Large genomic rearrangements of both BRCA2 and BRCA1 are a feature of the inherited breast/ovarian cancer phenotype in selected families

INTRODUCTION

A strong family history of breast and/or ovarian cancer can often be explained by small insertions, deletions, or substitutions in BRCA1 or BRCA2 and large genomic rearrangements in BRCA1. However, there is little evidence that genomic rearrangements are a major factor in BRCA2 associated breast cancer and the frequencies of rearrangements in BRCA1 in large clinic based populations are unknown.

OBJECTIVE

To investigate the frequency of large genomic rearrangements in BRCA1 and BRCA2 in a large clinic based population at high risk of developing breast and/or ovarian cancer.

METHODS

Multiplex ligation dependent probe amplification was used to comprehensively screen BRCA1 and/or BRCA2 in 312 index cases.

RESULTS

Three novel deletions detected in BRCA2 were found exclusively in families with at least one case of male breast cancer. Novel rearrangements in BRCA1 were detected mostly in families with both breast and ovarian cancer. Families with these mutations were significantly younger at average age of cancer diagnosis.

CONCLUSION

Screening for large genomic rearrangements in both BRCA1 and BRCA2 is strongly supported by this study, in particular in multiple case breast/ovarian families with a young age of onset (BRCA1) and families containing at least one case of male breast cancer (BRCA2).

A strategy for the determination of enzyme kinetics using electrospray ionization with an ion trap mass spectrometer

A simple and rapid means of enzyme kinetic analysis was achieved using electrospray ionization mass spectrometry and a one-point normalization factor. The model system used, glutathione S-transferase from porcine liver, is a two-substrate enzyme catalyzing the conjugation of glutathione with a variety of compounds containing an electrophilic center. An internal standard that is structurally similar to the product was added to the reaction quench solution, and a single-point normalization factor was used to determine the product concentration without the need of a calibration curve. Kinetic parameters, such as Km, Vmax and Ki (for thyroxine), obtained by electrospray mass spectrometry agreed with those obtained from traditional UV-vis spectroscopy, and competitive vs noncompetitive inhibition reactions could be delineated via mass spectrometry. These results suggest that our method can be applied to enzymatic processes in which spectrophotometric or spectrofluorometric assays are not feasible or when the relevant substrates do not incorporate chromophores or fluorophores. This new method is competitive with traditional UV assays in that it is facile and it involves very little analysis time.

Biosynthesis of sialylated lipooligosaccharides in Haemophilus ducreyi is dependent on exogenous sialic acid and not mannosamine. Incorporation studies using N-acylmannosamine analogues, N-glycolylneuraminic acid, and 13C-labeled N-acetylneuraminic acid

Haemophilus ducreyi is a Gram-negative bacterium that causes chancroid, a sexually transmitted disease. Cell surface lipooligosaccharides (LOS) of H. ducreyi are thought to play important biological roles in host infection. The vast majority of H. ducreyi strains contain high levels of sialic acid (N-acetylneuraminic acid, NeuAc) in their LOS. Here we investigate the biosynthetic origin of H. ducreyi sialosides by metabolic incorporation studies using a panel of N-acylmannosamine and sialic acid analogues. Incorporation of sialosides into LOS was assessed by matrix-assisted laser desorption and electrospray ionization mass spectrometry. A Fourier transform ion cyclotron resonance mass spectrometer provided accurate mass measurements, and a quadrupole time-of-flight instrument was used to obtain characteristic fragment ions and partial carbohydrate sequences. Exogenously supplied N-acetylmannosamine analogues were not converted to LOS-associated sialosides at a detectable level. In contrast, exogenous (13)C-labeled N-acetylneuraminic acid ([(13)C]NeuAc) and N-glycolylneuraminic acid (NeuGc) were efficiently incorporated into LOS in a dose-dependent fashion. Moreover, approximately 1.3 microM total exogenous sialic acid was sufficient to obtain about 50% of the maximum production of sialic acid-containing glycoforms observed under in vitro growth conditions. Together, these data suggest that the expressed levels of sialylated LOS glycoforms observed in H. ducreyi are in large part controlled by the exogenous concentrations of sialic acid and at levels one might expect in vivo. Moreover, these studies show that to properly exploit the sialic acid biosynthetic pathway for metabolic oligosaccharide engineering in H. ducreyi and possibly other prokaryotes that share similar pathways, precursors based on sialic acid and not mannosamine must be used.

Design, formation and properties of tetrahedral M(4)L(4) and M(4)L(6) supramolecular clusters

The rigid tris- and bis(catecholamide) ligands H(6)A, H(4)B and H(4)C form tetrahedral clusters of the type M(4)L(4) and M(4)L(6) through self-assembly reactions with tri- and tetravalent metal ions such as Ga(III), Fe(III), Ti(IV) and Sn(IV). General design principles for the synthesis of such clusters are presented with an emphasis on geometric requirements and kinetic and thermodynamic considerations. The solution and solid-state characterization of these complexes is presented, and their dynamic solution behavior is described. The tris-catecholamide H(6)A forms M(4)L(4) tetrahedra with Ga(III), Ti(IV), and Sn(IV); (Et(3)N)(8)[Ti(4)A(4)] crystallizes in R3(-)c (No. 167), with a = 22.6143(5) A, c = 106.038(2) A. The cluster is a racemic mixture of homoconfigurational tetrahedra (all Delta or all Lambda at the metal centers within a given cluster). Though the synthetic procedure for synthesis of the cluster is markedly metal-dependent, extensive electrospray mass spectrometry investigations show that the M(4)A(4) (M = Ga(III), Ti(IV), and Sn(IV)) clusters are remarkably stable once formed. Two approaches are presented for the formation of M(4)L(6) tetrahedral clusters. Of the bis(catecholamide) ligands, H(4)B forms an M(4)L(6) tetrahedron (M = Ga(III)) based on an "edge-on" design, while H(4)C forms an M(4)L(6) tetrahedron (M = Ga(III), Fe(III)) based on a "face-on" strategy. K(5)[Et(4)N](7)[Fe(4)C(6)] crystallizes in I43(-)d (No. 220) with a = 43.706(8) A. This M(4)L(6) tetrahedral cluster is also a racemic mixture of homoconfigurational tetrahedra and has a cavity large enough to encapsulate a molecule of Et(4)N(+). This host-guest interaction is maintained in solution as revealed by NMR investigations of the Ga(III) complex.

