Functional Relationship and Gene Ontology Classification of Breast Cancer Biomarkers

Breast cancer is a complex disease that still imposes a significant healthcare burden on women worldwide. The etiology of breast cancer is not known but significant advances have been made in the area of early detection and treatment. The advent of advanced molecular biology techniques, mapping of the human genome and availability of high throughput genomic and proteomic strategies opens up new opportunities and will potentially lead to the discovery of novel biomarkers for early detection and prognostication of breast cancer. Currently, many biomarkers, particularly the hormonal and epidermal growth factor receptors, are being utilized for breast cancer prognosis. Unfortunately, none of the biomarkers in use have sufficient diagnostic, prognostic and/or predictive power across all categories and stages of breast cancer. It is recognized that more useful information can be generated if tumors are interrogated with multiple markers. But choosing the right combination of biomarkers is challenging, because 1) multiple pathways are involved, 2) up to 62 genes and their protein products are potentially involved in breast cancer-related mechanisms and 3) the more markers evaluated, the more the time and cost involved. This review summarizes the current literature on selected biomarkers for breast cancer, discusses the functional relationships, and groups the selected genes based on a Gene Ontology™ classification.

Observations of differences in laterality imbalance of breast biopsies and breast disease between Caucasian and African American women

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Background: A number of published reports have indicated that the left breast is at greater risk of cancer than the right breast (laterality imbalance) in women of all ages. In addition, a woman’s left breast is usually larger than her right breast. In the Clinical Breast Care Project, more than 2400 subjects have been enrolled following HIPAA compliant, IRB approved protocols. Of these, 1200 have undergone a biopsy and completed demographic and pathological questionnaires. We investigated whether there is a laterality imbalance among the patients with respect to ethnicity, menopausal status or pathological diagnoses. Methods: Female patients with biopsies on only one breast whose pathological questionnaire was completed within 90 days of the demographical questionnaire were included in this analysis but patients who were surgically post-menopausal were excluded. Multiple biopsies on one breast for each woman were counted as one event. For statistical analysis, Pearson’s chi-square test in SPSS was used. Results: Of the 1200 patients, 708 (546 caucasian; CA and 172 African American; AA) satisfied the above criteria. Although the total number of biopsy events are essentially evenly distributed on either breast for either ethnicity, statistical analysis showed that post menopausal CA women have fewer biopsy events on the left breast (41%, n=264) than their pre-menopausal counterparts (52%, n = 282; p < 0.05); On the contrary, post-menopausal AA women have significantly more biopsy events on the left breast (62%, n=50) than their pre-menopausal counterparts (42%, n = 122; p = 0.02). Further analysis based on pathological diagnoses indicated that benign, pre-menopausal, AA patients have fewer events on the left breast (42%, n = 98) compared to CA (54%, n = 211; p < 0.05). Discussions: Despite the small sample size, the data nonetheless suggest that there are significant, menopausal status dependent, laterality imbalances of breast disease biopsy among CA and AA women. These differences await evaluation.

No significant financial relationships to disclose.

Functional relationship and gene ontology classification of breast cancer biomarkers

Breast cancer is a complex disease that still imposes a significant healthcare burden on women worldwide. The etiology of breast cancer is not known but significant advances have been made in the area of early detection and treatment. The advent of advanced molecular biology techniques, mapping of the human genome and availability of high throughput genomic and proteomic strategies opens up new opportunities and will potentially lead to the discovery of novel biomarkers for early detection and prognostication of breast cancer. Currently, many biomarkers, particularly the hormonal and epidermal growth factor receptors, are being utilized for breast cancer prognosis. Unfortunately, none of the biomarkers in use have sufficient diagnostic, prognostic and/or predictive power across all categories and stages of breast cancer. It is recognized that more useful information can be generated if tumors are interrogated with multiple markers. But choosing the right combination of biomarkers is challenging, because 1) multiple pathways are involved, 2) up to 62 genes and their protein products are potentially involved in breast cancer-related mechanisms and 3) the more markers evaluated, the more the time and cost involved. This review summarizes the current literature on selected biomarkers for breast cancer, discusses the functional relationships, and groups the selected genes based on a Gene Ontology classification.

