Physical mapping of distinct 7q22 deletions in uterine leiomyoma and analysis of a recently annotated 7q22 candidate gene.

Uterine leiomyoma (UL) is a benign, smooth muscle tumor of the uterus affecting a significant proportion of women of reproductive age. Deletions involving chromosome 7q22 are common in UL and vary in length. Previously reported 7q22 deletion intervals were physically mapped using information from the recently completed human genome sequence. Four distinct deletion intervals, which included a microdeletion reported by our laboratory, were identified. This microdeletion contains two known genes, ORC5L and LHFPL3. The single deleted marker in the microdeletion was mapped within the LHFPL3 locus. The ORC5L gene has been studied in UL. Conversely, LHFPL3 has been annotated only recently, and has therefore not been studied in UL. The predicted LHFPL3 protein sequence contained a polyalanine domain, and a signature sequence for the PMP22 Claudin protein family. Members of this family are transmembrane proteins with roles in differentiation, proliferation, and extracellular matrix formation, and have been implicated in other tumors. Differences in LHFPL3 expression were observed in both human and Eker rat UL. Our results provide evidence for four distinct 7q22 deletion intervals, each with multiple candidate genes, including the recently identified LHFPL3 gene.

An improved assay for genotyping the common Alu insertion in the tissue-type plasminogen activation gene PLAT.

An improved assay for genotyping the common Alu insertion in the tissue-type plasminogen activator (PLAT) locus is described in this report. The assay is a valuable asset to clinical researchers interested in exploring disease associations with this allele. The automation and improved accuracy will facilitate future population-based studies, as well as clinical screening.

PCR-RFLP genotyping assay for the Bcl I polymorphism of the beta-fibrinogen gene.

Polymorphisms of the beta-fibrinogen gene have been shown to affect plasma fibrinogen levels and risk of coronary artery disease (CAD). We were interested in developing an automated, PCR-based genotyping assay for the purpose of exploring relationships between CAD and CAD-associated aortic stiffness and the Bcl I allele of the beta-fibrinogen gene. We have developed a rapid PCR-RFLP assay for the Bcl I polymorphism of the beta-fibrinogen gene. We carried out direct PCR of genomic DNA to facilitate sequencing of the flanking region of the beta-fibrinogen gene. Using this new sequence information, primers were designed which border the site of the Bcl I polymorphism. One of the primers was labeled with a fluorophore to facilitate detection of the fragments. DNA fragment analysis was carried out using an automated capillary electrophoresis instrument (ABI310). We have developed an improved PCR-RFLP high-sample-throughput assay for the semiautomated detection of the Bcl I polymorphism of the beta-fibrinogen gene. This assay will support screening of large sample sizes required for population studies.

Allelic loss analysis by capillary electrophoresis: an accurate, automated method for detection of deletions in solid tumors.

In this report, we describe a fast and accurate capillary electrophoresis, PCR-based method for detecting loss of allelic heterozygosity in solid tumor samples. This automated method requires small sample sizes, and data can be obtained in less than 15 min. The method is particularly powerful for uncovering deletions in tumor sample preparations containing significant normal tissue contamination.

Insulin increases leptin mRNA expression in abdominal subcutaneous adipose tissue in humans.

Insulin regulates expression and production of leptin in rodents but whether this is also true in humans remains unclear. To test the effects of acute hyperinsulinemia on expression of leptin mRNA in humans, percutaneous needle biopsies of abdominal subcutaneous adipose tissue were performed at baseline and immediately following a 200-min two-step hyperinsulinemic-euglycemic glucose clamp in 16 Pima Indians (8M/8F). Leptin mRNA was quantified by reverse transcription, PCR amplification and expressed relative to actin mRNA. Leptin mRNA levels were higher in women than men (25.6 +/- 1.7 v 16.9 +/- 2.1 relative units, P = 0.003) at baseline. Baseline levels were directly related to percentage body fat (r = 0.54, P = 0. 03) and fasting plasma glucose concentrations (r = 0.57, P = 0.02) and were negatively correlated to glucose disposal at physiologic insulin concentrations (750 +/- 40 pmol/L) during the clamp (r = -0. 51, P = 0.04). Acute hyperinsulinemia (final insulin concentration 11560 +/- 950 pmol/L) increased leptin mRNA levels in 13 of 16 individuals an average of 13% (21.3 +/- 1.7 to 24.2 +/- 1.2 relative units, P = 0.01). Changes in leptin mRNA were directly related to glucose disposal rates during physiologic hyperinsulinemia (r = 0.54, P < 0.04). These results suggest that the expression of leptin mRNA is regulated by insulin in humans, as it is in rodents.

