Diversity in the immune system: “Preconceived ideas” or ideas preconceived?

Two concepts of the evolution and regulation of expression of the combining site repertoire of the immune system, are compared. One view is based on the Associative Recognition Theory as formulated by the author and the other is based on the Idiotype Network Idea as conceived by Jerne. The two concepts are analyzed from the point of view of their logic, internal consistency and factual support.     

Spontaneous missense mutation of an immunoglobulin in a mouse myeloma cell line.

The characterisation of the alteration in amino acid sequence of the immuno globulin heavy chain of IF4, a charge mutant of the myeloma line MOPC 21, is described. This was achieved by comparing the sequence of mutant IF4 heavy chain with the known sequence of the wild type. The peptic fragment (Fab′)₂ from whole immunoglobulin, and all the ten CNBr fragments of MOPC 21 wild-type and mutant IF4 heavy chains, were identified and characterised. The only difference was in a tryptic peptide of the C-terminal CNBr fragment which had the same amino acid composition, but different electrophoretic mobilities. Thermolysin digestion products showed that asparagine 415 of wild-type heavy chain had been replaced by an aspartate in the mutant. Analysis of newly synthesized immunoglobulins from wild type and mutant showed the same charge difference, which did not seem therefore to result from deamidation.Fingerprints of the [³²P]mRNA of IF4 heavy chain were prepared. The T₁ ribonuclease oligonucleotide that includes the coding sequence for residue 415 in wild type was not found in mutant IF4.The mechanism is most likely a missense point mutation (A to G transition) in the MOPC 21 heavy chain structural cistron.     

高效液相色谱法在脱氧核糖核酸酶解动力学研究中的应用

为了更好地对脱氧核糖核酸酶解动力学过程进行研究,建立脱氧核糖核酸（DNA）酶解液中4种脱氧核苷酸（腺嘌呤脱氧核苷酸（dAMP）、鸟嘌呤脱氧核苷酸（dGMP）、胞嘧啶脱氧核苷酸（dCMP）、胸腺嘧啶脱氧核苷酸（dTMP））的高效液相测定方法,能将酶解液中4种脱氧核苷酸完全分离并准确定量。在此基础上,对DNA酶解的动力学进行初步研究,其反应机理为不存在底物和产物抑制的双底物顺序反应,动力学方程为x=1／bin（1＋abt）（其中a=0．3723p0—0．974;b=-0．0493p0^2＋1．1150p0-1．1103）,该方程可以很好地描述DNA酶解过程,误差仅为3．31％.     

Enzymatic synthesis of 2'-deoxynucleoside diphosphates and triphosphates

2'-Deoxynucleoside diphosphates and triphosphates were synthesized from 2'-deoxy-nucleoside monophosphates by using nucleoside monophosphate kinase and nucleoside diphosphate kinase enzymes. This biocatalytic procedure is superior to chemical methods for obtaining these compounds and can be extended to other applications. © Rapid Science Ltd. 1998     

Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase

Numerous template-dependent DNA polymerases are capable of catalyzing template-independent nucleotide additions onto blunt-end DNA. Such non-canonical activity has been hypothesized to increase the genomic hypermutability of retroviruses including human immunodeficiency viruses. Here, we employed pre-steady state kinetics and X-ray crystallography to establish a mechanism for blunt-end additions catalyzed by Sulfolobus solfataricus Dpo4. Our kinetic studies indicated that the first blunt-end dATP incorporation was 80-fold more efficient than the second, and among natural deoxynucleotides, dATP was the preferred substrate due to its stronger intrahelical base-stacking ability. Such base-stacking contributions are supported by the 41-fold higher ground-state binding affinity of a nucleotide analog, pyrene nucleoside 5'-triphosphate, which lacks hydrogen bonding ability but possesses four conjugated aromatic rings. A 2.05 A resolution structure of Dpo4*(blunt-end DNA)*ddATP revealed that the base and sugar of the incoming ddATP, respectively, stack against the 5'-base of the opposite strand and the 3'-base of the elongating strand. This unprecedented base-stacking pattern can be applied to subsequent blunt-end additions only if all incorporated dAMPs are extrahelical, leading to predominantly single non-templated dATP incorporation.     

Mitotic control of dTTP pool: a necessity or coincidence?

The fidelity of DNA replication in eukaryotic cells requires a balanced dNTP supply in the S phase. During the cell cycle progression, the production of dTTP is highly regulated to coordinate with DNA replication. Intracellular thymidine is salvaged to dTTP by cytosolic thymidine kinase (TK1) and thymidylate kinase (TMPK), both of which expression increase in the G1/S transition and diminish in the mitotic phase via proteolytic destruction. Anaphase promoting complex/cyclosome (APC/C)-mediated ubiquitination targets TK1 and TMPK to undergo proteasomal degradation in mitosis, by which dTTP pool is minimized in the early G1 phase of the next cell cycle. In this review, we will focus on regulation of TK1 in the post-S phase and the importance of mitotic proteolysis in controlling dNTP balance, replication stress and genomic stability. Finally, we discuss how thymidine pool and oligomeric forms of TK1 can affect mitotic control of dTTP. This article is for the special issue of IMB 20^th anniversary.     

