Shotgun sequencing of the human transcriptome with ORF expressed sequence tags

Theoretical considerations predict that amplification of expressed gene transcripts by reverse transcription-PCR using arbitrarily chosen primers will result in the preferential amplification of the central portion of the transcript. Systematic, high-throughput sequencing of such products would result in an expressed sequence tag (EST) database consisting of central, generally coding regions of expressed genes. Such a database would add significant value to existing public EST databases, which consist mostly of sequences derived from the extremities of cDNAs, and facilitate the construction of contigs of transcript sequences. We tested our predictions, creating a database of 10,000 sequences from human breast tumors. The data confirmed the central distribution of the sequences, the significant normalization of the sequence population, the frequent extension of contigs composed of existing human ESTs, and the identification of a series of potentially important homologues of known genes. This approach should make a significant contribution to the early identification of important human genes, the deciphering of the draft human genome sequence currently being compiled, and the shotgun sequencing of the human transcriptome.

Association of the alpha-spectrin R28H mutation with allele alphaLELY and with alphaI/alphaII domain haplotypes in three Brazilian families

We have studied three Brazilian kindreds presenting spectrin alpha/74 hereditary elliptocytosis (HE) due to a G-->A substitution, responsible for the R28H mutation. The mutant allele was associated with alphaI domain haplotype 1 (XbaI-/MspI-/PvuII+) in all three families and with two different alphaII domain haplotypes (1/RIT, 4/RVR). This result may reflect that this mutation occurs in a "hot spot" and may have arisen more than once or that a crossing over event may have occurred between the two domains studied. We detected one new haplotype in the alphaI domain (haplotype 3 -XbaI(+)/MspI(-)/PvuII(+)). The mutant allele was associated with the lack of the alphaII domain Alu insertion in all three cases. Allele alphaLELY, detected by PCR and restriction enzyme digestion, was present in the heterozygous form in patient 1 (alphaHE/alphaLELY) and in the homozygous form in patients 2 and 3(alphaHE-LEL/alphaLELY). It was found to be associated with domain haplotypes I (RIT) and 4 (RVR) and with the presence and absence of the Alu insertion. This may have arisen through recombination events, since this polymorphism is located in the alphaIV-alphaV domain junction, which is far distant from the alphaII domain.

Frequencies of platelet-specific alloantigen systems 1-5 in three distinct ethnic groups in Brazil

The human platelet antigen (HPA) systems are related to immune platelet disorders as well as to the development of occlusive vascular disease. Several distinct biallelic HPA systems are known, and a heterogeneous distribution of HPA alleles has been described among distinct ethnic groups. In this study we genotyped 320 carefully selected individuals from three distinct ethnic groups in Brazil (Caucasians, Blacks and Amazonian Indians) for the HPA-1, -2, -3, -4 and -5 systems. A similar prevalence for all HPA alleles was found in Brazilians of Caucasian and Black descent. These data contrast with those reported for similar ethnic groups in other countries. Among the Amazonian Indians, no b allele of the HPA-1, -4 and -5 systems was identified. The data presented here could be useful in the diagnosis of alloimmune platelet disease, in genetic counselling and in the development of screening programmes for HPA-related diseases.

Mutation analysis of the HFE gene in Brazilian populations

We analyzed the frequency of the C282Y and H63D mutations in the HFE gene in 227 individuals from Brazil comprising 71 Caucasians, 91 racially mixed Caucasian African-derived Amerindians (both populations from Southeast Brazil), 85 African-derived subjects (from Northeast Brazil) and 75 Parakanã Indians. Allelic frequency of the mutation C. 845G(A (C282Y) was 1.4% in the Caucasian population, 1.1% in the African-derived population, 1.1% in the racially mixed normal controls and 0% in the Parakanã Indians. In the African-derived population, the C282Y mutation was present on chromosomes bearing the haplotype 6/1h according to Beutler and West (1997). Allelic frequency of the mutation C. 187C(G (H63D) was 16.3% in the Caucasian population, 7.5% in the African-derived population, 9.8% in the racially mixed controls and 0% in the Amerindians. The presence of these mutations in the African-derived population reflects the fact that these subjects may have undergone a non-identified racial admixture in their past history. The absence of both defects in the Amerindians suggests that these mutations have emerged after the migration of Polynesians to America, or that they may not have reached the Polynesian population until after the migration to America had occurred.

