Microarray profiles of ex vivo expanded hematopoietic stem cells show induction of genes involved in noncanonical Wnt signaling.

The low number of hematopoietic stem cells (HSC) in umbilical cord blood (UCB) is directly related to increased risk of transplant failure. Effective ex vivo expansion of HSC has been tried for many years, with conflicting results because of the inability to reproduce in vitro HSC proliferation in the same way it occurs in vivo. We compared freshly isolated HSC with their expanded counterparts by microarray analysis and detected activation of the noncanonical Wnt (wingless-type MMTV integration site family) pathway. Study of early alterations during ex vivo UCB-HSC expansion could contribute to improvement of ex vivo expansion systems.

Annexin A1 subcellular expression in laryngeal squamous cell carcinoma.

AIMS: Annexin A1 (ANXA1) is a soluble cytoplasmic protein, moving to membranes when calcium levels are elevated. ANXA1 has also been shown to move to the nucleus or outside the cells, depending on tyrosine-kinase signalling, thus interfering in cytoskeletal organization and cell differentiation, mostly in inflammatory and neoplastic processes. The aim was to investigate subcellular patterns of immunohistochemical expression of ANXA1 in neoplastic and non-neoplastic samples from patients with laryngeal squamous cell carcinomas (LSCC), to elucidate the role of ANXA1 in laryngeal carcinogenesis. METHODS AND RESULTS: Serial analysis of gene expression experiments detected reduced expression of ANXA1 gene in LSCC compared with the corresponding non-neoplastic margins. Quantitative polymerase chain reaction confirmed ANXA1 low expression in 15 LSCC and eight matched normal samples. Thus, we investigated subcellular patterns of immunohistochemical expression of ANXA1 in 241 paraffin-embedded samples from 95 patients with LSCC. The results showed ANXA1 down-regulation in dysplastic, tumourous and metastatic lesions and provided evidence for the progressive migration of ANXA1 from the nucleus towards the membrane during laryngeal tumorigenesis. CONCLUSIONS: ANXA1 dysregulation was observed early in laryngeal carcinogenesis, in intra-epithelial neoplasms; it was not found related to prognostic parameters, such as nodal metastases.

Expression differences of genes in the PI3K/AKT, WNT/b-catenin, SHH, NOTCH and MAPK signaling pathways in CD34+ hematopoietic cells obtained from chronic phase patients with chronic myeloid leukemia and from healthy controls.

PURPOSE: The fusion gene BCR-ABL has an important role to the progression of chronic myeloid leukemia (CML) and several signaling pathways have been characterized as responsible for the terminal blastic phase (BP). However, the initial phase, the chronic phase (CP), is long lasting and there is much yet to be understood about the critical role of BCR-ABL in this phase. This study aims to evaluate transcriptional deregulation in CD34+ hematopoietic cells (CD34+ cells) from patients with untreated newly diagnosed CML compared with CD34+HC from healthy controls. METHODS: Gene expression profiling in CML-CD34 cells and CD34 cells from healthy controls were used for this purpose with emphasis on five main pathways important for enhanced proliferation/survival, enhanced self-renewal and block of myeloid differentiation. RESULTS: We found 835 genes with changed expression levels (fold change ≥ ±2) in CML-CD34 cells compared with CD34 cells. These include genes belonging to PI3K/AKT, WNT/b-catenin, SHH, NOTCH and MAPK signaling pathways. Four of these pathways converge to MYC activation. We also identified five transcripts upregulated in CD34-CML patients named OSBPL9, MEK2, p90RSK, TCF4 and FZD7 that can be potential biomarkers in CD34-CML-CP. CONCLUSION: We show several mRNAs up- or downregulated in CD34-CML during the chronic phase.

Epidemiological studies in the information and genomics era: experience of the Clinical Genome of Cancer Project in São Paulo, Brazil.