A library approach to the generation of bisubstrate analogue sulfotransferase inhibitors

[reaction: see text]. A library of potential bisubstrate analogue inhibitors (1) targeting sulfotransferase enzymes was generated by the chemoselective ligation of the PAPS mimic 2 with a panel of 447 aldehydes. Preliminary screening has identified compounds that inhibit estrogen sulfotransferase (EST), an enzyme relevant to breast cancer.

Evidence of block and randomly sequenced chondroitin polysaccharides: sequential enzymatic digestion and quantification using ion trap tandem mass spectrometry

A method for determining the sequence type of the disaccharide repeat region of cartilage samples is introduced. The samples are sequentially subjected to selective and nonselective enzymatic digestion, and the isomeric products from each step are quantified using tandem mass spectrometry. The two-step digestion/quantification protocol identifies whether the global makeup of the polymer is "alternating", "random", or "blocked" with respect to the two main components of the cartilage, 4- and 6-sulfated disaccharides. Using this procedure, the sequence type of two biologically isolated chondroitin polysaccharides was identified. The results for chondroitin sulfate A, isolated from bovine trachea, are consistent with the 4- and 6-sulfated disaccharides randomly distributed throughout the repeat region of the polysaccharide. For chondroitin sulfate C, shark cartilage, the 6-sulfated disaccharides are adjacent to each other to a larger extent than one would expect for a randomly distributed polymer, indicating that "blocks" of repeating disaccharides with the same sulfation site are present.

Stabilization and linkage analysis of metal-ligated sialic acid containing oligosaccharides

The dissociation of metal-ligated sialyllactose and sialyl-N-acetyllactosamine was investigated. Metal-ligand derivatization of the carbohydrate samples with the diethylenetriamine ligand and one of four transition metals [Co(II), Ni(II), Cu(II), Zn(II)] suppressed sialic acid loss in the collision-induced dissociation process. Suppression of sialic acid loss allows sialic acid linkage information to be gained through tandem mass spectrometry. Sialic acid stabilization is postulated to occur due to the doubly charged metal ion which allows for deprotonation of the sialic acid moiety. Furthermore, a connection between the metal center and the amount of sialic acid loss was found. These results were rationalized using the Irving-Williams series and a competition between different sites of deprotonation. Analysis of the product ion spectra showed a clear differentiation of sialic acid linkage. Linkage determination is proposed to be effective due to the available conformations allowed by the different linkages. A more flexible linkage will allow more coordination of the sialic acid residue with the metal center, whereas a less flexible linkage will make this interaction unlikely.

Molecular orbital considerations in probing the stereoselective dissociations of cobalt-coordinated hexosamine monosaccharides

The mechanisms for the stereoselective dissociation pathways of isomeric [CoIII(diaminopropane)2(hexosamine-2H)]+ complexes are studied by ion trap and Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS). The exact masses of product ions were measured in order to determine the composition of each loss, and isotopic labeling experiments were used to determine which atoms were lost during dissociation. MS3 studies were used to probe the structures of the product ions from MS2 experiments. Based on the experimental evidence obtained, mechanisms explaining the dissociations are postulated. In deciphering the mechanisms, careful attention was paid to the molecular orbital alignment of the reacting bonds, and based on the molecular orbitals, transition state conformations were postulated. These transition states suggest how the observed stereoselectivity occurs. In each case, the carbohydrate/metal interaction was crucial in the dissociation processes.

Utilization of MS3 spectra for the multicomponent quantification of diastereomeric N-acetylhexosamines

A rapid and accurate means of quantifying mixtures of diastereomeric N-acetylhexosamine monosaccharides using MS3 product ions is introduced. The method involves derivatizing the monosaccharides with [Co(DAP)2Cl2]Cl (where DAP is diaminopropane), and subjecting the derivatized products to collision-induced dissociation (CID) in a quadrupole ion trap mass spectrometer. Each diastereomer provides unique MS3 product ion abundances. The abundances for the pure monosaccharide standards are used in a system of equations in order to quantify mixtures of these diastereomers. Using the system of equations is quite advantageous, as it is the only mass spectrometric method that has been shown to successfully quantify mixtures of more than two isomers. The utility of the method is demonstrated by successfully quantifying various two and three component mixtures of the diastereomeric monosaccharides. Furthermore, the method is used to quantify the recovery of a single diastereomeric monosaccharide from an acidic resin. Although the multicomponent quantification method described herein is used to quantify mixtures of N-acetylhexosamine diastereomers, it could be applied to any group of isomers, provided distinguishing CID spectra are obtained. This is the first known report of utilizing MS3 product ions for quantification of structural isomeric mixtures.

