TNF-alpha promoter single nucleotide polymorphisms are markers of human ancestry

We present a map of single nucleotide polymorphisms (SNPs) in the human tumor necrosis factor (TNF)-alpha promoter based upon exploratory sequencing of 333 human TNF-alpha gene promoters from individuals of distinct ancestral backgrounds. We detect 10 TNF-alpha promoter SNPs that occur with distinct frequencies in populations of different ancestry. Consistent with these findings, we show that two TNF-alpha SNPs, the -243 SNP and the -856 SNP, are the first SNP markers of a sub-Saharan African-derived extended haplotype and an Amerindian HLA haplotype, respectively. Comparisons of TNF-alpha promoter SNP allele frequencies can thus help elucidate variation of HLA haplotypes and their distribution among existing ethnic groups and shed light into the history of human populations.

Hepatitis B surface antigen- and tetanus toxoid-specific clonal expansion of CD4+ cells in vitro determined by TCRBV CDR3 length and nucleotide sequence

We demonstrate activation of primary human TCRBV-specific CD4+ cells in vitro towards hepatitis B surface antigen (HBsAg) and tetanus toxoid (TT) without the use of cell lines, clones or added cytokines. By multiplex PCR analysis and spectratyping, antigen-activated cells exhibited clonal T cell receptor expansion within specific and limited TCRBV families. The expanded CD4+ T cells were CD45RO. Three of four unrelated HBsAg responders showed CD4+ expansion within the TCRBV16 family. The response comprised predominantly single CDR3 sequences in all three donors and was completely monoclonal in one of them. However, the CDR3 lengths and sequences differed among the responders. Clonality induced by HBsAg in TCRBV16 was specific, reproducible and distinct from that induced by TT in terms of sequence, nucleotide addition and diversity (BD) or junctional (BJ) element usage. Thus, for the first time, we show monoclonal or oligoclonal expansion of primary human CD4- peripheral blood mononuclear cells (PBMC) in vitro in response to nominal protein antigen without manipulations utilizing exogenous IL-2. The ability to induce monoclonal/ oligoclonal responses to HBsAg now permits motif identification studies for determining the T cell role in nonresponsiveness to the HBsAg vaccine.

HLA-DRB1 leprogenic motifs in nigerian population groups

Amino acid residues involved in the peptide binding groove of HLA-DRB1 alleles were examined in three Nigerian ethnic groups with leprosy (n = 287) and 170 controls to determine the role of DRB1 alleles in disease outcome with Mycobacterium leprae. Nine positively charged motifs and two others with neutral charge to the binding groove were detected. These motifs occurred more frequently in leprosy (leprogenic) than was expected by chance (P < 0.0001). In contrast, five motifs with net negative or 'modified' neutral charges to the pocket were negatively associated with leprosy. We conclude that clinical outcome of infection with M. leprae is largely determined by a shared epitope in DRB1 alleles marked by several motifs. These motifs occur in otherwise normal DRB1 alleles, characterized by net positive or neutral charges in the binding groove. We hypothesize that these polarities cause poor binding of DRB1 to M. leprae. On presentation, the signal via the T cell receptor results in muted cell-mediated immunity. The resulting response translates to various forms of leprosy depending on degree of charge consonance between M. leprae and host DRB1 allele. Other factors within or without the HLA complex, such as the T cell receptor repertoire, may also influence the resulting disease.

Carboxyhaemoglobin levels in some Lagos dwellers--a pilot study

Carboxyhaemoglobin (COHb) concentrations were determined by differential spectrophotometry in blood of 60 healthy adult subjects from various locations in Lagos. Half of these were either occasional or regular tobacco cigarette smokers. Our findings showed that the Lagos dweller has elevated COHb concentration ranging between 7.6%-9.9%, several folds higher than permitted by Air Quality Standards. The range and scatter of COHb in smokers were wider (7.4%-13.0%) than in non smokers. In particular, COHb concentrations were significantly higher in regular smokers than in non smokers by Fisher's exact test (p < 0.0006). Elevated COHb concentrations among smokers were related to frequency of tobacco use (p < 0.01). There was however no statistically significant difference in COHb concentrations when the regular and occasional smokers were taken as a group and compared with the non smokers. Haematocrit measurements showed that a degree of anaemia was present in most of the subjects tested irrespective of smoking status (mean packed cell volume = 36.1). It is inferred from this data that the Lagos dweller has high ambient concentrations of COHb and that these may be further aggravated by cigarette smoking.