Genomics is expanding the horizons of epidemiology, providing a new dimension for classical epidemiological studies and inspiring the development of large-scale multicenter studies with the statistical power necessary for the assessment of gene-gene and gene-environment interactions in cancer etiology and prognosis. This paper describes the methodology of the Clinical Genome of Cancer Project in São Paulo, Brazil (CGCP), which includes patients with nine types of tumors and controls. Three major epidemiological designs were used to reach specific objectives: cross-sectional studies to examine gene expression, case-control studies to evaluate etiological factors, and follow-up studies to analyze genetic profiles in prognosis. The clinical groups included patients' data in the electronic database through the Internet. Two approaches were used for data quality control: continuous data evaluation and data entry consistency. A total of 1749 cases and 1509 controls were entered into the CGCP database from the first trimester of 2002 to the end of 2004. Continuous evaluation showed that, for all tumors taken together, only 0.5% of the general form fields still included potential inconsistencies by the end of 2004. Regarding data entry consistency, the highest percentage of errors (11.8%) was observed for the follow-up form, followed by 6.7% for the clinical form, 4.0% for the general form, and only 1.1% for the pathology form. Good data quality is required for their transformation into useful information for clinical application and for preventive measures. The use of the Internet for communication among researchers and for data entry is perhaps the most innovative feature of the CGCP. The monitoring of patients' data guaranteed their quality.

Ten novel mutations in the phenylalanine hydroxylase gene (PAH) observed in Brazilian patients with phenylketonuria.

In the present study we report on the identification of ten novel mutations in the phenylalanine hydroxylase (PAH) gene of Brazilian patients with phenylketonuria (PKU): IVS5-54A>G, IVS6+17G>T, E205A, F240S, K274E, I318T, L321L, C357G, IVS11+17G>A and S411X. These mutations were detected during the characterization of the PAH genotypes of 115 patients with PKU from the southeast region of Brazil. The results obtained confirm the high heterogeneity of the PAH gene and provide information about the distribution of PKU mutations in the Brazilian population.

A functional single nucleotide polymorphism in the thrombin-activatable fibrinolysis inhibitor (TAFI) gene associates with outcome of meningococcal disease.

In meningococcal sepsis, disseminated intravascular coagulation with deposition of fibrin and formation of microthrombi occurs in various organs and enhanced inhibition of fibrinolysis is associated with adverse outcome. Recently, TAFI (thrombin-activatable fibrinolysis inhibitor) was identified as a link between coagulation and fibrinolysis, as TAFI can be activated by thrombin and once activated potently attenuates fibrinolysis. On the basis of this one would predict that DNA polymorphisms that increase TAFI activity would deteriorate the outcome in meningococcal sepsis. Therefore, we studied the prevalence of the Thr325Ile dimorphism in the TAFI gene, which is associated with increased TAFIa stability and activity in 50 patients who survived meningococcal disease, in 176 first-degree relatives of a consecutive patient series with meningococcal disease and 212 controls from the same geographic region. The TAFI 325 Ile/Ile genotype was slightly more common among parents of patients with meningococcal disease than in controls (11% vs. 7.1%, P= 0.24). This difference was pronounced among the subgroup of parents of non-surviving patients (19.2%, P= 0.03). Patients whose parents were carriers of the TAFI 325 Ile/Ile genotype had a 1.6-fold (95% CI 0.7-3.7) higher risk to contract meningococcal disease and a 3.1-fold (95% CI 1.0-9.5) increased risk to die from the infection compared with all other genotypes. Survivors had a genotype frequency (4.0%) that was lower than in the general population. TAFI 325 variants affect the outcome of meningococcal disease.

PCR template preparation for capillary DNA sequencing.

Fluorescence-based capillary DNA sequencing has facilitated the early completion of several complex sequencing projects. While capillary systems offer great benefits in terms of ease of use and automation, we find that they are sufficiently different from slab gel separation methodologies, demanding re-examination of the protocols used to generate and use DNA sequencing templates. We have recently initiated a large-scale Human Open Reading Frame EST project involving 30 laboratories feeding 11 MegaBace 1000 capillary sequencers. The group has already produced more than 300,000 valid sequences. The most successful template preparation protocol we have found is described here. We have found that a crucial step is the standardization of the quantity and quality of the templates, which have been achieved by overnight bacterial culture followed by PCR using limiting amounts of primers. Using this protocol, there is no need for post-PCR purification, and the final preparation cost is US $0.09/template. After sequencing 10,848 templates using this protocol, 78% of the reads were accepted (after discarding vectors without inserts and inserts smaller than 100 nucleotides), and 85% of the total number of bases had Phred scores of 15 or above.