Mass spectrometry and immobilized enzymes for the screening of inhibitor libraries

A technique has been developed to rapidly screen enzyme inhibitor candidates from complex mixtures, such as those created by combinatorial synthesis. Inhibitor libraries are screened by using immobilized enzyme technologies and electrospray ionization ion cyclotron resonance mass spectrometry. The library mixture is first sprayed into the mass spectrometer, and compounds are identified. The library is subsequently incubated with the immobilized enzyme of interest under the correct conditions (buffer, pH, temperature) by using an excess of enzyme to ensure a surplus of sites for ligand binding. The immobilized enzyme/inhibitor mixture is centrifuged, and an aliquot of supernatant is again analyzed by electrospray ionization mass spectrometry. Potential inhibitors are quickly identified by comparison of the spectra before and after incubation with the immobilized enzyme. Non-inhibitors show no change in ion intensity after incubation, whereas weak inhibitors exhibit a visible decrease in ion abundance. Once inhibitor candidates have been identified, the library is reinjected into the mass spectrometer, and tandem mass spectrometry is used to determine the structure of the inhibitor candidates as needed. This method has been successfully demonstrated by identifying inhibitors of the enzymes pepsin and glutathione S-transferase from a 19- and 17-component library, respectively. It is further shown that the immobilized enzyme can be recycled and reused for continuous screening of additional new libraries without adding additional enzyme.

Mass spectral characterization of lipooligosaccharides from Haemophilus influenzae 2019

Lipooligosaccharide (LOS) glycoforms from Haemophilus influenzae 2019 were profiled using the high-resolution and accurate mass capabilities of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. Sequence and linkage for two previously unknown LOS glycoforms were subsequently obtained through MSn analyses on FT-ICR and quadrupole ion trap (qIT) instruments. MSn analysis of negative ion precursors confirmed structural details within the lipid moiety, while CID spectra of sodiated precursor ions provided monosaccharide sequence and linkage for the oligosaccharide portion of the molecule. Results obtained in this study indicate that extensive heterogeneity exists within the oligosaccharide moieties in LOS from H. influenzae 2019. More importantly, the data suggest that additional hexose moieties, which are added onto the LOS, are not simple extensions of one particular core structure but rather that structural isomers with different connectivities are present within the heterogeneous mixture.

Detection and quantification of the sulfated disaccharides in chondroitin sulfate by electrospray tandem mass spectrometry

A new method of identifying and quantifying the disaccharide building blocks of glycosaminoglycans is introduced. The polysaccharides are subjected to an enzymatic digestion that releases the sulfated disaccharides. The disaccharides are then identified using a combination of electrospray ionization mass spectrometry and tandem mass spectrometry. Quantification of the isomeric disaccharides is also achieved by tandem mass spectrometry, using a recently developed methodology which quantifies mixtures of isomers without the use of chromatography or prior separation. Using mass spectrometry to characterize the components of glycosaminoglycans significantly reduces both sample consumption and analysis time of traditional methods.

Combined partial acid hydrolysis and electrospray ionization-mass spectrometry for the structural determination of oligosaccharides

A general oligosaccharide acid hydrolysis method, amenable to electrospray ionization mass spectrometry (ESI-MS), is described that allows for hydrolysis of glycosidic bonds for both hexose- and N-acetylhexosamine-containing oligosaccharides. The partial acid hydrolysis of oligosaccharides is obtained by using an acid-exchange resin as the acid catalyst. A ladder sequence of the glycan is produced in solution that is directly analyzed by ESI tandem mass spectrometry, employing both ion trap and Fourier transform ion cyclotron resonance mass spectrometers, to provide sequence and linkage information. Unlike traditional acid hydrolysis procedures, there is minimal degradation of monosaccharide residues or deacetylation of N-acetylhexosamines by employing this technique. It is further demonstrated that the stereochemistry of the released monosaccharides and the anomeric configuration within disaccharides is determined by direct derivatization of the hydrolysate with Zn(dien)-Cl2 followed by ESI-MS/MS.

STAT: a saccharide topology analysis tool used in combination with tandem mass spectrometry

Sequential stages of mass spectrometry (MSn) have the potential to provide a great deal of structural information in glycan analysis. The saccharide topology analysis tool (STAT) presented here is a Web-based computational program that can quickly extract sequence information from a set of MSn spectra for an oligosaccharide of up to 10 residues. After information such as precursor ion mass, possible monosaccharide moieties, charge carrier, and product ion mass has been input, all possible connectivities are generated and evaluated against the MSn data. The list of possible structures is given a rating based on the likelihood that it is the correct sequence. Examples are given to demonstrate the feasibility of applying STAT to MSn data generated from bacterial lipooligosaccharides and an N-linked glycan. The major advantage of STAT is that the list of possible structures is generated quickly and the rating system pushes the more likely structures to the top of the list. Combining the data generated by STAT with data on the branching patterns of the glycan serves to eliminate all but a handful of structures. These remaining structures could then be used to guide further structural analysis.

Multicomponent quantification of diastereomeric hexosamine monosaccharides using ion trap tandem mass spectrometry

A rapid means of stereochemical differentiation and quantification for the hexosamine monosaccharides was achieved using electrospray ionization quadrupole ion trap mass spectrometry. The hexosamine monosaccharides, glucosamine, galactosamine, and mannosamine, were derivatized with [Co(DAP)2Cl2]Cl, and the complex [Co(DAP)2(HexNH2)]Cl was generated. Subjecting this complex to collision-induced dissociation provided a unique product ion spectrum for each of the diastereomeric monosaccharide complexes, thus differentiating the stereoisomers. Furthermore, the stereoisomers were quantified. This was achieved by using the relative abundances of product ions from pure standards and using these values to determine the ratio of isomeric products in a mixture. The utility of this quantification method was demonstrated by successfully determining the composition of two- and three-component mixtures of the hexosamines.

Differentiation of diastereomeric N-acetylhexosamine monosaccharides using ion trap tandem mass spectrometry

A quadrupole ion trap mass spectrometer equipped with electrospray ionization was used to distinguish three diastereomeric monosaccharides, N-acetylglucosamine, N-acetylgalactosamine, and N-acetylmannosamine. The saccharides were derivatized to form the metal complex [CoIII(DAP)2HexNAc]Cl3 which, when collisionally activated, produced dramatically different product ion spectra. The product ion spectra generated for the three monosaccharide diastereomers were then used to confirm the stereochemistry of N-acetylhexosamines from a hydrolyzed oligosaccharide. Finally, the origin of each product ion was determined through isotopic labeling studies, and mechanisms were proposed which explain each resulting dissociation.