Molecular cloning and demonstration of an aminopeptidase activity in a filarial nematode glycoprotein

ES-62 is an abundant phosphorylcholine-containing secreted glycoprotein of the filarial nematode Acanthocheilonema viteae. Using an antiserum directed against the parasite molecule, 3 cDNAs of size, approximately 1.5-1.6 kbp were isolated from an A. viteae expression library. Sequence analysis in combination with N-terminal amino acid sequencing of purified ES-62 revealed that each clone contained a full-length cDNA for ES-62 corresponding to 474 amino acid residues but differed in their 5' and 3' untranslated regions. Characterisation of the 5' end of ES-62 mRNA using 5' rapid amplification of cDNA ends showed that it coded for a signal sequence. Several tryptic peptides were independently sequenced using quadruple-time-of-flight mass spectrometry and used to confirm the cDNA sequence. The mature protein was found to contain three potential N-linked glycosylation sites. Comparison of the derived amino acid sequence of ES-62 with the SwissProt database identified a sequence (between amino acid residues approximately 250 and 350 of mature ES-62) with significant similarity to several bacterial/fungal aminopeptidases. Incubation of ES-62 with leucine-7-amino-4-methylcoumarin as substrate confirmed that ES-62 possessed aminopeptidase activity.

The gamma-subunit of the rod photoreceptor cGMP-binding cGMP-specific PDE is expressed in mouse lung

The type 6 phosphodiesterase (PDE-6) from retinal rod photoreceptors is an alpha beta gamma 2 heterotetramer. The alpha- and beta-subunits contain catalytic sites for cGMP hydrolysis, whereas the gamma-subunits (P gamma) serve as a protein inhibitor of the enzyme. P gamma is believed to be expressed only in photoreceptors. Using RT-PCR, we have amplified the complete coding sequence for P gamma from mouse lung RNA. The expression of P gamma in this tissue may be related to its ability to interact the type 5 phosphodiesterase (PDE-5), which is the predominant cGMP binding protein in lung. We therefore suggest that P gamma may have a wider signaling role in mammalian cells than previously appreciated.

Photoreceptor rim protein: partial sequences of cDNA show a high degree of similarity to ABC transporters

PURPOSE

To isolate and sequence cDNA for bovine rim protein, a large membrane-bound glycoprotein found in photoreceptor outer segments.

METHODS

Bovine rim protein was N-terminally sequenced (22 residues) and fragments were prepared by partial proteolysis. Two internal sequences of 21 and 18 amino acid residues were obtained from 35 kDa and 32 kDa fragments, respectively. Sense and anti-sense oligonucleotide primers were constructed, based on the peptide sequences derived from the 35 kDa and 32 kDa fragments, respectively, and the polymerase chain reaction (PCR) was used to amplify a 150 bp sequence from bovine retinal cDNA.

RESULTS

The amplified sequence coded for the remainder of the peptide sequence determined from the 35 kDa fragment, which was not present in the primer, confirming that it was derived from the rim protein. The 150 bp sequence was translated to give a 50 amino acid peptide. Part of this peptide was compared with Dna sequence databases using the TFastA program, which found 94.6% identity with an EST derived from human retina and 86.1% identity to the mouse abc1 transporter.

CONCLUSIONS

It is proposed that rim protein is a member of the ATP transporter family of proteins. It may be involved in transport of molecules involved in visual transduction across the photoreceptor disk membrane.

Identification of the products of the haptoglobin-related gene

A novel haptoglobin, which is undetectable using conventional peroxidase staining techniques, has been detected using immunoblotting. The behaviour of this novel haptoglobin after electrophoresis under native, denaturing and reducing conditions indicates that it is the product of the haptoglobin-related gene. This protein is detectable in normal human plasma.