Analysis of the 677 C-->T mutation of the methylenetetrahydrofolate reductase gene in different ethnic groups.

A recently described mutation in the methylenetetrahydrofolate reductase (MTHFR) gene (a C to T transition at nucleotide 677) is associated with a thermolabile phenotype and decreased enzyme activity. In homozygotes, the mutation is also related to hyperhomocysteinemia and increased risk for atherosclerotic disease and (apparently) venous thrombosis. The prevalence of this mutation in different human populations is unknown. We have investigated the frequency of the 677 C-->T mutation in the MTHFR gene in 337 individuals (674 chromosomes) belonging to four ethnic groups: Whites, African and Brazilian Blacks, Asians and Amerindians. The frequencies of the positive allele among Whites and Asians were similar to those previously reported for Caucasian populations. The positive allele seems to be slightly rarer among the Amerindians (frequency 24.0%) in comparison to Whites and Asians, with a heterogeneous distribution among the five Indian tribes analysed. In contrast, the mutation has a very low prevalence in Blacks, especially among the African Blacks, for whom the mutation was absent in homozygosity. Our data indicate that the 677 C-->T MTHFR mutation has a significantly heterogeneous distribution among different ethnic groups, a fact that may contribute to explain geographical or racial differences in the risk for vascular disease.

Ethnic heterogeneity of the factor XIII Val34Leu polymorphism.

A polymorphism in the coagulation factor XIII gene (FXIII Val34Leu) has been recently described to confer protection for arterial and venous thrombosis and to predispose to intracerebral hemorrhage. At present it is known that FXIII Val34Leu is prevalent in Caucasians, but information upon its distribution in different ethnic groups is scarce. We investigated the prevalence of FXIIIVal34Leu in 450 unrelated subjects of four ethnic groups: 97 Caucasians (Brazilians of European descent and Portuguese), 149 Blacks (Brazilians, and Africans from Cameroon, Zaire and Angola), 40 Asians (Japanese descendents) and 164 Amerindians from South America. PCR amplification of exon 2 of FXIII gene followed by MseI restriction-digestion was employed to define the genotypes. FXIIIVal34Leu was detected in 44.3% of the Caucasians, in 28.9% of the Blacks, in 2.5% of the Asians and in 51.2% of the Amerindians. These data confirm that FXIII Val34Leu is highly prevalent in Caucasians and indicate that it is rarer in populations of African origin. The very high frequency among Amerindians indicates that FXIII Val34Leu is not absent among Asians, and since it has a very low prevalence in Japanese, a heterogeneity in its distribution in Asia may be inferred. Taken together, our data showed that FXIII Val34Leu exhibits a significant ethnic heterogeneity, a finding that is relevant for studies relating this polymorphism with thrombotic and bleeding disorders.

Factor XIII Val34Leu is a genetic factor involved in the etiology of venous thrombosis.

A mutation in the factor XIII gene (FXIII Val34Leu) gene was recently reported to confer protection against myocardial infarction, but its relationship with venous thrombosis is unknown. In addition, a mutation in the 5'-untranslated region of the FXII gene (46 C->T) was identified which is associated with low plasma levels of the protein. Its prevalence in patients with venous thrombosis is also unknown. We investigated the frequency of the FXIII Val34Leu and FXII 46 C->T mutations in 189 patients with deep venous thrombosis and in 187 age-, gender- and race-matched controls. FXIII Val34Leu was detected in 38.6% of the patients and in 41.2% of the controls. Interestingly, homozygosity for the FXIII mutation was found in 1.6% of the patients and in 9.6% of the controls, yielding an odds ratio (OR) for venous thrombosis of 0.16 (95% CI: 0.05-0.5). The OR for heterozygotes was 1.1 (95% CI: 0.7-1.7). The FXII 46 C->T mutation was detected in 46.0% of the patients and in 48.6% of the controls. The OR for heterozygotes was 0.9 (95% CI: 0.6-1.4) and for homozygotes the OR was 0.8 (95% CI: 0.3-1.9). Our data indicate that the FXII 46 C->T mutation is unlikely to be a major risk factor for venous thrombotic disease. In contrast, the homozygous state for FXIII Val34Leu is a strong protective factor against venous thrombosis, which emerges as a novel genetic factor involved in the aetiology of thrombophilia.