Determining anomericity of the glycosidic bond in Zn(II)-diethylenetriamine-disaccharide complexes using MSn in a quadrupole ion trap

Zinc-diethylenetriamine (Zn-dien) N-glycoside complexes of four 1,4 and four 1,6 linked disaccharides are prepared. Each reaction mixture is ionized by electrospray and the resulting species [Zn(dien)(disaccharide)-H]+ is allowed to undergo collision-induced dissociation in a quadrupole ion trap. An MS3 analysis is used to differentiate alpha versus beta anomericity of the glycosidic bond in the disaccharide moiety. In addition, the MS2 and MS3 spectra can be used together to determine the linkage position of this glycosidic bond.

Evidence for linkage position determination in cobalt coordinated pentasaccharides using ion trap mass spectrometry

A methodology to determine the linkage position of oligosaccharides is presented. In order to illustrate this technique, several oligosaccharides and disaccharides were ionized by electrospray and analyzed in a Paul trap mass spectrometer. Multiple stage tandem mass spectrometry experiments were used to determine linkage and structural information for the following four cobalt coordinated and singly charged ([M + Co-H]+) pentasaccharides: Lacto-N-fucopentaose I, II, III, and V. In order to differentiate between linkage positions, multiple low energy collision induced experiments with mass selected C type ions have been carried out in an ion trap mass spectrometer. Because of the coordination with cobalt, which directs the dissociation pathways, these C type ions undergo specific fragmentation reactions upon low energy collision induced dissociation. These dissociation pathways are unambiguously dependent on their linkage position, thus allowing differentiation between 1-->2, 1-->3, 1-->4, and 1-->6 linkage positions throughout the oligomers. Studies on various linked disaccharides and N-acetyl-disaccharides, which are smaller constituents of the pentasaccharides, were used to verify and confirm the results obtained from the pentasaccharides.

Evidence for linkage position determination in cobalt coordinated pentasaccharides using ion trap mass spectrometry

A methodology to determine the linkage position of oligosaccharides is presented. In order to illustrate this technique, several oligosaccharides and disaccharides were ionized by electrospray and analyzed in a Paul trap mass spectrometer. Multiple stage tandem mass spectrometry experiments were used to determine linkage and structural information for the following four cobalt coordinated and singly charged ([M + Co-H]+) pentasaccharides: Lacto-N-fucopentaose I, II, III, and V. In order to differentiate between linkage positions, multiple low energy collision induced experiments with mass selected C type ions have been carried out in an ion trap mass spectrometer. Because of the coordination with cobalt, which directs the dissociation pathways, these C type ions undergo specific fragmentation reactions upon low energy collision induced dissociation. These dissociation pathways are unambiguously dependent on their linkage position, thus allowing differentiation between 1-->2, 1-->3, 1-->4, and 1-->6 linkage positions throughout the oligomers. Studies on various linked disaccharides and N-acetyl-disaccharides, which are smaller constituents of the pentasaccharides, were used to verify and confirm the results obtained from the pentasaccharides.

Stereochemical differentiation of mannose, glucose, galactose, and talose using zinc(II) diethylenetriamine and ESI-ion trap mass spectrometry

Diastereomeric diethylenetriamine N-glycoside zinc(II) complexes are investigated using electrospray ionization followed by tandem mass spectrometry in a quadrupole ion trap. Dissociation ions specific to stereochemical differences at C2 and C4 in hexose complexes are observed in the MS2 and MS3 spectra, thus allowing unambiguous differentiation of glucose, galactose, mannose, and talose. Labeling studies incorporating 2H and 13C are used to probe the mechanisms of dissociation involved with these diastereomers, and MS2 studies on deoxyglucose complexes are implemented to support proposed sites of deprotonation within the complexes.

Immunohistochemical detection of progesterone receptors in archival breast cancer

The progesterone receptor (PR) is an important marker of response to endocrine agents in breast cancer. Immunohistochemical demonstration of PR in formalin fixed tissue has previously proved difficult, and heat pretreatment is considered necessary to retrieve the antigen. There are few data on the effectiveness of autoclaving in unmasking PR, however, and it is not known whether all PR epitopes are equally unmasked. The objectives of this study were to compare the efficacy of autoclaving and microwaving to retrieve PR antigen in archival breast tumors, to determine whether there is an epitope-dependent variability in the pretreatment required, and to examine different slide types and adhesives to reduce the problem of section loss frequently associated with these procedures. Paraffin embedded sections were cut at 2 or 4 microm, mounted onto various slide types with or without the addition of adhesive, and heat pretreated prior to immunoperoxidase staining. Whereas PR immunoreactivity was clearly demonstrated in tissue after both autoclaving and microwaving, autoclaving produced a significantly stronger staining intensity under the conditions used in this study. The duration of autoclaving required to reveal PR fully differed for different epitopes examined. In the absence of heat pretreatment, PR was not detected. Section retention was improved by the use of adhesives and by cutting tissue at 2 microm. Maximum retention was obtained using positively charged slides coated with Mayer albumen adhesive. We conclude that for maximal tissue preservation autoclave pretreatment is the preferred method of PR antigen retrieval from archival breast tumors, that there is epitope-dependent variability in pretreatment required, and that section loss during this procedure can be minimized by choice of slide type, the use of adhesive, and by cutting sections at 2 microm.

