gene

We studied the methylation pattern of the alpha 2 (type 1) collagen gene in DNA from five cell types with varying rates of type I collagen synthesis: chick embryo fibroblast (CEF), CEF transformed by Rous sarcoma virus, erythrocyte, brain and sperm. The methylation-sensitive restriction enzymes, Msp I, Hpa II, Ava I and Sma I were used to detect methylation in three regions of the alpha 2 (type I) collagen gene: a 5.7 kb region, which includes the start site of transcription and the first two exons of the collagen gene; a 5.2 kb region containing exons in the middle of the gene; and a 3.5 kb region containing exons in the 3' portion of the gene. The DNA around the start site of transcription is not methylated whether or not the cells synthesize collagen. In contrast, the DNA from the central and 3' region of the gene is methylated to about the same extent whether or not the cells make collagen. Our data indicate that a gene that is methylated can be actively transcribed and that the level of expression of the alpha 2 (type I) collagen gene seems to be independent of methylation.

A simple method for the preparation of antibodies to the mitochondrial biotin-dependent carboxylases

Heterologous antiserum to the 3 biotin-dependent carboxylases was prepared by selective removal of these enzymes from human liver on an avidin-sepharose column. A carboxylase-avidin-sepharose matrix was used as an antigen to produce anti-carboxylase antibodies. The resultant antisera can be used to purify the specific carboxylases, to prepare monoclonal antibodies to these enzymes or to study inherited carboxylase deficiencies and biotin-dependent intermediary metabolism.

Biochemical characterization of propionyl CoA carboxylase deficiency: heterogeneity within a single genetic complementation group

Liver tissues and fibroblasts from patients with propionic acidemia assigned to the pcc BC genetic complementation group have previously been shown to contain normal or near-normal quantities of structurally altered propionyl CoA carboxylases (PCC). Biochemical comparisons of PCCs from extracts of three livers and one placenta belonging to the pcc BC complementation group revealed that the Km values for the enzyme's major substrates, propionyl CoA, bicarbonate, and ATP, and its monovalent activator, potassium, were similar to those of normal PCC. PCC in extracts of one of the livers, however, had an altered isoelectric point (pI = 5.4) compared to that of PCC from normal and other PCC-deficient tissues (pK = 4.6-4.7). Thermostability in the presence of sucrose or ATP differed among several of the mutant PCCs, including the PCC with an altered pI, and from that of normal PCC. To confirm these results and to determine whether valid inferences may be derived from comparisons of mutant and normal PCC in crude extracts, PCC was purified from normal liver and from one of the PCC-deficient livers. The biochemical parameters of the purified carboxylases were similar to those observed in liver extracts. These studies furthermore confirmed that, whether purified or in extracts, PCC from the pcc BC group reflects structural mutations. Nevertheless, the abnormal enzyme structure appears to have no corresponding effect on the clinical features of the disorder in various affected individuals. Moreover, there is biochemical heterogeneity within the pcc BC complementation group that probably represents different interallelic gene mutations.

Magnesium and magnesium adenosine triphosphate activation of human propionyl CoA carboxylase and beta-methylcrotonyl CoA carboxylase

Free magnesium and MgATP2- are required for activation of the mitochondrial enzymes pyruvate carboxylase, propionyl CoA carboxylase and beta-methylcrotonyl CoA carboxylase. Previous studies have demonstrated that free Mg2+ interacts with either a Mg2+- binding site or one of the two MgATP2- sites that are required for the allosteric activation of pyruvate carboxylase. We have shown that similar Mg2+ and MgATP2- interactions occur to activate propionyl CoA carboxylase and beta-methylcrotonyl CoA carboxylase. Thus, Mg2+ and MgATP2- activation, because it is common to structurally similar carboxylases, may constitute a general mode of carboxylase activation.

Immunological studies of propionyl CoA carboxylase in livers and fibroblasts of patients with propionic acidemia

Antiserum prepared against homogeneous pig heart propionyl CoA carboxylase cross-reacted with human propionyl CoA carboxylase, and was used to demonstrate the presence of immunological cross-reacting material in extracts from the livers of three patients and from fibroblasts of four patients with propionic acidemia representing three major propionyl CoA carboxylase-deficient genetic complementation groups, pcc A, pcc C and bio. Since the quantity of cross-reacting material in the propionyl CoA carboxylase-deficient livers and enzyme-deficient fibroblast cell lines was comparable to that in normal tissues while showing less than five percent of the normal enzyme activity, these patients must synthesize normal or near-normal quantities of an enzymatically inactive propionyl CoA carboxylase protein. In addition, no appreciable change in the amount of cross-reacting material was found in the biotin-responsive bio fibroblasts after incubation with supplemental biotin despite a sixteen-fold increase in enzyme activity suggesting that the defect in the bio mutant involves the activation rather than the synthesis of a pre-existing normal apoenzyme.

Step conductance increases in bilayer membranes induced by antibody-antigen-complement action

A sharp rise in the electrical conductance of lipid bilayer membranes was observed following the addition of antigen (bovine serum), antibody (rabbit anti-bovine serum), and complement to the neighboring aqueous phases. At low concentrations, step increases in the conductivity occurred which are consistent with the appearance of about 2.2 nm holes in the membrane. Probably attack or lysis of the lipid bilayer by complement is responsible.