Employing a blood based gene expression signature to detect early stage breast cancer

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Background: Existing methods to detect breast cancer (BC) in asymptomatic patients have limitations, and there is a need to develop more accurate and convenient methods. We recently demonstrated the potential use of gene expression profiling in peripheral blood cells (PBC) for early detection of BC (1) and repeated this with a larger study using the Agilent platform with an accuracy of 75± 7%. Objective: 2 studies are presented that investigate: i) whether effective normalization of experimental conditions can improve diagnostic accuracy, ii) whether a blood based signature developed for BC can discriminate other forms of cancer, and iii) whether an expression signature developed using stage 0 patients can be used to predict BC in stage I disease, and vice versa. Material and Methods: Study I enrolled 60 females with BC and 60 healthy females. Study II enrolled 20 females with early stage BC (10 stage 0 and 10 stage I), 20 healthy females, and 8 females with colon cancer. Gene expression analysis was conducted using the ABI HGSM v2.0 with 32,878 oligo probes. Expression data were analyzed by PLSR for model building and results validated using cross-validation and test set validation. Results: Effective normalization of the data led to improved diagnostic performance. The signature developed using 20 BC and 20 non-BC samples classified 7/8 colon cancer patients as non-BC. The signature developed using stage 0 vs non-BC detected cancer in stage I patients, and the signature developed for stage 1 detected cancer in stage 0 patients. Conclusion: A blood-based gene expression signature can be developed for early stage breast cancer, which is specific and able to distinguish between other forms of malignancy such as colon cancer. The gene expression pattern is systemically affected in early stage BC patients in which there is typically no direct contact of blood cells with cancer cells. References: 1. Sharma P et al. (2005) Breast Cancer Res. 7 (5): R 634–44 2. Aaroe J et al (2006), poster no:125, 97th AACR Annual Meeting, Washington DC, USA Some RT-PCR analyses were performed by Marion Hirt IMGM Laboratories, Martinsried, Germany.

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Isolation of the first putative peroxidase cDNA from a conifer and the local and systemic accumulation of related proteins upon pathogen infection

Peroxidases are associated with the active defence reactions in higher plants in response to foreign organisms. They are involved in the oxidation of phenolic compounds in cell walls, polymerization of lignin and suberin, and in several other oxidation processes but the exact function of individual peroxidases is not known. We have isolated a cDNA encoding the putative defence-related and basic plant peroxidase SPI2 (spruce pathogen-induced 2), with an estimated molecular mass of 34 kDa, from roots of Norway spruce (Picea abies) seedlings. This is the first description of the isolation of a complete cDNA encoding a putative peroxidase from a gymnosperm. The transcript was present in the roots of healthy seedlings, and during infection with the pathogen Pythium dimorphum there was a rapid initial increase followed by a dramatic reduction of the transcript. The 34 kDa mature SPI2 protein was detected in both the developing root and shoot of healthy seedlings and increased amounts of SPI2 and increased accumulation of highly basic peroxidase isoforms was observed in roots after infection. In addition, two SPI2-related proteins with apparent molecular masses of 38 and 39 kDa, were also detected. Both these proteins accumulated in roots only after infection, and the 39 kDa protein was in addition detected in shoots of root-infected seedlings. Thus, both SPI2 and the SPI2-related proteins accumulate as a local response, in roots, and as a systemic response to infection the 39 kDa protein accumulates in the shoot.

Mechanical injury and fungal infection induce acquired resistance in Norway spruce

Norway spruce trees (Picea abies (L.) Karst.) pretreated by wounding and fungal infection showed highly enhanced resistance to a subsequent challenge inoculation with the pathogenic bluestain fungus Ceratocystis polonica (Siem.) C. Moreau. This is the first time the effectiveness of the constitutive and inducible defenses has been shown to depend on prior wounding and infection in conifers, although such acquired resistance has previously been found in several angiosperms. Trees that were pretreated with a combination of 12 bark wounds (1.6 x 10 cm), four fungal inoculations and four sterile inoculations 1-15 days before mass inoculation with C. polonica at 400 inoculations per square meter over a 0.8 m stem section had significantly shorter necroses in the phloem, less bluestained sapwood, and less dead cambium than untreated control trees. Pretreatment with four fungal or sterile inoculations alone did not lead to enhanced resistance. Pretreatment by bark wounding alone seemed to provide an intermediate degree of resistance compared to bark wounding, fungal inoculations and sterile inoculations combined. All trees had a marked increase in the number of resin ducts in the year of inoculation compared with previous years, suggesting that formation of traumatic resin ducts play an important role in the development and maintainance of enhanced resistance.