Analysis of loss of heterozygosity and KRAS2 mutations in ovarian neoplasms: clinicopathological correlations

The molecular events that give rise to ovarian epithelial neoplasms are not well understood. In particular, it is not known whether adenocarcinomas arise from benign or low malignant potential (LMP) precursors. We have examined a large series of benign (25) and LMP (31) ovarian tumors for loss of heterozygosity (LOH) at multiple loci on 17 chromosomes. LOH was observed in benign tumors on chromosomes 6 (14%) and 9 (5%) and on the X chromosome (33%) only. LOH on these chromosomes was also detected in a small number of LMP neoplasms, suggesting that these may derive sometimes from benign precursors. In addition, we examined LOH in 93 adenocarcinomas. Analysis of associations between LOH events showed that LOH on chromosomes 5 and 17 (P = 0.0002) and on chromosomes 17 and 18 (P = 0.00007) were associated significantly with each other, which suggests that these may represent cooperative, progressive events. No novel significant associations were identified between LOH events and stage, grade, or histology, which would indicate the existence of genetic heterogeneity in ovarian neoplasms. KRAS2 mutations were detected more often in LMP neoplasms than in malignant tumors (P = 0.004) and were detected more often in Stage I/II malignant tumors than in Stage III/IV malignant tumors (P = 0.033), suggesting that LMP tumors with KRAS2 mutations are unlikely to progress to frank malignancy. Univariate (but not multivariate) survival analysis showed that LOH of chromosomes 11 (P = 0.039) and 17 (P = 0.04) was associated with a significantly worse prognosis. Replication of these novel findings is necessary, and the identification, isolation, and characterization of the critical genes affected by LOH will determine their importance in the pathogenesis of ovarian malignancies.

Allelic loss on chromosome 7q in ovarian adenocarcinomas: two critical regions and a rearrangement of the PLANH1 locus

The presence of a tumour suppressor gene on chromosome 7q is indicated by cytogenetic, loss of heterozygosity (LOH) and chromosome transfer studies. One candidate gene in this region is Plasminogen Activator Inhibitor-1 (PAI-1). The PAI-1 gene product is involved in proteolysis and may therefore influence tumour spread and invasion. We have analysed a series of 139 ovarian epithelial tumours at four loci in the region 7q21-q31 which includes the PAI-1 gene. The highest rates of loss were found in malignant tumours (FIGO stages I-IV) at markers D7S471 (38%, 20/52 informative cases) and D7S522 (34%, 15/44). No loss was seen in benign tumours and only one out of 27 (4%) informative LMP tumours demonstrated LOH. The smallest region of overlap (SRO) lies between D7S471 and PAI-1. We also identified a rearrangement in one tumour in the PAI-1 gene, suggesting that this may be the inactivated gene in this region. In addition LOH at the more distal marker, D7S522, which lies outside the SRO, shows significant association with stage (P=0.0343) and with LOH on chromosome 13 (P=0.0024). This is in contrast to all other markers examined. These data suggest the presence of two critical regions on 7q which may be important in subsets of epithelial ovarian tumours.

Differentiation of stereochemistry of glycosidic bond configuration: Tandem mass spectrometry of diastereomeric cobalt-glucosyl-glucose disaccharide complexes

Configurations of glycosidic linkages (α or β) in a series of 1,3-, 1,4-, and 1,6-glucosyl-glucose disaccharides were differentiated by tandem mass spectrometry. Diastereomeric octahedral complexes, [Co(+3) (acac)2/disaccharide](+), were generated in situ via fast-atom bombardment ionization. Mass-analyzed, ion kinetic energy spectra of the metastable complexes obtained in the absence of collision gas indicated that the major product ion results from the loss of an acetylacetonate ligand, which thus generates the ion [Co(+2)(acac)/disaccharide](+). Kinetic energy release measurements for this dissociation display a consistently greater value for complexes that possess an α-linked disaccharide relative to those that possess β-linked disaccharides, regardless of linkage position.

MDR1 and multidrug resistance-associated protein (MRP) gene expression in epithelial ovarian tumors

Clinical drug resistance poses a major problem in the successful treatment of ovarian cancer. Two genes, MDR1 and MRP, have been found to play a role in the multidrug resistance phenotype of a number of human tumors. Using a sensitive semiquantitative PCR assay we examined 53 primary untreated ovarian tumors for expression of both MDR1 and MRP genes. Approximately one-third of the tumors expressed MDR1 while all the tumors expressed varying levels of the MRP gene.

LC/MS/MS of carbohydrates with postcolumn addition of metal chlorides using a triaxial electrospray probe

A new technique for on-line postcolumn addition (PCA) formation and tandem electrospray mass spectrometry of carbohydrate-metal complexes is presented. A metal chloride solution is added to a carbohydrate sample directly within the ion source of the mass spectrometer. Using a triaxial electrospray probe, this technique can be applied to form carbohydrate-metal complexes on-line, without the need of previously mixing the carbohydrate and metal chloride. Two basic tasks may be accomplished: structural analysis and sensitivity enhancement. The performance of this approach is demonstrated through PCA of LiCl, NaCl, KCl, RbCl, CsCl, and CoCl2, introduced via the triaxial probe after chromatographic separation of two four-component carbohydrate mixtures. Each metal-carbohydrate complex is subsequently analyzed by on-line MS and MS/MS. This technique is used to enhance sensitivity and also, in the case of cobalt coordination, to assist in carbohydrate structural elucidation. On-line LC/MS with PCA of LiCl was achieved with as little as 1.7 pmol of oligosaccharide (average consumed amount, 1.7 pmol with 1 microL of a 10 pmol/microL carbohydrate test mixture injection).

