Duyen Ngo

Fetal hemoglobin in sickle cell anemia

Fetal hemoglobin (HbF) is the major genetic modulator of the hematologic and clinical features of sickle cell disease, an effect mediated by its exclusion from the sickle hemoglobin polymer. Fetal hemoglobin genes are genetically regulated, and the level of HbF and its distribution among sickle erythrocytes is highly variable. Some patients with sickle cell disease have exceptionally high levels of HbF that are associated with the Senegal and Saudi-Indian haplotype of the HBB-like gene cluster; some patients with different haplotypes can have similarly high HbF. In these patients, high HbF is associated with generally milder but not asymptomatic disease. Studying these persons might provide additional insights into HbF gene regulation. HbF appears to benefit some complications of disease more than others. This might be related to the premature destruction of erythrocytes that do not contain HbF, even though the total HbF concentration is high. Recent insights into HbF regulation have spurred new efforts to induce high HbF levels in sickle cell disease beyond those achievable with the current limited repertory of HbF inducers.

Medical hyperspectral imaging to facilitate residual tumor identification during surgery

Introduction: Adequate evaluation of breast tumor resection at surgery continues to be an important issue in surgical care, as over 30% of postoperative tumors recur locally unless radiation is used to destroy remaining tumor cells in the field. Medical Hyperspectral Imaging (MHSI) delivers near-real time images of biomarkers in tissue, providing an assessment of pathophysiology and the potential to distinguish different tissues based on spectral characteristics. Method: We have used an experimental DMBA-induced rat breast tumor model to examine the intraoperative utility of MHSI, in distinguishing tumor from normal breast and other tissues. Rats bearing tumors underwent surgical exposure and MHSI imaging, followed by partial resection of the tumors, then MHSI imaging of the resection bed, and finally total resection of tumors and of grossly normal-appearing glands. Resected tissue underwent gross examination, MHSI imaging, and histopathological evaluation. Results: An algorithm based on spectral characteristics of tissue types was developed to distinguish between tumor and normal tissues. Tissues including tumor, blood vessels, muscle, and connective tissue were clearly identified and differentiated by MHSI. Fragments of residual tumor 0.5 - 1 mm in size intentionally left in the operative bed were readily identified. MHSI demonstrated a sensitivity of 89% and a specificity of 94% for detection of residual tumor, comparable to that of histopathological examination of the tumor bed (85% and 92%, respectively). Conclusion: We conclude that MHSI may be useful in identifying small residual tumor in a tumor resection bed and for indicating areas requiring more extensive resection and more effective biopsy locations to the surgeon. 3

Fetal haemoglobin levels and haematological characteristics of compound heterozygotes for haemoglobin S and deletional hereditary persistence of fetal haemoglobin

Compound heterozygotes for sickle haemoglobin (HbS) and hereditary persistence of fetal haemoglobin (HPFH) have high fetal haemoglobin (HbF) levels but few, if any, sickle cell disease‐related complications. We studied 30 cases of HbS‐HPFH (types 1 and 2), confirmed by molecular analysis, and report the haematological features and change in HbF levels over time. These results were compared to those of patients with sickle cell anaemia or HbS‐β0 thalassaemia, including a subgroup of patients carrying the XmnI polymorphism, known to be associated with elevated HbF. Among the HbS‐HPFH patients, HbF level was 50–90% during infancy and declined steeply within the first few years of life, stabilizing between ages 3 and 5 years, at approximately 30%. Mean HbF of individuals age 5 or older was 31 ± 3%, average haemoglobin concentration was 130 ± 10 g/l and average mean corpuscular volume (MCV) was 75 ± 4 fl. Univariate and multivariate regression analyses significantly associated HbF with age, haemoglobin concentration, and MCV (P < 0·001). There was a strong inverse association between HbF and age (r = −0·9, P < 0·001). Despite having a much higher HbF level, patients with HbS‐HPFH have a similar age‐related pattern of HbF decline and associations as patients with sickle cell anaemia or HbS‐β0 thalassaemia.

Prohibitin and the SWI/SNF ATPase subunit BRG1 are required for effective androgen antagonist-mediated transcriptional repression of androgen receptor-regulated genes

Androgen antagonists or androgen deprivation are the primary therapeutic modalities for the treatment of prostate cancer. Invariably, however, the disease becomes progressive and unresponsive to androgen ablation therapy (hormone refractory). The molecular mechanisms by which androgen antagonists inhibit prostate cancer proliferation are not fully defined. In this study, we identify two molecules which are required for effective prostate cancer cell responsiveness to androgen antagonists. We establish that androgen receptor (AR)-dependent transcriptional suppression by androgen antagonists requires the tumor suppressor prohibitin. This requirement for prohibitin was demonstrated using structurally-distinct androgen antagonists, stable and transient knockdown of prohibitin and transfected and endogenous AR-responsive genes. The SWI-SNF complex core ATPase BRG1, but not its closely-related counterpart ATPase BRM, is required for this repressive action of prohibitin on AR-responsive promoters. Androgen antagonists induce recruitment of prohibitin and BRG1 to endogenous AR-responsive promoters and induce a physical association between AR and prohibitin and BRG1. The recruitment of prohibitin to endogenous AR-responsive promoters is dependent upon antagonist-bound AR. Prohibitin binding in the prostate-specific antigen (PSA) promoter results in the recruitment of BRG1 and the dissociation of p300 from the PSA promoter. These findings suggest that prohibitin may function through BRG1-mediated local chromatin remodeling activity and the removal of p300-mediated acetylation to produce androgen antagonist-mediated transcriptional repression. Furthermore, in addition to its necessary role in AR-mediated transcriptional repression, we demonstrate that prohibitin is required for full and efficient androgen antagonist-mediated growth suppression of prostate cancer cells.