Familial hypercholesterolemia in Brazil.

The Brazilian population has heterogeneous ethnic origins and is unevenly distributed in a country of continental dimensions. In addition to the Portuguese colonists until the end of the World War II Brazil received almost 5 million immigrants who settled mainly in the south and southeast. This features of the Brazilian population have two important consequences for the inherited diseases that are associated with an ethnic background: their frequencies are different in various regions of the country reflecting a variety of ethnic origins and variable degrees of admixtures. There was no report about the molecular basis of hypercholesterolemia in Brazil until our report in 1996 that the Lebanese allele is the most common cause of the disease in our country: 10 out of the 30 families were of Arab origin, and the Lebanese allele was detected in 9 of the 10 unrelated families of Arab origin. In addition, the abnormal gene is associated with the same haplotype at the LDL-R locus in all but one family, suggesting single origin for this mutation. Recently we described seven mutations in exons 4, 7, 12 and 14 and a new mutation in exon 15. In another region of our state, eight mutation already described and seven new mutations were described and interesting no common mutations were find. We can conclude that the complex history and structure of the Brazilian population, which was formed by the contribution of a large number of ethnic components that are in a state of increasing miscegenation, is reflected in the frequency and regional distribution of the more common hereditary diseases.

Gene polymorphisms in the TNF locus and the risk of myocardial infarction.

We investigated two genetic polymorphisms in the tumor necrosis factor locus (TNF-alpha -308 G-->A and LT-alpha +252 A-->G) as risk factors for coronary atherothrombotic disease (CAD) by determining its prevalence in 148 survivors of myocardial infarction (MI) with angiographically-proven severe CAD, and in 148 age-, gender- and race-matched controls. The odds ratio (OR) for MI related to the mutant TNF-alpha and LT-alpha alleles was 0.8 (CI95: 0.4-1.3) and 1. 3 (CI95: 0.8-2.0), respectively. We also sought interaction of smoking and metabolic risk factors for MI with each mutant genotype. Smokers not carrying the LT-alpha +252 A-->G mutation had a risk of MI of 2.7 (CI95: 1.4-5.4) whereas in smoking carriers the risk was 6. 9 (CI95: 3.4-14.1). An interactive effect of the LT-alpha mutation may also exist with dyslipidemia (OR for MI in non-carriers was 12 [CI95: 3.2-41.3] and in carriers the OR was 39, [CI95: 5.1-301] and with obesity (OR for MI was 2.7, [CI95: 1-7.2] in non-carriers and in carriers the OR was 6 [CI95: 2.1-16.8]). Lastly, the OR for MI in obese non-carriers of TNF-alpha -308 G-->A was 2.8 (CI95: 1.3-6) and in obese carriers the OR was 14.5 (CI95: 1.8-113). Although significant interactive effects could not be detected, the findings suggest that interaction of polymorphisms in the TNF locus with major risk factors for CAD may exist, and should be explored in larger studies.

Hereditary haemoglobin disorders in Brazil.

