Standardized protocols for differentiation of THP-1 cells to macrophages with distinct M(IFNγ+LPS), M(IL-4) and M(IL-10) phenotypes.

In vitro models of differing macrophage functions are useful since human monocyte-derived macrophages are short-lived, finite and vary from donor to donor. Published protocols using the promonocytic cell line THP-1 have tended to result in cells that closely resemble classically-activated macrophages, differentiated in IFNγ and LPS. However, no protocol, to date, has fully recapitulated polarization of THP-1 to the M(IL-4) or M(IL-10) macrophage phenotypes seen when human monocyte-derived macrophages are exposed to each cytokine. Here we present protocols that can be used to prepare M(IL-4) polarized THP-1 that transcribe CCL17, CCL26, CD200R and MRC1 and M(IL-10) cells which transcribe CD163, C1QA and SEPP1. We show that the inhibitory Fcγ Receptor IIb is preferentially expressed on the surface of M(IL-4) cells, altering the balance of activating to inhibitory Fcγ Receptors. Adoption of standardized experimental conditions for macrophage polarization will make it easier to compare downstream effector functions of different macrophage polarization states, where the impact of PMA exposure is minimized and rest periods and cytokine exposure have been optimized.

Inferring relative proportions of DNA variants from sequencing electropherograms.

MOTIVATION: Determination of the relative copy number of single-nucleotide sequence variants (SNVs) within a DNA sample is a frequent experimental goal. Various methods can be applied to this problem, although hybridization-based approaches tend to suffer from high-setup cost and poor adaptability, while others (such as pyrosequencing) may not be accessible to all laboratories. The potential to extract relative copy number information from standard dye-terminator electropherograms has been little explored, yet this technology is cheap and widely accessible. Since several biologically important loci have paralogous copies that interfere with genotyping, and which may also display copy number variation (CNV), there are many situations in which determination of the relative copy number of SNVs is desirable. RESULTS: We have developed a desktop application, QSVanalyzer, which allows high-throughput quantification of the proportions of DNA sequences containing SNVs. In reconstruction experiments, QSVanalyzer accurately estimated the known relative proportions of SNVs. By analyzing a large panel of genomic DNA samples, we demonstrate the ability of the software to analyze not only common biallelic SNVs, but also SNVs within a locus at which gene conversion between four genomic paralogs operates, and within another that is subject to CNV. AVAILABILITY AND IMPLEMENTATION: QSVanalyzer is freely available at http://dna.leeds.ac.uk/qsv/. It requires the Microsoft .NET framework version 2.0, which can be installed on all Microsoft operating systems from Windows 98 onwards. CONTACT: msjimc@leeds.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Ongoing activation of p53 pathway responses is a long-term consequence of radiation exposure in vivo and associates with altered macrophage activities.

The major adverse consequences of radiation exposure, including the initiation of leukaemia and other malignancies, are generally attributed to effects in the cell nucleus at the time of irradiation. However, genomic damage as a longer term consequence of radiation exposure has more recently been demonstrated due to untargeted radiation effects including delayed chromosomal instability and bystander effects. These processes, mainly studied in vitro, are characterized by un-irradiated cells demonstrating effects as though they themselves had been irradiated and have been associated with altered oxidative processes. To investigate the potential for these untargeted effects of radiation to produce delayed damaging events in vivo, we studied a well-characterized model of radiation-induced acute myeloid leukaemia in CBA/Ca mice. Haemopoietic tissues of irradiated CBA/Ca mice exhibit enhanced levels of p53 stabilization, increased levels of p21(waf1), and increased amounts of apoptosis, as expected, in the first few hours post-irradiation, but also at much later times: weeks and months after the initial exposure. Because these responses are seen in cells that were not themselves directly irradiated but are the descendants of irradiated cells, the data are consistent with an initial radiation exposure leading to persistently increased levels of ongoing DNA damage, analogous to radiation-induced chromosomal instability. To investigate the potential source of ongoing oxidative processes, we show increased levels of 3-nitrotyrosine, a marker of damaging nitrogen/oxygen species in macrophages. Not all animals show increased oxidative activity or p53 responses as long-term consequences of irradiation, but increased levels of p53, p21, and apoptosis are directly correlated with increased 3-nitrotyrosine in individual mice post-irradiation. The data implicate persistent activation of inflammatory-type responses in irradiated tissues as a contributory bystander mechanism for causing delayed DNA damage.

FcgammaRIIIA-158V and rheumatoid arthritis: a confirmation study.

OBJECTIVES: To develop a robust assay for genotyping the FcgammaRIIIA-158V/F polymorphism and to confirm the putative association between the FcgammaRIIIA-158V allele and rheumatoid arthritis (RA). METHODS: This allelic association study examined the FcgammaRIIIA-158V/F polymorphism for association with RA. A novel single-stranded conformational polymorphism assay was used to genotype 828 RA patients and 581 controls from the UK. RESULTS: The FcgammaRIIIA-158V allele was associated with both RA (P=0.02) and nodules (P=0.04). Individuals homozygous for this higher affinity allele had a significantly increased risk of RA (OR 1.53, 95% CI 1.08-2.18) and the development of nodules (OR 2.20, 95% CI 1.20-4.01). There was no evidence of an interaction with the shared epitope. CONCLUSIONS: We have developed a novel assay to genotype the FcgammaRIIIA-158F/V polymorphism and confirmed that homozygosity for the FcgammaRIIIA-158V allele is associated with UK Caucasian RA, particularly in those individuals with nodules, suggesting FcgammaRIIIA may play a role in determining disease severity or in the development of nodules per se.

The South Australian Breast X-Ray Service: results from a statewide mammographic screening programme.

The South Australian Breast X-Ray Service is a centralised breast cancer screening programme in the State of South Australia. In its first 5 years of operation nearly 100 000 screens were performed. This study reports the clinical performance of the programme and compares it with other published series. Women aged 40 years and over were screened with two-view mammography every 2 years. Radiologists double-read the screening films and multidisciplinary teams assessed the recalled women at a single centre. In the prevalent round 76 106 women were screened, and subsequently 21 506 of them were rescreened. The recall rate for further investigation was 4.9% in the prevalent round and 2.4% in the incident rounds. The cancer detection rate per 1000 women was 7.0 in the prevalent screening round and 3.4 in the incident rounds. Forty-two per cent of invasive carcinomas measured < or = 10 mm in the prevalent screening round and the median tumour size was 12 mm. The benign to malignant biopsy ratio was 1:1.4 in the prevalent round and 1:2.8 in the incident rounds. In the prevalent round 77% of invasive tumours were lymph node negative and this proportion increased to 86% in the incident rounds.