Detection of cytomegalovirus infections by PCR in renal transplant patients

Cytomegalovirus (CMV) is the single most important infectious agent affecting recipients of organ transplants. To evaluate the incidence and the clinical importance of CMV infection in renal transplants in Brazil, 37 patients submitted to renal allograft transplants were tested periodically for the presence of cytomegalovirus DNA in urine using the polymerase chain reaction (PCR), and for the presence of IgM and IgG antibodies against CMV by enzyme-linked immunosorbent assay (ELISA) and indirect immunofluorescence (IIF). The PCR-amplified products were detected by gel electrophoresis and confirmed by dot-blot hybridization with oligonucleotide probes. Thirty-two of the 37 patients (86.4%) were positive by at least one of the three methods. In six patients, PCR was the only test which detected the probable CMV infection. Ten patients had a positive result by PCR before transplantation. In general, the diagnosis was achieved earlier by PCR than by serologic tests. Active infection occurred more frequently during the first four months after transplantation. Sixteen of the 32 patients (50%) with active CMV infection presented clinical symptoms consistent with CMV infection. Five patients without evidence of active CMV infection by the three tests had only minor clinical manifestations during follow-up. Our results indicate that PCR is a highly sensitive procedure for the early detection of CMV infection and that CMV infection in renal transplant patients is a frequent problem in Brazil.

Spontaneous erythroid colony formation in Brazilian patients with sickle cell disease

The ability of circulating progenitor cells to develop erythroid colonies was studied in vitro in the presence or absence of growth factors (5637-CM and erythropoietin) in 63 patients with sickle cell disease (SCD) (36 homozygotes for hemoglobin [Hb] S, 13 double heterozygotes for Hb S and beta thalassemia, and 14 SC patients) in Southeast Brazil. In the presence of growth factors, SCD patients (all genotypes) presented significantly higher numbers of circulating burst-forming unit-erythroid (BFU-E/5 x 10(5) MNC), when compared with control subjects. However, when the progenitor cells were cultured in the absence of added stimulus, high numbers of BFU-E were observed only in the genotypes SS and S/beta thalassemia. SC patients presented a similar response to the control subjects. Moreover, there was an inverse correlation between spontaneous (without stimulus) BFU-E and Hb levels in SCD patients. These results suggest that the formation of spontaneous BFU-E observed in SCD may be due to an expanded erythropoiesis secondary to hemolysis.

Lutzomyia longipalpis: pH in the gut, digestive glycosidases, and some speculations upon Leishmania development

Screening for digestive glycosidases in different parts of the gut and associated organs of Lutzomyia longipalpis is reported. Searches for the enzymes were made in blood-fed and non-blood-fed females and the enzymes were characterized as soluble or membrane-bound molecules. A total of four different activities were detected, corresponding to the following specificities: an alpha-glucosidase, an N-acetyl-beta-d-glucosaminidase, an N-acetyl-beta-d-galactosaminidase, and an alpha-l-fucosidase. Their possible role and importance for Leishmania development are discussed and the alpha-glucosidase enzyme was partially characterized. The pH inside the gut of non-blood-fed phlebotomines was measured with pH indicator dyes. The pH ranges obtained for crop, midgut, and hindgut were, respectively, higher than pH 6, pH 6, and lower than pH 6. A hypothesis concerning these data and Leishmania development is proposed.

The relationship of bone marrow histology with the molecular pattern in chronic myeloid leukemia