The data on the incidence and variability of hereditary haemoglobin (Hb) disorders in Brazil are reviewed. The most common abnormalities are HbS, HbC and beta-thalassaemias. Both homozygotes and compound heterozygotes for these genes (i.e., HbS/HbC disease, S/beta-thalassaemia, C/beta-thalassaemia) are common, owing to the free miscegenation of populations of Mediterranean and African ancestry. The diversity of beta-thalassaemias is similar to that observed in other regions. beta(0)-Thalassaemia is more frequent than the beta(+) variant among affected individuals. Most patients are descendants of Italian immigrants but occasional cases have other racial origins. Patients with thalassaemia major are mostly beta (0) homozygotes, while thalassaemia intermedia is more heterogeneous, including a variety of genotypes. alpha-Thalassaemias are not common although cases of HbH disease have been reported. Isolated examples of several Hb variants have been described, and two abnormal Hb were first found in Brazil: Hb Porto Alegre and Hb Niteroi.

An HbF enrichment procedure for the HPLC analysis of gamma chains.

A rapid and inexpensive method is described for the enrichment of fetal hemoglobin (HbF) which eliminates the interference of other hemoglobins in the HPLC analysis of gamma chains when HbF is less than or equal to 20-30% of the total Hb. The enrichment procedure, which is carried out on 1 ml hemolysate, is based on the alkaline denaturation of the other Hbs followed by Zn2+ precipitation. Samples are injected into the HPLC apparatus without further treatment. The method was validated by HPLC analysis of hemolysates with high levels of HbF and mixtures prepared by diluting the high HbF hemolysates with adult hemolysates. The relative proportions of gamma chains as well as their chromatographic behavior were unaltered by the HbF enrichment procedure. The method is illustrated by the analysis of hemolysates of normal newborns and of patients with thalassemia, sickle cell diseases and aplastic anemia containing 3.4 to 100% HbF. For the four hemolysates containing greater than 20% HbF, the same quantitative and chromatographic results were obtained by direct analysis and after enrichment. Although reproducible and accurate results were obtained for the enrichment method and HPLC analysis when HbF was greater than or equal to 3%, at lower concentrations the variability of both was unacceptably high, indicating the need for additional or improved methodology for hemolysates containing very low levels of HbF.

Hyperhomocysteinemia increases the risk of venous thrombosis independent of the C677T mutation of the methylenetetrahydrofolate reductase gene in selected Brazilian patients.

Fasting total homocysteine (tHcy) and the methylenetetrahydrofolate reductase (MTHFR) C677T mutation were evaluated in 91 patients with venous thromboembolism and without acquired thrombophilia, and in 91 age-matched and sex-matched controls. Hyperhomocysteinemia was detected in 11 patients (12.1%) and in two controls (2.2%), yielding an odds ratio (OR) for venous thrombosis of 6.1 [95% confidence interval (CI), 1.3-28.4]. After excluding 21 patients and four controls with other known genetic risk factors for venous thrombosis, the OR was not substantially changed (7.0; 95% CI, 1.5-33.1). The prevalence of the MTHFR 677TT genotype was not significantly different in patients (9.9%) and in controls (5.5%), with an OR for venous thrombosis of 1.8 (95% CI, 0.6-5.8). Subjects with the MTHFR 677TT genotype showed higher levels of tHcy compared with the 677CC genotype in patients (P = 0.010) and in controls (P = 0.030). In conclusion, we found that fasting hyperhomocysteinemia is a risk factor for venous thrombosis in patients without known acquired thrombophilia and other genetic risk factors for venous thrombosis. Although tHcy levels are significantly higher in those homozygous for the MTHFR C677T mutation, this genotype does not increase the thrombotic risk in our study population.

G gamma-levels of the HbF of patients with bone marrow failure syndromes.

1. The gamma chain composition of 17 patients with varying degrees of bone marrow failure was determined by high performance liquid chromatography. All 10 patients with anemia had high G gamma levels (48.1-68.5%), while 5/7 patients in remission had G gamma in the range 30.0-38.8%. 2. There was also an association of higher G gamma values with higher HbF levels. The average value of G gamma in the HbF of patients with active aplastic or hypoplastic anemia differed from those obtained both for normal adult and for newborn HbF. 3. Thus, in spite of activation of both the G gamma and A gamma genes, the former are more effectively expressed as HbF increases.

The evaluation of spleen function in man.