Fetal hemoglobin in sickle cell anemia: genetic studies of the Arab-Indian haplotype.

Sickle cell anemia is common in the Middle East and India where the HbS gene is sometimes associated with the Arab-Indian (AI) β-globin gene (HBB) cluster haplotype. In this haplotype of sickle cell anemia, fetal hemoglobin (HbF) levels are 3-4 fold higher than those found in patients with HbS haplotypes of African origin. Little is known about the genetic elements that modulate HbF in AI haplotype patients. We therefore studied Saudi HbS homozygotes with the AI haplotype (mean HbF 19.2±7.0%, range 3.6 to 39.6%) and employed targeted genotyping of polymorphic sites to explore cis- and trans- acting elements associated with high HbF expression. We also described sequences which appear to be unique to the AI haplotype for which future functional studies are needed to further define their role in HbF modulation. All cases, regardless of HbF concentration, were homozygous for AI haplotype-specific elements cis to HBB. SNPs in BCL11A and HBS1L-MYB that were associated with HbF in other populations explained only 8.8% of the variation in HbF. KLF1 polymorphisms associated previously with high HbF were not present in the 44 patients tested. More than 90% of the HbF variance in sickle cell patients with the AI haplotype remains unexplained by the genetic loci that we studied. The dispersion of HbF levels among AI haplotype patients suggests that other genetic elements modulate the effects of the known cis- and trans-acting regulators. These regulatory elements, which remain to be discovered, might be specific in the Saudi and some other populations where HbF levels are especially high.

Fetal hemoglobin in sickle cell anemia: Molecular characterization of the unusually high fetal hemoglobin phenotype in African Americans

Fetal hemoglobin (HbF) is a major modifier of disease severity in sickle cell anemia (SCA). Three major HbF quantitative trait loci (QTL) are known: the Xmn I site upstream of (G)γ- globin gene (HBG2) on chromosome 11p15, BCL11A on chromosome 2p16, and HBS1L-MYB intergenic polymorphism (HMIP) on chromosome 6q23. However, the roles of these QTLs in patients with SCA with uncharacteristically high HbF are not known. We studied 20 African American patients with SCA with markedly elevated HbF (mean 17.2%). They had significantly higher minor allele frequencies (MAF) in two HbF QTLs, BCL11A, and HMIP, compared with those with low HbF. A 3-bp (TAC) deletion in complete linkage disequilibrium (LD) with the minor allele of rs9399137 in HMIP was also present significantly more often in these patients. To further explore other genetic loci that might be responsible for this high HbF, we sequenced a 14.1 kb DNA fragment between the (A)γ-(HBG1) and δ-globin genes (HBD). Thirty-eight SNPs were found. Four SNPs had significantly higher major allele frequencies in the unusually high HbF group. In silico analyses of these four polymorphisms predicted alteration in transcription factor binding sites in 3.

BCL11A enhancer haplotypes and fetal hemoglobin in sickle cell anemia

BACKGROUND Fetal hemoglobin (HbF) levels in sickle cell anemia patients vary. We genotyped polymorphisms in the erythroid-specific enhancer of BCL11A to see if they might account for the very high HbF associated with the Arab-Indian (AI) haplotype and Benin haplotype of sickle cell anemia. METHODS AND RESULTS Six BCL112A enhancer SNPs and their haplotypes were studied in Saudi Arabs from the Eastern Province and Indian patients with AI haplotype (HbF ~20%), African Americans (HbF ~7%), and Saudi Arabs from the Southwestern Province (HbF ~12%). Four SNPs (rs1427407, rs6706648, rs6738440, and rs7606173) and their haplotypes were consistently associated with HbF levels. The distributions of haplotypes differ in the 3 cohorts but not their genetic effects: the haplotype TCAG was associated with the lowest HbF level and the haplotype GTAC was associated with the highest HbF level and differences in HbF levels between carriers of these haplotypes in all cohorts were approximately 6%. CONCLUSIONS Common HbF BCL11A enhancer haplotypes in patients with African origin and AI sickle cell anemia have similar effects on HbF but they do not explain their differences in HbF.