The chromosomal abnormality in chronic myeloid leukemia (CML) results from a reciprocal translocation between chromosomes 9 and 22 transferring the c-abl proto-oncogene from chromosome 9 to the restricted breakpoint region on chromosome 22 M (bcr). In this study the breakpoint was determined within the M-bcr in 35 CML patients in the chronic phase, by Southern blotting analysis, and it was then correlated with bone marrow Granulocytic-Megakaryocytic (GRAN-MEG) and Granulocytic (GRAN) histological subgroups, as well as with the clinical findings and laboratory parameters. In the 35 patients analyzed, 46% were grouped as 5' and 54% as 3'. There was an increase in bone marrow basophils in 5' breakpoint patients compared to 3' breakpoint (p = 0.042) but the M-bcr breakpoint site did not differ significantly in the subgroup GRAN or GRAN-MEG (p = 0. 12). In conclusion, the patient population had a higher frequency of M-bcr breakpoint in zone 4 and 3' position; there was no correlation between 5' and 3' positions and clinical or haematological features, except a significant increase in bone marrow basophil cells in 5' breakpoint patients compared to 3' breakpoint. Although a higher frequency of the 3' breakpoint was found in patients with a low number of megakaryocytes compared to the cases with a granulocytic-megakaryocytic proliferation, this difference was not statistically significant.

Prevalence of homozygosity for the deleted alleles of glutathione S-transferase mu (GSTM1) and theta (GSTT1) among distinct ethnic groups from Brazil: relevance to environmental carcinogenesis?

Environmental related diseases due to occupational carcinogens and toxic substances are a serious problem particularly in developing countries. The glutathione S-transferase system is fundamental for the detoxification of numerous carcinogens and mutagens. The individual inherited susceptibility to chemical carcinogenesis due to glutathione S-transferase mu (GSTM1) and theta (GSTT1) varies significantly among distinct ethnic groups. In this study we determined the prevalence of the null genotype of the GSTM1 and GSTT1 genes among individuals from three distinct Brazilian racial groups using a multiplex-PCR methodology. The results showed that the highest prevalence of the null genotype for the GSTM1 occurred among Caucasians (55%, allele frequency = 0.74), followed by 33% among Brazilian Black subjects (allele frequency = 0.57), and 20% among Amazonian Indians (allele frequency = 0.45). For GSTT1 a homogenous distribution of the null genotype was found among Caucasian and African descendants (18.5 and 19% homozygotes, respectively, allele frequency = 0.43), with a lower prevalence among Amazonian Indians (11% of homozygotes, allele frequency = 0.34). Whether the deficiency of the GST system contributes to a predisposition to environmental related carcinogenesis in specific populations in Brazil remains to be determined.

Molecular analysis of the retinoblastoma (RB1) gene in acute myeloid leukemia patients

The pathogenesis of acute leukemia is still poorly understood. In the past few years several groups have reported deletion of the RB1 gene or altered pRB expression in certain hematologic malignancies, suggesting a possible role of RB1 gene inactivation in the process of leukemogenesis. Most studies regarding structural abnormalities of the RB1 gene indicate that gross deletions or rearrangements are present in a small percentage of patients with acute myeloid leukemia (AML), as is the case with retinoblastoma, where the majority of RB1 gene abnormalities are attributed to point mutations. To investigate if such point mutations in the RB1 gene may have a role in leukemogenesis in AML, we screened the RB1 gene of 36 AML patients using conformation-sensitive gel electrophoresis (CSGE). No point mutations were found in the 27 exons, their flanking intron regions or in the promoter region in any of the 36 patients. Thus, according to our findings, the susceptibility in these patients for developing AML does not appear to be related to point mutations in the RB1 gene. While screening for point mutations, we identified a number of new and previously noted neutral sequence variations indicating the efficiency and sensitivity of CSGE in identifying small changes in the RB1 gene.

Prothrombin mutant, factor V Leiden, and thermolabile variant of methylenetetrahydrofolate reductase among patients with sickle cell disease in Brazil

The prevalence of the prothrombin gene variant (allele 20.210 A), factor V Leiden mutation, and homozygosity for transition 677C-->T in the methylenetetrahydrofolate reductase (MTHFR) gene was determined among patients with sickle cell disease (SCD). The group included 73 patients with median age of 32.3 years with a diagnosis of sickle cell anemia in 53 patients, hemoglobinopathy SC in 16 patients, and four with S/beta(0) thalassemia. Vascular complications such as ischemic stroke or deep vein thrombosis were diagnosed in nine patients. Heterozygosity for the prothrombin gene variant or factor V Leiden mutation was identified in four patients. However, only one patient, who developed ischemic stroke, was identified as a carrier of factor V Leiden mutation. None of the patients presented homozygosity for the thermolabile variant of the MTHFR. These data suggest a low clinical impact of inherited hypercoagulability risk factors in developing thrombosis, occlusive stroke, or mortality data among patients with SCD in Brazil.

