Allelic resolution NGS HLA typing of Class I and Class II loci and haplotypes in Cape Town, South Africa

The development of next-generation sequencing (NGS) methods for HLA genotyping has already had an impact on the scope and precision of HLA research. In this study, allelic resolution HLA typing was obtained for 402 individuals from Cape Town, South Africa. The data were produced by high-throughput NGS sequencing as part of a study of T-cell responses to Mycobacterium tuberculosis in collaboration with the University of Cape Town and Stanford University. All samples were genotyped for 11 HLA loci, namely HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3, -DRB4, and -DRB5. NGS HLA typing of samples from Cape Town inhabitants revealed a unique cohort, including unusual haplotypes, and 22 novel alleles not previously reported in the IPD-IMGT/HLA Database. Eight novel alleles were in Class I loci and 14 were in Class II. There were 62 different alleles of HLA-A, 72 of HLA-B, and 47 of HLA-C. Alleles A∗23:17, A∗43:01, A∗29:11, A∗68:27:01, A∗01:23, B∗14:01:01, B∗15:10:01, B∗39:10:01, B∗45:07, B∗82:02:01 and C∗08:04:01 were notably more frequent in Cape Town compared to other populations reported in the literature. Class II loci had 21 different alleles of DPA1, 46 of DPB1, 27 of DQA1, 26 of DQB1, 41 of DRB1, 5 of DRB3, 4 of DRB4 and 6 of DRB5. The Cape Town cohort exhibited high degrees of HLA diversity and relatively high heterozygosity at most loci. Genetic distances between Cape Town and five other sub-Saharan African populations were also calculated and compared to European Americans.

Radiosensitization mediated by a transfected anti-erbB-2 single-chain antibody in vitro and in vivo

PURPOSE

The erbB-2 receptor is overexpressed in several human cancers, including ovarian, prostate, and breast. We have developed plasmid and adenoviral vectors expressing an anti-erbB-2 single chain antibody (sFv), directed to the endoplasmic reticulum (ER) of target cells, that is cytotoxic to tumor cells overexpressing erbB-2 through induction of apoptosis. The anti-erbB-2 sFv also sensitizes erbB-2 overexpressing cells to the cytotoxic effects of cisplatin. On this basis, we hypothesized that human ovarian cancer cells expressing anti-erbB-2 sFv with downregulated erbB-2 product, p185erbB-2, also would be sensitized to ionizing radiation. Therefore, we designed experiments to test the ability of the anti-erbB-2 sFv to radiosensitize human ovarian cancer cells in vitro and in vivo.

METHODS AND MATERIALS

To test our hypothesis, we established subcutaneous (s.c.) tumors in the flanks of nude mice with SKOV3.ip1 human ovarian cancer cells and SKOV3 cells stably expressing the ER directed anti-erbB-2 sFv (SKOV3/pGT21). The tumors were treated with 10 Gy 60Co, or received no radiation. We then determined the regression rate, delay in regrowth, and time to tumor doubling of the tumors treated with radiation in the transfected group and controls. In addition, SKOV3.ip1 and SKOV3/pGT21 tumors were dissected from the irradiated animals and assayed for differences in p185erbB-2 expression at 12 weeks after irradiation by immunohistochemistry. Further, in vitro clonogenic survival assays were performed on the parental SKOV3.ip1 and SKOV3/pGT21 cell lines.

RESULTS

A statistical analysis of the combined data was done for two in vivo experiments. The analysis of the combined data showed that animals with irradiated tumor SKOV3/pGT21 had a significantly higher regression rate (p = 0.0055), longer delay in regrowth (p = 0.0001) and time to tumor doubling (p = 0.0004), than those animals with tumor SKOV3.ip1 that received radiation. We observed a similar significant effect for the same parameters in the unirradiated tumor SKOV3/pGT21 compared to unirradiated tumor SKOV3.ip1. Immunohistochemical analysis of the SKOV3/pGT21 tumor cells demonstrated focal accumulation of p185erbB-2 in scattered clumps of cells and less p185erbB-2 membrane expression than cells of SKOV3.ip1 tumors. However, SKOV3.ip1 and SKOV3/pGT21 cells had similar in vitro sensitivity to radiation.

CONCLUSIONS

These data support the hypothesis that tumors with reduced p185erbB-2 expression mediated by the anti-erbB-2 sFv are rendered more susceptible in vivo to the cytotoxic effects of ionizing radiation than tumors that maintain their normal expression of p185erbB-2. However, a similar effect was not observed with the same tumor cells in vitro. Thus, as has been described by others (1, 2), in vitro and in vivo results do not always correlate. Therefore, appropriate assays to assess clinical relevance need to be determined for each particular system studied.

Effect of high-fat diet on cholesterol distribution in plasma lipoproteins, cholesterol esterifying activity in leucocytes, and erythrocyte membrane components studied: importance of body weight

Effects of isocaloric changes in dietary fat on plasma lipoproteins and lipids and enzymes of erythrocytes and leucocytes were assessed. Subjects with a higher Brocca index showed increase in total and LDL cholesterol, significant reduction in HDL cholesterol, and increased total cholesterol:HDL cholesterol ratio after high-fat diet consumption. Due to high-fat diet feeding, erythrocyte membrane and leucocyte cholesterol and phospholipid contents were increased, cholesterol:phospholipid molar ratio was elevated, and erythrocyte enzymes (G6PD and 6PGD) and leucocyte enzymes (CEH and CES) were elevated. Erythrocyte membrane glycoprotein components showed marked increase, indicating possible alterations of membrane surfaces. The metabolic alterations were reversed slowly after resumption of the normal (low-fat) diet. Body weight plays an important role in the alterations in major lipoprotein cholesterol contents in response to changes in dietary fat composition. Cellular changes indicate alterations in structure and function of blood cells due to high-fat diet feeding.