Automated, PCR-RFLP genotyping of the urokinase gene.

The urokinase-type plasminogen activator (u-PA) has been suggested to play a role in the early initiation and progression of atherosclerosis and coronary artery disease (CAD) (Grenett et aL, 1998). Recently, a common genetic polymorphism in the untranslated region of the u-PA gene was shown to be associated with syptomatic CAD. To study the possible role of this common genetic polymorphism in the u-PA gene, we have developed an automated, PCR-based assay. Automation of the PCR-RFLP genotyping of the BamHI polymorphism of the urokinase gene will support the screening of the large sample sizes required to do the population-based studies necessary to uncover disease susceptibility associations.

Development of a highly accurate, rapid PCR-RFLP genotyping assay for the methylenetetrahydrofolate reductase gene.

The C677T mutation of the methylenetetrahydrofolate (MTHFR) gene is a nutrient-oriented, "eco" genetic mutation that is associated with elevated levels of homocysteine and an increased risk for coronary heart disease. The purpose of this study was to optimize and automate an assay for PCR-restriction fragment length polymorphism (RFLP) genotyping of the MTHFR gene. We developed an automated assay for the PCR-RFLP genotyping of the MTHFR gene. The DNA was amplified with MTHFR-specific PCR primers, and the resulting PCR product was then digested using the restriction enzyme Hinf I. We then analyzed the restriction fragments on the ABIPrism310 Genetic Analyzer, an automated capillary electrophoresis instrument. Reaction conditions were optimized to achieve an approximately equal ratio of the expected 198-bp and 175-bp Hinf I restriction fragments obtained from a DNA sample that was heterozygous for the C677T mutation. We have developed a high-throughput, accurate method to genotype DNA obtained from blood samples or other sources in less than 1 day. Automation of the PCR-RFLP genotyping of the MTHFR gene can be achieved successfully using the capillary electrophoresis-based ABIPrism310 Genetic Analyzer. In conclusion, automation of the PCR-RFLP genotyping of the MTHFR gene will support the screening of large sample sizes, either for routine clinical diagnostic testing or for large population studies.

Insulin-inducible changes in the relative ratio of PTP1B splice variants.

The skeletal muscle activity of protein tyrosine phosphates 1B (PTP1B), a modulator of insulin and IGF-1 signaling, is reduced in obese nondiabetic subjects and in subjects with type 2 diabetes in comparison with leaner, nondiabetic controls. PTP1B mRNA, like many other signaling molecules, including the insulin receptor, is alternatively spliced. Since we have shown that the ratio of the insulin receptor splice variants is modulated by insulin in vitro and is related to insulin levels in vivo, we hypothesized that the relative ratios of the alternatively spliced PTP1B mRNA might also vary in humans in proportion to the degree of hyperinsulinemia. This was tested in 21 nondiabetic Pima Indians, a population at increased risk for obesity and type 2 diabetes. The relative ratio of the PTP1B splice variants was quantified using RT-PCR of total RNA extracted from fractionated monocytes. The ratio of the splice variants was positively correlated with fasting plasma insulin concentration (r = 0.757; P = 0.0001), 2-h plasma insulin concentration following an oral glucose tolerance test (r = 0.614; P = 0.01, n = 16), and percentage of body fat (r = 0.746; P = 0.0001). These data indicate that variability in the ratio of the two splice variants is due, in part, to in vivo levels of chronic hyperinsulinemia. This simple, noninvasive assay is therefore a potential biomarker for chronic hyperinsulinemia, similar to the HbAlc assay in use to monitor glucose management in diabetic patients.

The etiology of obesity: relative contribution of metabolic factors, diet, and physical activity.