Insulin-like growth factor I (Igf-1) gene polymorphism in patients with non-metastatic breast cancer

We aimed to assess the association between IGF-I gene (CA repeats) polymorphism in breast cancer patients and their clinicopathological features, as well as disease recurrence and survival. Seventy-six non-metastatic breast cancer patients were enrolled in the present study. The IGF-I (CA) repeats were studied with polymerase chain reaction by using proper primers belonging to these gene areas from DNA samples. Results show that the non 19- non 19 homozygote were more common in patients without lymph node involvement (p=0.04), with low histological grade (p=0.04), with positive hormone receptor status (p=0.01), and in patients without recurrence (p=0.06). These results suggest that the non 19-non 19 carriers have some favorable prognostic factors, and IGF-I gene polymorphism (CA repeats) may affect disease recurrence and overall survival.     

Enzymatic incorporation and fluorescent labelling of cyclooctyne-modified deoxyuridine triphosphates in DNA

The amino group of 5-aminopropargyl-2′-deoxyuridine-5′-triphosphate was labelled with dibenzocyclooctyne (DIBO) and two derivatives of bicyclo [6.1.0] non-4-yne (BCN) with short and long linkers to produce three different cycloalkyne-modified deoxyuridine triphosphates. BCN was successfully incorporated into DNA at multiple sites by enzyme-mediated primer extension and the polymerase chain reaction (PCR). Efficient fluorescent labelling of the BCN-DNA and DIBO-DNA with Cy3-azide was demonstrated.     

Semaphorin-plexin signalling genes associated with human breast tumourigenesis

Introduction

Gene expression profiling has enabled us to demonstrate the heterogeneity of breast cancers. The potential of a tumour to grow and metastasise is partly dependant on its ability to initiate angiogenesis or growth and remodelling of new blood vessels, usually from a pre-existing vascular network, to ensure delivery of oxygen, nutrients, and growth factors to rapidly dividing transformed cells along with access to the systemic circulation. Cell-cell signalling of semaphorin ligands through interaction with their plexin receptors is important for the homeostasis and morphogenesis of many tissues and has been widely studied for a role in neural connectivity, cancer, cell migration and immune responses. This study investigated the role of four semaphorin/plexin signalling genes in human breast cancers in vivo and in vitro.

Materials and methods

mRNA was extracted from formalin fixed paraffin embedded archival breast invasive ductal carcinoma tissue samples of progressive grades (grades I-III) and compared to tissue from benign tumours. Gene expression profiles were determined by microarray using the Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and validated by Q-PCR using a Corbett RotorGene 6000. Following validation, the gene expression profile of the identified targets was correlated with those of the human breast cancer cell lines MCF-7 and MDA-MD-231.

Results

The array data revealed that 888 genes were found to be significantly (p ≤ 0.05) differentially expressed between grades I and II tumours and 563 genes between grade III and benign tumours. From these genes, we identified four genes involved in semaphorin-plexin signalling including SEMA4D which has previously been identified as being involved in increased angiogenesis in breast cancers, and three other genes, SEMA4F, PLXNA2 and PLXNA3, which in the literature were associated with tumourigenesis, but not directly in breast tumourigenesis. The microarray analysis revealed that SEMA4D was significantly (P = 0.0347) down-regulated in the grade III tumours compared to benign tumours; SEMA4F, was significantly (P = 0.0159) down-regulated between grades I and II tumours; PLXNA2 was significantly (P = 0.036) down-regulated between grade III and benign tumours and PLXNA3 significantly (P = 0.042) up-regulated between grades I and II tumours. Gene expression of SEMA4D was validated using Q-PCR, demonstrating the same expression profile in both data sets. When the sample set was increased to incorporate more cases, SEMA4D continued to follow the same expression profile, including statistical significance for the differences observed and small standard deviations. In vitro the same pattern was present where expression for SEMA4D was significantly higher in MDA-MB-231 cells when compared to MCF-7 cells. The expression of SEMA4F, PLXNA2 and PLXNA3 could not be validated using Q-PCR, however in vitro analysis of these three genes revealed that both SEMA4F and PLXNA3 followed the microarray trend in expression, although they did not reach significance. In contrast, PLXNA2 demonstrated statistical significance and was in concordance with the literature.

Discussion

We, and others, have proposed SEMA4D to be a gene with a potentially protective effect in benign tumours that contributes to tumour growth and metastatic suppression. Previous data supports a role for SEMA4F as a tumour suppressor in the peripheral nervous system but our data seems to indicate that the gene is involved in tumour progression in breast cancer. Our in vitro analysis of PLXNA2 revealed that the gene has higher expression in more aggressive breast cancer cell types. Finally, our in vitro analysis on PLXNA3 also suggest that this gene may have some form of growth suppressive role in breast cancer, in addition to a similar role for the gene previously reported in ovarian cancer. From the data obtained in this study, SEMA4D may have a role in more aggressive and potentially metastatic breast tumours.

Conclusions

Semaphorins and their receptors, the plexins, have been implicated in numerous aspects of neural development, however their expression in many other epithelial tissues suggests that the semaphorin-plexin signalling system also contributes to blood vessel growth and development. These findings warrant further investigation of the role of semaphorins and plexins and their role in normal and tumour-induced angiogenesis in vivo and in vitro. This may represent a new front of attack in anti-angiogenic therapies of breast and other cancers.