Prevalence of the mutation C677 --> T in the methylene tetrahydrofolate reductase gene among distinct ethnic groups in Brazil

Vascular disease is a serious public health problem in the industrialized world, and is a frequent cause of death among the adult population of Brazil. Mild hyperhomocysteinemia has been identified as a risk factor for arterial disease, venous thrombosis, and neural tube defects. Individuals homozygous for the thermolabile variant of methylenetetrahydrofolate reductase (MTHFR-T) are found in 5-15% of the general population and have significantly elevated plasma homocysteine levels which represent one of the genetic risk factors for vascular diseases. We have analyzed the prevalence of individuals homozygous for the MTHFR-T in 327 subjects representing the three distinct ethnic groups in Brazil. The prevalence of homozygotes for the mutated allele MTHFR-T was high among persons of Caucasian descent (10%) and considerably lower among Black (1.45%) and Indians persons populations (1.2%). These data suggest that screening for the MTHFR-T allele should help in identifying individuals with a high risk of vascular disease among populations with a heterogeneous background.

Increased tyrosine phosphorylation of band 3 in hemoglobinopathies

In order to investigate the tyrosine phosphorylation of band 3, we performed immunoblotting of intact red cells using anti-phosphotyrosine antibody of 21 patients with sickle cell disorders (11 SS, 5 Sbeta, 5 SC), 7 patients with beta thalassemias (5 beta thal intermedia, 2 deltabeta thal), 10 normal controls, and 1 patient with hereditary spherocytosis. They had not received transfusion for the last 4 months and all were clinically stable. Our results showed an increased tyrosine phosphorylation of two proteins, in the 100 and 80 kD regions, in sickle cell and beta-thalassemic red cells when compared to the normal controls and to the patient with hereditary spherocytosis. Immunoprecipitation of the lysed red cells with anti-band 3 antibody and immunoblotting with anti-phosphotyrosine antibody confirmed that the 100 kD tyrosine phosphorylated protein was band 3. In the sickle cell disease group, the band 3 tyrosine phosphorylation varied from 2- to 10-fold increase compared to control (x +/- SD; SS = 7.8- +/- 2.7-fold; SC = 3.8- +/- 1.3-fold; Sbeta = 5.2- +/- 2.0-fold). It was also higher in the beta-thalassemic group (beta-thal = 4.3- +/- 3.7-fold). There was no significant difference in tyrosine phosphorylation among the various groups tested, except when we compared the phosphorylation in intact red cells of patients with sickle cell anemia and hemoglobinopathy SC (U = 6, P < 0.02). The tyrosine phosphorylation of band 3 was increased in hemoglobinopathies even in the absence of high reticulocyte count. At least two mechanisms might be involved in the increased tyrosine phosphorylation of band 3 in these hemoglobin disorders, probably related to the endogenous reactive oxygen intermediates generated by the abnormal erythrocyte: an inhibition of protein tyrosine phosphatase activity or an activation of the protein tyrosine kinase p72syk.

Haplotype analysis and Agamma gene polymorphism associated with the Brazilian type of hereditary persistence of fetal hemoglobin

We have identified three unrelated individuals and three members of a family with the non-deletion form of Agamma-hereditary persistence of fetal hemoglobin (HPFH). Molecular analysis showed that each individual is a heterozygote for a previously described -195 Agamma (C-->G) mutation. The beta-globin gene cluster was studied using the polymerase chain reaction and related techniques. Haplotyping using nine restriction sites identified two closely related chromosomes with the -195Agamma mutation, differing only in a single site 3' to the beta-globin gene. Further analysis of beta-globin framework indicated that the HPFH allele segregates with haplotype V, according to Orkin's classification. The second haplotype probably originated by a point mutation or DNA rearrangement of a pre-existing -195Agamma chromosome. We also determined the sequences from -622 to +55 bp upstream to the Agamma gene and part of the Agamma IVS-2. We found four polymorphisms associated to the -195Agamma promoter region. All -195Agamma chromosomes had a G at positions -588 and +25 relative to the Agamma gene. One individual was also homozygous for polymorphisms at -398 (G-->A), and another at -369 (C-->G). Cloning and sequencing of the polymorphic patterns of the 3' region of Agamma IVS-2 showed that the mutated allele is linked to beta-globin chromosome B. Some correlations between chromosome characteristics and Agamma point mutations were also observed.