Three major factors modulate body weight: metabolic factors, diet, and physical activity, each influenced by genetic traits. Despite recent advances in these areas, the prevalence of obesity in Westernized societies has increased. In contrast to monogenic animal models and rare human genetic syndromes, predisposition to common forms of obesity is probably influenced by numerous susceptibility genes, accounting for variations in energy requirements, fuel utilization, muscle metabolic characteristics, and taste preferences. Although recent increases in obesity prevalence cannot be explained by changes in the gene pool, previously "silent" genetic variants may now play important permissive roles in modern societies. Available data suggest that variations in resting energy expenditure, thermic effect of food, and fuel utilization exist but, by themselves, are unlikely to explain the onset of obesity. Regarding diet, the best available trend survey data indicate that fat and energy intake have fallen, in this and other Westernized countries. Diverging trends of decreasing energy intake and increasing body weight suggest that reduced physical activity may be the most important current factor explaining the rising prevalence of obesity. Subsistence in modern societies requires extreme adaptations in previously useful energy-conserving diet and exercise behaviors. Recognizing the difficulties in sustaining energy-restricted diets in the presence of fast foods and social feasts, the current trend toward increasing body weight is not likely to be reversed solely through recommendations for further reductions in energy intake. In all likelihood, activity levels will have to increase in response to an environment engineered to be more physically demanding.

Molecular analysis of chromosome 7q21.3 in uterine leiomyoma: analysis using markers with linkage to insulin resistance.

Recent sibling-pair linkage analyses have indicated possible linkage of noninsulin dependent diabetes mellitus (NIDDM) with a number of markers on the long arm of chromosome 7. A coincidental and recent discovery is that specific genetic anomalies identified on chromosome 7 in uterine leiomyoma tumor cells in many cases correspond, cytogenetically, to the same region where genetic linkage to insulin resistance has been identified. In the present study, 15 closely spaced microsatellite markers were used to finely map deletion breakpoints and to test for allelic loss of 7q markers in 12 uterine leiomyoma tumor samples with cytogenetically defined deletions. Of the 9 informative tumor samples, three exhibited breakpoints in the same region where genetic linkage to insulin resistance has been identified (between PON and UT901). Because breakpoints in neoplasias often occur within or adjacent to expressed sequences, these breakpoints may provide a molecular tool to aid in the identification of candidate genes for insulin resistance.

Insulin-inducible changes in insulin receptor mRNA splice variants.

Alternative splicing of insulin receptor pre-mRNA has been shown to be regulated in a tissue-specific and developmental manner. We investigated whether the receptor ligand might regulate the relative distribution of alternatively spliced mRNA in insulin-sensitive cells and found that changes in the relative expression of the two alternatively spliced insulin receptor RNA isotypes expressed in hepatocytes are regulated by insulin. In addition, we observed significant differences (p < or = 0.001) in insulin receptor isotype expression in subjects who were hyperinsulinemic and insulin-resistant versus subjects who were insulin-sensitive. These results support a role for insulin in the regulation of the relative expression of alternatively spliced mRNA expressed in insulin-responsive cells and tissues.

Isolation and characterization of dnaJ null mutants of Escherichia coli.

Bacteriophage lambda requires the lambda O and P proteins for its DNA replication. The rest of the replication proteins are provided by the Escherichia coli host. Some of these host proteins, such as DnaK, DnaJ, and GrpE, are heat shock proteins. Certain mutations in the dnaK, dnaJ, or grpE gene block lambda growth at all temperatures and E. coli growth above 43 degrees C. We have isolated bacterial mutants that were shown by Southern analysis to contain a defective, mini-Tn10 transposon inserted into either of two locations and in both orientations within the dnaJ gene. We have shown that these dnaJ-insertion mutants did not grow as well as the wild type at temperatures above 30 degrees C, although they blocked lambda DNA replication at all temperatures. The dnaJ-insertion mutants formed progressively smaller colonies at higher temperatures, up to 42 degrees C, and did not form colonies at 43 degrees C. The accumulation of frequent, uncharacterized suppressor mutations allowed these insertion mutants to grow better at all temperatures and to form colonies at 43 degrees C. None of these suppressor mutations restored the ability of the host to propagate phage lambda. Radioactive labeling of proteins synthesized in vivo followed by immunoprecipitation or immunoblotting with anti-DnaJ antibodies demonstrated that no DnaJ protein could be detected in these mutants. Labeling studies at different temperatures demonstrated that these dnaJ-insertion mutations resulted in altered kinetics of heat shock protein synthesis. An additional eight dnaJ mutant isolates, selected spontaneously on the basis of blocking phage lambda growth at 42 degrees C, were shown not to synthesize DnaJ protein as well. Three of these eight spontaneous mutants had gross DNA alterations in the dnaJ gene. Our data provide evidence that the DnaJ protein is not absolutely essential for E. coli growth at temperatures up to 42 degrees C under standard laboratory conditions but is essential for growth at 43 degrees C. However, the accumulation of extragenic suppressors is necessary for rapid bacterial growth at higher temperatures.