Isolation and characterization of a cDNA encoding a plant defensin-like protein from roots of Norway spruce

We are studying the interaction between the roots of Norway spruce seedlings (Picea abies L. Karst) and a highly pathogenic isolate of Pythium dimorphum. Here, we report the isolation of a cDNA from spruce roots encoding a protein with high sequence similarity to plant defensins, designated as SPI1 (Spruce Pathogen Induced No.1). The transcript hybridizing to the SPII cDNA probe is highly induced in uninfected roots when the seedlings are transferred from solid to liquid incubating malt medium (hypoxic conditions). However, when the seedlings are transferred from solid to liquid malt media containing a saturating amount of P. dimorphum hyphae, the amount of transcript is unchanged the first day after infection, but then decreases on day 1, and is no longer detectable 2 days after infection. Since plant defensins may play a role in plant defence, their negative regulation upon infection might reflect a strategy employed by this pathogenic fungus to evade the effect of toxic gene products.

PCR amplification and sequences of cDNA clones for the small and large subunits of ADP-glucose pyrophosphorylase from barley tissues

Several cDNAs encoding the small and large subunit of ADP-glucose pyrophosphorylase (AGP) were isolated from total RNA of the starchy endosperm, roots and leaves of barley by polymerase chain reaction (PCR). Sets of degenerate oligonucleotide primers, based on previously published conserved amino acid sequences of plant AGP, were used for synthesis and amplification of the cDNAs. For either the endosperm, roots and leaves, the restriction analysis of PCR products (ca. 550 nucleotides each) has revealed heterogeneity, suggesting presence of three transcripts for AGP in the endosperm and roots, and up to two AGP transcripts in the leaf tissue. Based on the derived amino acid sequences, two clones from the endosperm, beps and bepl, were identified as coding for the small and large subunit of AGP, respectively, while a leaf transcript (blpl) encoded the putative large subunit of AGP. There was about 50% identity between the endosperm clones, and both of them were about 60% identical to the leaf cDNA. Northern blot analysis has indicated that beps and bepl are expressed in both the endosperm and roots, while blpl is detectable only in leaves. Application of the PCR technique in studies on gene structure and gene expression of plant AGP is discussed.

Primary structure of a novel barley gene differentially expressed in immature aleurone layers

As a direct approach to elucidate the molecular biology of barley aleurone cell development, we differentially screened an aleurone cDNA library made from poly(A)+ RNA of immature grains for clones representing transcripts present in the aleurone but not in the starchy endosperm. For one of these clones, B22E, which hybridies to a 0.7 kb transcript, Northern and in situ hybridization revealed that expression is under complex spatial, temporal and hormonal control in barley grains. cDNAs corresponding to B22E transcripts were isolated from aleurone/pericarp and embryo of developing grains, and from germinating scutella. Among these were the nearly full-length aleurone/pericarp clone pB22E.a16 (541 bp). cDNAs matching the sequence of this clone (type 1 transcript) were found for all tissues investigated. In addition, cDNAs with an extra 12 bp insertion (type 2 transcript) were obtained from germinating scutella. The two different transcripts can encode novel barley proteins of 115 and 119 amino acids, respectively. A gene designated B22EL8 was isolated and sequenced; it encodes the type 1 B22E transcript and contains two introns of 145 and 125 bp. Particle bombardment of barley aleurone with a B22EL8 promoter-GUS (beta-glucuronidase) construct demonstrates that the promoter (3 kb) is active in developing barley grains. The promoter is not, however, active in the seeds of tobacco plants transgenic for the B22EL8 gene, indicating the existence of sequences specific for monocots. A comparison of 1.4 kb of upstream sequence of B22E with the maize c1 promoter reveals a number of short, identical sequences which may be responsible for aleurone cell-specific gene transcription.

Plant ADP-glucose pyrophosphorylase--recent advances and biotechnological perspectives (a review)

Recent advances in studies on plant ADP-glucose pyrophosphorylase (AGP), the key enzyme of starch biosynthesis, are presented. AGP constitutes the first committed and highly regulated step of starch synthesis in all plant tissues. The importance of AGP in carbohydrate metabolism and several of its features, such as potent regulation by cellular effectors (3-phosphoglycerate and Pi), an unusual two subunit-types structure, tissue-specific and developmentally-regulated expression, and presence of the AGP-deficient mutants, make it an attractive, but complex, target for biotechnological manipulations. Some strategies for future research on AGP are discussed.