Characterization of non-flocculent cells isolated from a culture of flocculent Saccharomyces cerevisiae NCYC 1001

During cultivation of a flocculent yeast, Saccharomyces cerevisiae 1001, two cell fractions, flocs and free cells, appeared in the medium. Free cells contained cells with a normal ability to flocculate, less flocculent cells and not-flocculent cells. When the non-flocculent cells and not-flocculent cells. When the non-flocculent cell fraction from the postexponential phase of growth was collected and used as an inoculum, the culture showed synchronous growth. The floc forming ability of the yeast cells from this culture increased gradually with the number of divisions.

Maintenance of expression of differentiated function of kidney cells following transformation by SV40 early region DNA

This study describes the isolation and characterization of epithelial cell lines that maintain their differentiated phenotype following the stable integration of SV40 genes. Epithelial cells were derived from a defined location of rabbit kidney, the thick ascending limb of Henle's loop, and were co-transfected with genes from the early region of SV40 together with pSV2-neo DNA (which confers resistance to the antibiotic G418). These cells were shown to be resistant to G418, express SV40 large T-antigen and continued to express differentiated characteristics typical of cells of their origin. Such characteristics include the expression of high levels of activity of both Na,K-ATPase and the functionally important Na,K,Cl-co-transport system, the synthesis of Tamm-Horsfall glycoprotein and the presence of a barium-sensitive K+ channel on the apical membrane surface.

Expression of the alpha-fetoprotein gene in pluripotent and committed cells

We have studied the structure and expression of the alpha-fetoprotein gene in various cell types which differ in their capacity to synthesize alpha-fetoprotein. In all cells and tissues examined the levels of alpha-fetoprotein RNA found in the nucleus and cytoplasm were consistent with the hypothesis that alpha-fetoprotein expression is transcriptionally regulated. The alpha-fetoprotein gene was insensitive to deoxyribonuclease I in both undifferentiated embryonal carcinoma cells and in differentiated tissues which do not express alpha-fetoprotein, whereas in endoderm cells derived from the embryonal carcinoma cells and in alpha-fetoprotein-producing tissues the gene was sensitive to deoxyribonuclease I.

Changes in polypeptide pattern in ASV-transformed rat cells are correlated with the degree of morphological transformation

Normal rat kidney cells (NRK) have been transformed with an avian sarcoma virus (ASV) mutant that induces a temperature-sensitive transformed phenotype. When compared in vitro different ASV-transformed clones showed different degrees of morphological transformation at the permissive temperature, while they all reverted to normal at 39 degrees C. Comparisons of the polypeptide patterns of the different cells showed two things. First, a group of about 30 polypeptides, amounting to 5% of all the polypeptides analyzed in normal cells, were affected in all ASV-transformed clones and also in two papovavirus-transformed clones and also in two papovavirus-transformed NRK clones. Second, the patterns were found to differ between the clones in that varying numbers of polypeptides were found to be affected depending on the clone; the number of polypeptide changes showed a good correlation with the degree of morphological transformation. At the nonpermissive temperature the polypeptide patterns of ts ASV-transformed cells were indistinguishable from that of the untransformed cells, which is in agreement with the morphological data.

Regulation of the synthesis of Sindbis virus-specified RNA: role of the virion core protein

Cells infected with seven different RNA+ mutants of Sindbis virus were found to accumulate a virus-specified polypeptide of mol. wt. 144000 (p144) during incubation at the non-permissive temperature, while at the same time synthesis of the virus structural proteins was drastically reduced. Mapping of the tryptic peptides of p144 showed that it contained the amino acid sequences of all the virus structural proteins. At the non-permissive temperature cells infected with the same seven mutants (out of 28 examined) also showed increased synthesis of 26S RNA, the mRNA for the virus structural proteins, relative to 42S RNA, and the virus genome, compared with infections by wild-type virus. We propose that both these phenotypic effects are the results of a single mutational step and that the primary defect in the processing of the virus structural protein precursor induces the relatively increased rate of synthesis of structural protein mRNA. Temperature-shift experiments with mutant-infected cells showed that p144 itself is not the agent of this effect. The failure of exposure to zinc ions to alter the RNA ratio in wild-type virus-infected cells suggested that the virus envelope proteins are not involved either, since their synthesis is preferentially inhibited under these circumstances. It is possible that it is the failure to synthesize the proper quantity of core protein in the mutant-infected cells which causes the shift of RNA synthesis in favour of structural protein mRNA.