Enzymology of the pre-priming steps in lambda dv DNA replication in vitro.

We have examined some of the early pre-priming steps of bacteriophage lambda dv DNA replication in vitro. Previous experiments have shown that bacteriophage lambda replication requires host RNA polymerase-dependent RNA synthesis near or at the origin of replication (ori lambda) to initiate DNA synthesis. Using a crude Fraction II enzymatic system we have shown that during RNA polymerase action, at least the bacteriophage lambda O and lambda P replication proteins as well as the host dnaB protein must be present to initiate ori lambda-specific DNA replication. The presence of three other host initiation proteins, dnaG primase, dnaJ, and dnaK, is not required during RNA polymerase action. Because of the apparent absence of a requirement for the dnaJ and dnaK pre-priming proteins during the transcriptional activation step, we propose that the early events of lambda dv DNA replication, prior to action by the dnaG primase, can be divided into two recognizable steps: an early step which requires at least RNA polymerase, lambda O, lambda P, and dnaB, and a subsequent step which requires the action of at least the dnaJ and dnaK proteins.

Structural differences in the subfragment 1 and rod portions of myosin isozymes from adult and developing rat skeletal muscles.

During development of fast contracting skeletal muscle in the rat hindleg, embryonic and neonatal forms of the myosin heavy chain are present prior to the accumulation of the adult fast type ( Whalen , R. G., Sell, S. M., Butler-Browne, G.S., Schwartz, K., Bouveret, P., and Pinset -H arstr öm, I. (1981) Nature (Lond.) 292, 805-809). Polypeptide mapping of the heavy chain subunit using partial proteolysis in the presence of sodium dodecyl sulfate has shown differences in the cleavage patterns for these various heavy chains. Using this technique, we have now examined subfragments, which represent functional domains, from several different myosin isozymes. The heavy chains of the S-1 subfragments containing either light chain 1 or light chain 3 are indistinguishable for the neonatal or fast myosin isozymes. We also isolated the S-1 fragments and the alpha-helical COOH-terminal half of the molecule (rod) from rat embryonic, neonatal, and adult fast and slow myosin, as well as myosin from cardiac ventricles. All of these S-1 and rod fragments were different, indicating that the previously reported differences among these different myosin heavy chain isozymes are located in both the S-1 and rod subfragments for all myosins examined. However, the polypeptide maps of neonatal and adult fast S-1 show clear similarities, as do the maps of slow and cardiac S-1. These similarities in the two pairs of polypeptide maps were confirmed by the results of immunoblotting experiments using antibodies to adult fast and to slow myosin.

Myosin from fetal hearts contains the skeletal muscle embryonic light chain.

The contractile proteins of adult skeletal and cardiac muscle tissue are very similar. Some of these proteins are identical in amino acid sequence or differ only slightly. Various structural studies have shown that the heavy and light chains of myosin are also homologous in skeletal and cardiac muscles. In developing skeletal muscles, certain myosin subunits are present which are not found in the corresponding adult muscle. Whether fetal cardiac muscle also contains myosin subunits homologous to these early forms is not known. We now report that ventricular myosin of fetal rats has a light chain polypeptide corresponding to the skeletal muscle embryonic light chain. This result provides further evidence that a form of myosin light chain, not detectable in adult skeletal or ventricular myosin, is characteristic of the early stages of striated muscle development.

Contractile protein isozymes in muscle development: identification of an embryonic form of myosin heavy chain.

The nature of the myosin heavy chain in embryonic muscle tissue, cultured muscle cells, and several adult muscles was investigated. After denaturation with sodium dodecyl sulfate, purified rat myosins were subjected to partial proteolytic cleavage or immunological analysis using microcomplement fixation. Three types of myosin heavy chains could be demonstrated by both approaches. Whereas adult muscles contain fast- or slow-type myosin heavy chains, embryonic tissue and cultured muscle cells harbor a distinct embryonic form. The existence of this distinct form further characterizes the isozymic transitions of contractile proteins during muscle development.