Genetic analysis of beta-thalassemia major and beta-thalassemia intermedia in Brazil

The development of methodologies to identify the molecular lesions responsible for different types of beta-thalassemia has made it possible to correlate these data with clinical and hematological severity. We examined DNA from 35 patients with beta-thalassemia, residents of the State of São Paulo, Brazil, for some types of genetic modifying factors: beta-thalassemia mutations, the upstream Xmnl GY-globin gene polymorphisms, and alpha-globin gene deletions. Additionally, the beta-like gene cluster haplotypes and the presence of the AYT variant were studied. The following mutations were present in the 70 chromosomes studied: 54.3% codon 39 (C-->T) (beta degree); 18.6% IVS-I-6 (T-->C) (beta+); 18.6% IVS-I-110 (G-->A) (beta+), and 4.3% IVS-I-1 (G-->T) (beta degree). Haplotype II was associated with the nonsense mutation at codon 39, haplotype I with the IVS-I-110 and codon 39 mutations, and haplotypes VI and VII with the IVS-I-6 mutation. The Xmnl polymorphism was detected in three out of 31 patients studied. No alpha-thalassemia was detected among the thalassemia intermedia patients. The AYT variant was present in 87.1% of 31 thalassemia patients and was associated with the codon 39/haplotype II and IVS-I-6/haplotype VI mutations. This is the first study of the Brazilian population that has analyzed the beta-thalassemia mutations and other molecular variants, and has correlated them with the clinical manifestations.

Early circulating erythroid progenitor cells and expression of erythropoietin receptors in sickle cell disease

The ability of circulating progenitor cells from 22 patients with sickle cell disease (SCD) to develop erythroid colonies was studied in vitro in the presence or absence of growth factors (5637-CM and erythropoietin). In both conditions, SCD patients presented significantly higher numbers of circulating burst-forming unit-erythroid (BFU-E/5x10[5]MNC) when compared to control subjects. The study of the expression of erythropoietin receptors revealed an increased level in SCD patients. Moreover, there was a correlation between both stimulated and autocrine (without stimulus) BFU-E and the expression of erythropoietin receptors. These results are of particular interest since they indicate that the phenomenon of spontaneous BFU-E-derived colonies observed in SCD patients may be due to an increased expression of erythropoietin receptors.

Presence of allele alphaLELY in an Amazonian Indian population

Allele alphaLELY is a low-expression allele of the erythroid spectrin alpha-chain that is characterized by a C --> G mutation at position alpha1857 in exon 40 and a C --> T (nt -12) mutation in intron 45. This second mutation is probably responsible for the partial skipping of exon 46. This exon is essential for the nucleation of the alpha-chains by the beta-chains during erythropoeisis. Although allele alphaLELY remains asymptomatic in both heterozygotes and homozygotes, it enhances the expression of deleterious alpha-alleles that occur and, as such, has clinical importance. In this study, the frequency of allele alphaLELY was estimated in two ethnically different Brazilian populations: a random sample of blood donors from Campinas, a city located in São Paulo State, in the southeastern region of Brazil, and a sample of Parakanã Indians (Tupi tribe), a very isolated population with a high degree of inbreeding. The frequency of allele alphaLELY in the blood donor's sample (n = 54) was 24.1% whereas in the indigenous sample (n = 41), it was 15.9%. These frequencies were not significantly different at the 5% level (chi2 = 1.931). Similarly, when the frequencies of our samples were compared with those of the four ethnic groups studied by Maréchal et al. [Br J Haematol 90:553-556, 1995], no significant differences were found at the 5% level (chi2 = 6.686). These results suggest that allele alphaLELY is a very ancient allele since it occurs with a relatively uniform and high frequency in all human ethnic groups studied so far. These findings confirm the importance of allele alphaLELY in influencing the expression of deleterious alpha-spectrin alleles. To our knowledge, these are the first data concerning allele alphaLELY in native Americans.