Synthesis of alphavirus-specified RNA

UV irradiation of chicken fibroblasts infected with Semliki Forest or Sindbis virus has been used to investigate the mechanism of synthesis of 42S and 26S RNA, the major plus-strand virus-specified RNAs formed during the multiplication of standard virus particles. From an analysis of the kinetics of UV inactivation of the synthesis of these two RNAs, we conclude (i) that 26S RNA is formed by internal transcriptive initiation from a point about two-thirds of the way from the 3' end of the 42S negative-strand template; (ii) that there exists a population of plus-strand synthesizing complexes whose members are each capable of synthesizing both 42S and 26S RNA; and (iii) that, on a time-averaged basis, each complex in wild-type virus-infected cells contains one virus polymerase mediating 42S RNA synthesis and three mediating 26S RNA synthesis. The RNA phenotypes of 15 RNA(-)ts mutants of Sindbis virus have been examined after temperature shift to the restrictive temperature. Under these conditions, cells infected with three mutants, N2, N7, and E268, synthesized four to six times as much 42S RNA (relative to 26S RNA) as wild-type virus-infected cells. These studies were extended by examining, in detail, the RNA and polypeptide phenotypes of mutants N2 and E268. These experiments showed that, in N2- and E268-infected cells, one of the virus-specified nonstructural (NS) polypeptides (NS p89; H. Brzeski and S. I. T. Kennedy, J. Virol. 22:420-429, 1977) is thermolabile after shift up to restrictive temperature. This finding, together with the observation that, after shift, the 26S/42S RNA ratio in N2-infected cells changes markedly in favor of 42S RNA synthesis, leads us to conclude that, of the three NS polypeptides, NS p89 modulates 26S RNA synthesis.

Synthesis of Sindbis virus nonstructural polypeptides in chicken embryo fibroblasts

The identification of eight previously undescribed polypeptides in chicken embryo cells infected with Sindbis virus is reported. Seven of these polypeptides were distinguishable from the virus structural polypeptides and their precursors by their molecular weights and tryptic peptide maps. The eighth was closely related to pE2 (Schlesinger and Schlesinger, 1973), a precursor to one of the virus particle glycoproteins. Pulse-chase experiments and the use of an inhibitor of proteolytic cleavage allowed a division of the seven nonstructural (NS) polypeptides into three stable end products (NS p89, NS p82, and NS p60) and four precursors (p230, p215, p150, and p76). The labeling kinetics after synchronous initiation of translation indicated that synthesis of the NS polypeptides started at a single site and showed that the order of the genes coding for the NS polypeptides was (5' leads to 3') NS p60, NS p89, and NS p82. Short-pulse experiments under conditions of both synchronized and nonsynchronized translation suggested that cleavage of the primary translation product of the NS genes occurred only after its synthesis was completed and that the first cleavage removed the C-terminal polypeptide. From these and other experiments, we propose a detailed scheme for the synthesis and processing of Sindbis virus NS polypeptides.

RNA polymerase components in Semliki Forest virus-infected cells: synthesis from large precursors

Two previously undescribed stable polypeptides (referred to as nsp 90 and nsp 63) appear in mammalian and avian cells infected with Semliki Forest virus. They are distinguishable from the virus structural proteins and their known precursors by their molecular weights and tryptic peptide maps, and are identical in size to two polypeptides found in purified preparations of virus-specific RNA polymerase. Data from pulse-chase experiments and from the use of inhibitors of proteolytic cleavage indicate that nsp 90 and nsp 63 are synthesized via a series of post-translational cleavages from three larger polypeptides, p200, p184 and p150. The labelling kinetics after synchronous initiation of protein synthesis are also consistent with the synthesis of nsp 90 and nsp 63 from a common initiation site, and show that nsp 63 is located close to this site. It is concluded that nsp 90 and nsp 63 are components of the virus-specific RNA polymerase, and are synthesized via a post-translational cleavage scheme entirely separate from that leading to the synthesis of the virus structural proteins.