The usual methods for the functional evaluation of the spleen in man are based on the measurement of a) spleen volume, b) spleen uptake of particles from the circulating blood, and c) morphological abnormalities of circulating erythrocytes. Analysis of clearance curves of damaged autologous erythrocytes, measurement of spleen size or volume by scintillation scanning and counting of erythrocytes with pits by interference contrast microscopy at present are the most widely used techniques. The most frequent causes of acquired functional abnormalities of the spleen are the sickle cell diseases, inflammatory intestinal diseases, immune complex diseases, chronic myelogenous leukemia, irradiation, hemophilia, and the hyposplenism of newborn infants and of the elderly. Usually there is a parallelism enlarged or normal-sized spleen with decreased function, has been observed in sickle cell syndromes and occasionally in chronic myelogenous leukemia and hemophilia.

Beta-thalassemia in Brazil.

1. Clinical, hematological, genetic and peripheral blood globin synthesis studies were carried out on 17 symptomatic Brazilian thalassemics and their parents who live in the northeast of São Paulo State. The group included 8 beta zero-thalassemia homozygotes, 7 carriers of at least one beta + gene, one delta beta zero/beta zero-thalassemia double heterozygote and one beta zero homozygote also carrying the alpha-chain variant Hb Hasharon (alpha 2(47) His beta 2). 2. The mean non-alpha/alpha ratio for globin biosynthesis of the patients lacking HbA (beta zero homozygotes and delta beta zero/beta zero double heterozygotes) was 0.26 +/- 0.11 (mean +/- SD), which is not statistically different from the value of 0.32 +/- 0.06 obtained for the carriers of at least one beta + gene. In contrast, the mean non-alpha/alpha ratio for the thalassemia major patients (0.22 +/- 0.07) was significantly lower than that obtained for the milder cases (0.34 +/- 0.06) although the beta/alpha ratios for the parents of the two groups were similar. 3. The heterogeneity within this group of Brazilian patients having two thalassemic genes, i.e. 60% who are beta zero homozygotes and 40% who are carriers of at least one beta + gene, is consistent with the Italian origin of most of these patients.

Dyserythropoiesis in iron deficiency and in beta-thalassemia.

Nuclear and cytoplasmic abnormalities were quantitated in bone marrow erythroblasts from 15 patients with iron deficient anemia, 5 beta-thalassemia homozygotes, 5 beta-thalassemia heterozygotes, 6 S/beta-thalassemia double heterozygotes and 9 controls. The frequency of dyserythropoietic changes in iron deficiency was 11.90 +/- 5.02% (mean +/- SD) which is significantly higher than 3.36 +/- 1.16% obtained for the control group. The degree of dyserythropoiesis was negatively correlated with hemoglobin level (rS = 0.757). The frequency of dyserythropoietic changes obtained for the beta-thalassemia heterozygotes (5.23 +/- 1.45%) and for S/beta-thalassemia (7.13 +/- 2.00%) was elevated compared with the controls (P less than 0.05 and P less than 0.01, respectively). The highest frequency of dyserythropoiesis (19.88 +/- 7.40%) occurred among beta-thalassemia homozygotes. In all cases studied the abnormalities were observed mainly in the late erythroblasts. In addition, a peculiar cytoplasmic inclusion was observed in Leishman-stained bone marrow or peripheral blood erythroblasts from beta-thalassemia homozygotes, which is probably the result of precipitation of excess alpha-chain. This abnormality of thalassemia erythroblasts in Leishman-stained smears had not been previously reported.

Hemoglobin H disease caused by two gene deletions.

1. A white Brazilian woman not of Asian origin was found to have Hb H disease of moderate severity. 2. Gene mapping demonstrated that the disease was caused by the association of two abnormal alpha-globin gene clusters on chromosome 16: one with a deletion which removed the two functional alpha genes and the other carrying the 3.7-kb rightward deletion, which leaves a single functional alpha gene. 3. These data illustrate the necessity for systematic molecular approaches to the diagnosis of this heterogeneous group of diseases.