Increased expression of the NME1 gene is associated with metastasis in epithelial ovarian cancer

The genetic events involved in the development of metastases of epithelial ovarian cancer are largely unknown. One gene postulated to play a role in tumour metastasis suppression is NME1 (nm23-H1), and an inverse relationship between NME1 expression and metastatic potential has been observed for some solid tumours. In this study we have investigated the levels of mRNA expression of the 2 isoforms of the NME gene, NME1 and NME2. A maximum of 45 tumours samples from 33 patients were available for Northern blot analysis. We observed variable levels expression of NME1 and NME2 mRNA. The average level of NME1, but not NME2, mRNA expression was statistically higher in metastatic biopsies when compared with primary tumour biopsies. To examine the possible tumour suppressor gene role of NME1 in ovarian tumours, 76 patients were investigated by Southern blot analysis to determine the rate of allelic deletion. Allele loss at 5 other chromosome 17 loci (D17S5, TP53, NF1, D17S74, D17S4) was also evaluated for many of these 76 patients. Allele loss was observed in 22/30 (73%) informative patients at the NME1 locus. We also observed high rates of allele loss at the other loci evaluated. No correlations with clinical stage, histological subtype or patient survival were observed in either mRNA or DNA analyses. We have established that tumour progression in ovarian cancer is accompanied by over-expression of the NME1 gene; however, despite high rates of allele loss at the NME1 locus, the concept that NME1 may be a candidate tumour suppressor gene in ovarian cancer cannot be confirmed by this study.

Chiral recognition in the gas phase: Mass spectrometric studies of diastereomeric cobalt complexes

Results of mass analyzed ion kinetic energy (MIKE) spectra and kinetic energy release (KER) measurements of diastereomeric octahedral cobalt complexes indicate that these diastereomers can be distinguished in the gas phase. Four alkyl tartrate esters were complexed to cobalt trisacetylacetonate (Co(acac)3) in the presence of a chiral auxiliary, RR- and SS-threohydrobenzoin. Different KER values of the product ion generated from [Co(acac)2/D- or L-diisopropyl tartrate](+) reflect differences in the precursor ion structure. The dissociation pathway resulting in this product ion is believed to arise via a hydride transfer from the acetylacetonate ligand to the metal center with subsequent loss of neutral organic species. It has been established that two conditions are necessary for observation of chiral recognition in this system; (1) the cobalt complex must be octahedral and (2) a chemical kinetic resolving agent must be present during formation of the complex.

Mechanism of gas-phase aldose-ketose isomerization: A study using tandem mass spectrometry and theoretical calculations

Fast-atom bombardment tandem mass spectrometry and the semiempirical molecular orbital method were used to investigate the mechanism of gas-phase aldose-ketose isomerization process in lithiated 1,3 linked disaccharide isomers. Both the 1,3 hydrogen shift and hydride transfer mechanisms were investigated. Our experimental and theoretical calculations support the latter. The hydride transfer mechanism in these lithium-coordrnated systems is similar to the xylose isomerase catalyzed aldose-ketose isomerization.

Differentiation of Ca(2+)- and Mg(2+)-coordinated branched trisaccharide isomers: an electrospray ionization and tandem mass spectrometry study

Three isomeric branched trisaccharides coordinated to calcium and magnesium were analyzed by electrospray ionization followed by tandem mass spectrometry. Studies were undertaken to optimize the singly charged metal coordinated precursor prior to MS/MS and MS/MS/MS experiments. The positioning of the glycosidic linkages between reducing and nonreducing rings could be determined in all three isomers, and the linkage of the fucose ring was obvious in two of the three isomers when calcium was used as the coordinating metal. The ionic radius and charge of the metal appear to be very important in obtaining structural information in these isomers.

Amplification of HER-2/neu oncogene in human ovarian cancer

Amplification and/or increased expression of the HER-2/neu oncogene has been reported to occur in ovarian tumors and possibly to correlate with biologic behavior and prognosis. The frequency with which amplification is reported to occur is quite variable ranging from 0-30% in different series and this variability is probably accounted for by technical and methodologic factors. The variability and lack of reproducibility has raised questions about the usefulness of assessing amplification of the HER-2/neu oncogene and in particular its clinical relevance. In this study by using strict criteria for amplification and using multiple controls we could demonstrate unequivocal amplification of the HER-2/neu oncogene by Southern blot analysis in only 11% of malignant ovarian tumors. The potential pitfalls with the techniques used to detect HER-2/neu oncogene amplification and overexpression are reviewed and possible ways to overcome some of the problems are suggested.

Characterization of phycocyanin produced by cpcE and cpcF mutants and identification of an intergenic suppressor of the defect in bilin attachment

Mutants of the cyanobacterium Synechococcus sp. PCC 7002 constructed by the insertional inactivation of either the cpcE or cpcF gene produce low levels of spectroscopically detectable phycocyanin. The majority of the phycocyanin produced in these strains appears to lack the alpha subunit phycocyanobilin (PCB) chromophore (Zhou, J., Gasparich, G. E., Stirewalt, V. L., de Lorimier, R., and Bryant, D. A. (1992) J. Biol. Chem. 267, 16138-16145). Purification of the phycocyanin produced in the mutants revealed two fractions each with an aberrant absorption spectrum. Tryptic peptide maps of the major fraction showed that the alpha-84 PCB peptide was absent. The two PCB peptides derived from the beta subunit were normal. Tryptic digests of the less abundant phycocyanin fraction contained a family of bilin peptides derived from the alpha subunit. Several distinct bilin adducts were present. A major component was a mesobiliverdin adduct, a previously described product of the in vitro reaction of PCB and apophycocyanin. The same results were obtained with both the cpcE mutant and the cpcF mutant. In vitro reactions with PCB and the fractions containing apo alpha subunit showed that the alpha-84 bilin attachment site was unmodified and competent for adduct formation. Pseudo-revertants of both strains were observed to arise at high frequency. Analysis of the phycocyanin from a cpcE pseudo-revertant, which produced a near wild-type level of phycocyanin with alpha subunit carrying PCB, revealed a single amino acid substitution, alpha-Tyr129----Cys. This residue, which is conserved in all phycocyanins sequenced to date, forms part of the alpha-84 bilin binding site and lies within 5 A of alpha-Cys84. A mutated cpcA gene containing this substitution was constructed by site-directed mutagenesis and transformed, along with cpcB, into a cpcBAC deletion strain containing an insertionally inactivated cpcE. This strain produces high levels of phycocyanin and the majority of the alpha subunit carries PCB at alpha-Cys84.