The Susceptibility of Photosynthesis to Photoinhibition and the Capacity of Recovery in High and Low Light Grown Cyanobacteria, Anacystis nidulans

The susceptibility of photosynthesis to photoinhibition and the rate of its recovery were studied in the cyanobacterium Anacystis nidulans grown at a low (10 micromoles per square meter per second) and a high (120 micromoles per square meter per second) photosynthetically active radiation. The rate of light limited photosynthetic O(2) evolution was measured to determine levels of photoinhibition and rates of recovery. Studies of photoinhibition and recovery with and without the translation inhibitor streptomycin demonstrated the importance of a recovery process for the susceptibility of photosynthesis to photoinhibition. We concluded that the approximately 3 times lower susceptibility to photoinhibition of high light than of low light grown cells, significantly depended on high light grown cells having an approximately 3 times higher recovery capacity than low light grown cells. It is suggested that these differences in susceptibility to photoinhibition and recovery depends on high light grown cells having a higher turnover rate of photosystem II protein(s) that is(are) the primary site(s) of photodamage, than have low light grown cells. Furthermore, we demonstrated that photoinhibition of A. nidulans may occur under physiological light conditions without visible harm to the growth of the cell culture. The results give support for the hypotheses that the net photoinhibitory damage of photosystem II results from the balance between the photoinhibitory process and the operation of a recovery process; the capacity of the latter determining significant differences in the susceptibility of photosynthesis to photoinhibition of high and low light grown A. nidulans.

Photoinhibition and Reactivation of Photosynthesis in the Cyanobacterium Anacystis nidulans

The susceptibility of photosynthesis to photoinhibition and its recovery were studied on cultures of the cyanobacterium Anacystis nidulans. Oxygen evolution and low temperature fluorescence kinetics were measured. Upon exposure to high light A. nidulans showed a rapid decrease in oxygen evolution followed by a quasi steady state rate of photosynthesis. This quasi steady state rate decreased with increasing photon flux density of the photoinhibitory light. Reactivation of photosynthesis in dim light after the photoinhibitory treatment was rapid: 85 to 95% recovery occurred within 2 hours. In the presence of the translation inhibitor, streptomycin (250 micrograms per milliliter), no reactivation occurred. We also found that the damage increased dramatically if the high light treatment was done with streptomycin added. A transcription inhibitor, rifampicin, did not inhibit the reactivation process. Based on these data we conclude that the photoinhibitory damage observed is the net result of a balance between the photoinhibitory process and the operation of the repairing mechanism(s).

Acclimation Processes in the Light-Harvesting System of the Cyanobacterium Anacystis nidulans following a Light Shift from White to Red Light

Cyanobacteria acclimate to changes in light by adjusting the amounts of different cellular compounds, for example the light-harvesting macromolecular complex. Described are the acclimatization responses in the light-harvesting system of the cyanobacterium Anacystis nidulans following a shift from high intensity, white light to low intensity, red light.The phycocyanin and chlorophyll content and the relative amount of the two linker peptides (33 and 30 kilodaltons) in the phycobilisome were studied. Both the phycocyanin and chlorophyll content per cell increased after the shift, although the phycocyanin increased relatively more. The increase in phycocyanin was biphasic in nature, a fast initial phase and a slower second phase, while the chlorophyll increase was completed in one phase. The phycocyanin and chlorophyll responses to red light were immediate and were completed within 30 and 80 hours for chlorophyll and phycocyanin, respectively. An immediate response was also seen for the two phycobilisome linker peptides. The amount of both of them increased after the shift, although the 33 kilodalton linker peptide increased faster than the 30 kilodalton linker peptide. The increase of the content of the two linker peptides stopped when the phycocyanin increase shifted from the first to the second phase. We believe that the first phase of phycocyanin increase was due mainly to an increase in the phycobilisome size while the second phase was caused only by an increase in the amount of phycobilisomes. The termination of chlorophyll accumulation, which indicates that no further reaction center chlorophyll antennae were formed, occurred parallel to the onset of the second phase of phycocyanin accumulation.