HLA class I phenotype and gene frequencies in parts of southern Nigeria

HLA-A, B and C antigens were determined in 101 healthy subjects from two major and several minor ethnic groups in some parts of Southern Nigeria. Compared to earlier data based on a panel of expatriate Nigerians, significant differences were observed in antigen phenotype and gene frequencies particularly at the HLA-A locus. At least three antigenic specificities not previously observed in the expatriate Nigerians were detected in the present study. These included HLA-B8. B14 and CW1. These antigens however occurred at low frequencies. The antigens A23 and B7 were in positive linkage disequilibrium along with others which involved CW4 with B53 or B35. It is concluded from our findings that HLA polymorphisms in Nigerians may not be completely reflected in major population group studies alone. It is possible that more specificities may be detected by continued testing of the minor ethnic groups. The importance of this could be immense in disease association studies involving HLA genes as well as in anthropology.

IgG2 associated hypergammaglobulinaemia in some Nigerians with HIV infection

Concentrations of immunoglobulins (IgA, IgG and IgM) were measured in Nigerians with (HIV) infection. Considerable elevations up to two-fold the reference values were observed for IgG and IgM in the patient group as a whole but elevations in IgA concentration were least marked albeit significantly different from the healthy subjects. Elevation of a particular isotype was not always concomitant with elevation of the other major classes in the same patient. Overall, these elevations were observed in both symptomatic and asymptomatic infected subjects. Further analysis of IgG hyperglobulinemia showed that increases in this major class may be due to increased IgG2 subclass concentrations. It is suggested that elevation of IgG2 subclass in Nigerians with HIV infection and not IgG1 or IgG3 may be due to genetic and environmental factors rather than variation in the strain of the virus.

Bf S gene frequency in Nigerians with HIV infection

Complement immunogenetic susceptibility to human immunodeficiency virus (HIV) infection was examined in 40 Nigerians with serological and/or clinical evidence of the infection. A mild increase in C4A null alleles (C4AQO) frequency was observed in the patient group compared to a group of healthy subjects (25 per cent vs 17 per cent) but overall the HIV infected and the reference groups did not differ significantly in the frequency of alleles of C4A or C4B. In contrast, properdin factor B (Bf) S gene frequency was significantly higher in the patients with HIV infection (p less than 0.025). There was a concomitant decrease in Bf F allele and gene frequencies (p less than 0.01, and p less than 0.05), respectively. Furthermore, blank Bf allotypes due to excessive complement consumption were detected in two asymptomatic patients. These findings suggest that Major Histocompatibility Complex (MHC) located complement genes may be important HIV infection. In particular Bf S gene or even C4AQO alleles may be permissive or influence outcome of infection with HIV.

Properdin factor B allotypes in diabetic Nigerians. A preliminary report on chromosome 6 markers

Properdin factor B(Bf) allotypes were determined in patients with insulin dependent (type 1) diabetes mellitus (n = 15); in patients with non-insulin dependent diabetes mellitus n = 15); and in healthy Nigerians (n = 252) from various tribal groups. In all three groups only commonly reported Bf allotypes namely BfF, F1, S and S1 were observed. More important, BfF1 allele was significantly increased in patients with insulin dependent (type 1) diabetes mellitus (expected 1/15, observed 5/15), X2 = P less than 0.005). It is suggested that this allele is probably the same as that reported in caucasoids and is part of a supratype or ancestral haplotype defined by HLA-B18, C4A3, C4A3, BQo, BfF1, DR3 marking type 1 (insulin dependent) diabetes mellitus.