Investigations of gas-phase lithium-peptide adducts: Tandem. mass spectrometry and semiempirical studies

Tandem mass spectrometry using a hybrid mass spectrometer of BEqQ geometry was used to investigate the gas-phase formation of the [An (+) Li - H)(+) ion from lithium-peptide adducts. High resolution mass measurements as well as precursor and product ion scans of five peptides indicate that one source of [An (+) Li - H) arises from [An (+) Li](+). Semiempirical calculations (MNOO) and metastable ion decomposition studies of the peptide Gly-Gly-Gly show that the lithium ion prefers to coordinate to the three internal carbonyls of the neutral molecule to give a species that is energetically more stable than the lithiated zwitterion by 305 kJ/mol. Theoretical and experimental evidence suggest that the monolithiated precursor ion population may be a distribution of structural isomers. (J Am Soc Mass Spectrom 1990, 1, 473-480).

Amplification of c-ras-Ki oncogene in human ovarian tumours

Amplification of the c-ras-Ki oncogene has been the most consistent finding reported in studies on oncogene activation in ovarian cancer, but for the most part the studies have been small and the results conflicting. In order to determine whether amplification occurred de novo in primary tumours or was associated with tumour progression and metastasis, 81 tumour samples from different sites in 26 patients with ovarian tumours and 7 xenografted ovarian tumour cell lines were assayed. Amplification of c-ras-Ki occurred infrequently and was apparent in a single metastatic site in a patient with poorly differentiated serous cystadenocarcinoma of the ovary. Ten-fold amplification of the c-ras-Ki oncogene was also evident in a benign ovarian fibroma. Amplification of the c-ras-Ki oncogene is rare in ovarian tumours and does not appear to play a fundamental role in tumor development or progression.

Chemical and toxicological characterization of residential oil burner emissions: I. Yields and chemical characterization of extractables from combustion of No. 2 fuel oil at different Bacharach Smoke Numbers and firing cycles

Particulates and complex organic mixtures were sampled from the exhaust of a flame retention head residential oil burner combusting No. 2 fuel oil at three firing conditions: continuous at Bacharach Smoke No. 1, and cyclic (5 min on, 10 min off) at Smoke Nos. 1 and 5. The complex mixtures were recovered by successive Soxhlet extraction of filtered particulates and XAD-2 sorbent resin with methylene chloride (DCM) and then methanol (MeOH). Bacterial mutagenicity [see Paper II (8)] was found in the DCM extractables. Samples of DCM extracts from the two cyclic firing conditions and of the raw fuel were separated by gravity column chromatography on alumina. The resulting fractions were further characterized by a range of instrumental methods. Average yields of both unextracted particulates and of DCM extractables, normalized to a basis of per unit weight of fuel fired, were lower for continuous firing than for cyclic firing. For cyclic firing, decreasing the smoke number lowered the particulates emissions but only slightly reduced the average yield of DCM extractables. These and similar observations, here reported for two other oil burners, show that adjusting the burner to a lower smoke number has little effect on, or may actually increase, emissions of organic extractables of potential public health interest. Modifications of the burner firing cycle aimed at approaching continuous operation offer promise for reducing the amount of complex organic emissions. Unburned fuel accounted for roughly half of the DCM extractables from cyclic firing of the flame retention head burner at high and low smoke number. Large (i.e., greater than 3 ring) polycyclic aromatic hydrocarbons (PAH) were not observed in the DCM extractables from cyclic firing. However, nitroaromatics, typified by alkylated nitronaphthalenes, alkyl-nitrobiphenyls, and alkyl-nitrophenanthrenes were found in a minor subfraction containing a significant portion of the total mutagenic activity of the cyclic low smoke samples (8). Oxygen-containing PAH, typified by phenalene-1-one and its alkyl derivatives, are important mutagens from cyclic firing at high smoke conditions. Thus, oil burner effluents differ markedly from those of several other combustors, including the automotive diesel engine, where multiring PAH, typified by fluoranthene and alkylated phenanthrenes, account for a significant portion of the effluent mutagenicity. Implications for combustion and emissions source identification are discussed.

Immunohistochemical detection of proliferating cells in vivo

Incorporation of the thymidine analogue 5-bromo-2'-deoxyuridine (BrUdR) into newly synthesized DNA provides the basis of a simple technique for identifying proliferating cells. BrUdR was administered to C57BL/6 mice by continuous infusion for 1-7 days, or by intraperitoneal injection for shorter intervals. Various tissue types, including gut, kidney, and liver, were excised, fixed in neutral buffered formalin, and paraffin-embedded for sectioning. De-paraffinized 4-micron tissue sections and bone marrow samples were incubated with an anti-BrUdR antibody and cells that had traversed S-phase during the BrUdR exposure period were identified immunohistochemically. Proliferation and migration of intestinal epithelial cells were identified by antibody staining after continuous in vivo exposure to BrUdR for 1-4 days, and BrUdR incorporation into proliferating marrow cells was detected within 30 min. Tissues such as normal liver, known to have low levels of proliferation, remained unstained after 3 days' exposure to BrUdR. After we established that normal proliferating cells could be identified using this technique, BrUdR was administered to mice bearing B16 melanomas. Again, proliferating tumor cells were clearly identified in histological sections. The nuclei from these paraffin-embedded tumors were also collected for flow cytometric analysis after de-waxing, rehydration, and pepsin treatment. This combination of techniques made possible the comparison in adjacent tissue sections of labeling index, obtained from stained sections, with percentage S-phase, measured using DNA flow cytometry. The % S-phase was consistently higher than the labeling index obtained with immunocytochemistry, and two-parameter DNA vs BrUdR flow cytometry showed that this difference could be accounted for by a population of unlabeled cells with an S-phase DNA content.

Metastatic adeno or undifferentiated carcinoma from an unknown primary site--natural history and guidelines for identification of treatable subsets

Two hundred and eighty-six patients presenting with metastatic adenocarcinoma or undifferentiated carcinoma whose primary site was not identified by clinical history, physical examination and chest radiograph have been studied. Median survival from presentation was 22 weeks. Factors independently predicting improved survival were lymph node presentations, good performance status and body weight loss of less than 10 per cent. In 88 (31 per cent) patients the primary tumour site was subsequently identified, in 58 (20 per cent) during life. Lung cancer was the most frequently identified primary tumour, and in only 32 (11 per cent) of the patients was a 'treatable' primary tumour (i.e. germ cell, breast, ovarian, prostate, thyroid cancer or lymphoma) identified. Among the treatable primary tumours were those in eight out of 16 female patients presenting with axillary metastases who were subsequently shown to have primary breast cancer and four of 13 females presenting with ascites who were found to have primary ovarian cancer. Prostatic cancer was confirmed in five out of 13 men with raised serum acid phosphatase. Of 22 patients with elevated serum alphafoetoprotein (AFP) or beta-human chorionic gonadotrophin levels (beta HCG) 18 had some features of the 'atypical teratoma syndrome'. Of the total of 32 patients with treatable tumour types, 29 (90 per cent) were identified during life. Median survival for patients with treatable tumour types identified during life was 104 weeks, compared with 22 weeks for the group as a whole. Retrospective immunocytochemical staining of the original biopsy showed that prostatic specific antigen and antibodies to beta HCG and AFP were diagnostically useful, but a series of organ site non-specific markers of histogenesis or cellular differentiation (carcinoembryonic antigen, secretory component for IgA, peanut lectin binding, epithelial membrane antigen and keratin) showed no significant correlations with identified primary sites, responsiveness to empirical chemotherapy or survival. Metastatic undifferentiated carcinoma or adenocarcinoma from an unknown primary site represents 6.5 per cent of all referrals to the medical oncology unit, Royal Prince Alfred Hospital, Sydney. We offer guidelines for the rapid identification of the limited number of primary sites for which effective and specific forms of systemic treatment are available.

Post-translational methylation of asparaginyl residues. Identification of beta-71 gamma-N-methylasparagine in allophycocyanin

A novel post-translationally modified residue, gamma-N-methylasparagine, was detected in the beta subunit of Anabaena variabilis allophycocyanin. Structure determination was accomplished by isolating a decapeptide, AP-beta (63-72) shown to have the following structure: Ser-Asp-Ile-Thr-Arg-Pro-Gly-Gly- Asn[N-CH3]-homoserine lactone Fast atom bombardment-mass spectrometry established that the residue corresponding to position 71 in the protein (DeLange, R. J., Williams, L. C., and Glazer, A. N. (1981) J. Biol. Chem. 256, 9558-9566) contained 13 mass units more than expected for aspartic acid though aspartic acid was recovered after acid hydrolysis. The 1H NMR spectrum of AP-beta (63-72) revealed a strong methyl single at 2.71 ppm characteristic of the methyl derivative of an amide nitrogen. Confirmation of this bond arrangement was obtained by detection of a stoichiometric amount of methylamine in acid hydrolysates of the peptide. This is the first report of gamma-N-methylasparagine in a protein. Amino acid analysis of A. variabilis allophycocyanin subunits showed that the derivative at position 71 can account for the total methylamine released from the beta subunit, while hydrolysis of the alpha subunit released no methylamine. The beta subunits of the allophycocyanins from the cyanobacterium Synechococcus PCC 6301 and the red alga Porphyridium cruentum each released 1 eq of methylamine upon acid hydrolysis. No methylamine was released from the alpha subunits.

Isolation and identification of 1(3),2-diacylglyceryl-(3)-O-4'-(N,N,N-trimethyl)homoserine from the soil amoeba, Acanthamoeba castellanii

A polar lipid accounting for 12.5% of the total lipid nitrogen has been isolated from the protozoan Acanthamoeba castellanii. On the basis of thin-layer chromatography and mass spectral analysis, the lipid has been identified as diacylglyceryltrimethylhomoserine (DGTS). Fast atom bombardment (FAB) mass spectra of DGTS are reported for the first time and are compared to the FAB mass spectra of phosphatidylcholines and the electron ionization (EI) and field desorption (FD) mass spectra of DGTS. Gas-liquid chromatographic-mass spectrometric (GLC-MS) analysis of the acyl chain composition of this lipid has shown that 87.5% consists of cis-9-octadecenoic acid. Plasma membrane isolated from this organism has shown that labeled DGTS appears in the plasma membrane but is not enriched in this fraction. DGTS has been isolated previously only from a limited number of green plants and one species of fungus. Identification of this lipid in Acanthamoeba indicates that this lipid is distributed among a diverse group of lower eucaryotes.

Metastatic adenocarcinoma of unknown primary site: abnormalities of cellular DNA content and survival

Using a new flow cytometric technique we measured the cellular DNA content of tumour biopsies taken from 152 patients presenting with metastatic adenocarcinoma or undifferentiated carcinoma of unknown primary site. One hundred and six (70%) contained populations of cells with an abnormal cellular DNA content and the remainder were diploid. The incidence of aneuploidy was similar for the two sexes and bore no obvious relationship to the various patterns of metastatic involvement. Median survival of patients with diploid tumours was 4.2 months and for patients with aneuploid tumours, 4.8 months. Nine of the 46 patients with diploid tumours (i.e. 18%) survived for more than 2 yr compared to 10 of 106 (9%) of those with aneuploid tumours. These results indicate that the incidence of aneuploidy in this heterogeneous group of patients is similar to that reported for adenocarcinomas of known histogenesis, such as breast or colorectal cancer. In contrast to many of these tumour types, however, patients with metastatic adenocarcinomas of unknown primary which are diploid do not on the whole have a more favourable prognosis.