A functional promoter polymorphism of the δ‐globin gene is a specific marker of the Arab‐Indian haplotype

Most sickle cell anemia (SCA) patients indigenous to the Eastern Province of Saudi Arabia have their HbS gene on the Arab-Indian (AI) HBB gene cluster haplotype. Their fetal hemoglobin (HbF) levels are near 20% and they have milder disease compared with SCA where the HbS gene is on African origin HBB haplotypes [1–9]. The AI haplotype is characterized by an Xmn1 restriction site at position 2158 50 to HBG2 (rs7482144), a Hinc2 site 50 to HBE (rs3834466) and other polymorphisms [10]. The causal elements that modify HbF might be in linkage disequilibrium with the b globin gene in this Saudi population. We first performed homozygosity mapping using genome-wide single nucleotide polymorphisms (SNPs) in AI HbS homozygotes [11,12] and identified a single large autozygous region including the HBB cluster and surrounding genes. By next generation sequencing, we examined this region in these same individuals and identified several variants that included a SNP in the HBD promoter region at position 268 bp 50 to HBD (CCAAC > TCAAC). We found this SNP only when the HbS gene was on an AI haplotype and not in SCA with other haplotypes. This SNP was functional in reporter assays in K562 cells and is an AI haplotype-specific marker. Table I summarizes the patient characteristics. Using genome-wide SNP data from a limited number of cases, a region of autozygosity was found only in AI HbS homozygotes on chromosome 11 (coordinates 5,196,450– 5,323,071). The region contains HBD, HBG1, HBG2, HBE1, and the Xmn1 50 HBG2 restriction site (rs7482144). By targeted deep sequencing of 400 kb of chromosome 11 (coordinates 5,143,424–5,543,424; average coverage 42x) in 4 AI patients 1,195 variants were found. A homozygous C-T variant 268 bp 50 HBD with high genotyping and mapping quality that was not in dbSNP build 135 or 1,000 Genomes, was present. Resequencing of 15.9 kb of chr11 (coordinates 5,253,531–5,269,435) by Sanger sequencing detected three new SNPs of which one was the 268 C > T SNP. We focused on this SNP because of its location within the Corfu deletion region and its location in the HBD promoter. The C > T SNP in the HBD promoter was found only in individuals with the AI haplotype. Saudi sickle cell trait carriers with the AI haplotype were heterozygous for this SNP; while siblings without HbS did not carry this mutation. Among 25 AI HbS-b thalassemia patients, 16 were heterozygous at this site (C/T) and 9 were homozygous (T/T). All AI HbS-b thalassemia patients who were homozygous T/T were also homozygous for the AI haplotype (Table I). Fifteen African American SCA patients with unusually high HbF, 54 Saudi SCA patients from the Southwestern Province (SW)—mainly Benin but including subjects with the Senegal haplotype—19 SW HbS-b thalassemia patients, 16 SW sickle cell trait cases, and 25 normal Saudi controls did not carry the 268 HBD SNP. This SNP was not found in 1,094 individuals in 1,000 Genomes May 2011 release. It is important to note that hemoglobin electrophoresis results in Table I were performed using different methods, so direct comparison of HbF and HbA2 between different groups will not be accurate. In addition, the effect of coinheritance of a-thalassemia, or presence of iron deficiency anemia on Hb A2 level was not assessed. Finally, HbA2 levels are artifactually high when HbS is present because of the co-elution of minor HbS species. For these reasons, it is not possible to estimate the effects of the 268 C-T SNP on these subjects HbA2 levels. Reduced expression of HBD relative to HBB in normal individuals is partly a result of a degenerate CCAAT box in the HBD promoter (CCAAC). The CCAAC motif is the site of the 268 C > T SNP (TCAAC) [13–15]. When we compared the activity of the wild-type HBD promoter with the promoter containing the 268 C > T SNP the variant promoter was associated with a significant decrease in the expression of a reporter construct suggesting that it could further impair already enfeebled HBD expression (Fig. 1). Although HBG is expressed at high levels in K562 cells, endogenous HBD is also expressed [16]. The expression studies were designed solely to test the hypothesis that the 268 C > T SNP downregulates the expression of the HBD promoter. The literature provides further evidence for a functional role of the 268 C > T SNP. Its presence was associated with d thalassemia in one individual with reduced HbA2 of 2% and a slightly increased HbF of 1.3% [13]. Moreover, mutations at positions 230, 231, 236, 255, 265, 276, and 277 in the HBD promoter were reported in HbVar database (http://globin.cse.psu.edu/) to cause d thalassemia [14,17–19], and HbF levels of 3.3–4.7% have been noted in some hematologically normal individuals with homozygous d thalassemia [19,20]. A mechanism for increased HbF in the presence of less common HBD promoter mutations is unknown. Any role for the 268 C-T SNP as a modifier of HbF in AI haplotype HbS sickle cell disease is unknown. Perhaps HBD promoter SNPs reduce the interaction of the locus control region and the transcription apparatus with this promoter permitting enhanced interactions with HBG promoters [21]. The paradox of the Corfu deletion first suggested the potential of the HBD-HBG1 intergenic area, the site of the 268 C-T SNP, as a silencer of HBG expression [22]. One potential functional area is the polypyrimidine (PYR) binding site about 960 bp upstream of HBD; however, polymorphisms

Genomic approaches to identifying targets for treating β hemoglobinopathies

Sickle cell disease and β thalassemia are common severe diseases with little effective pathophysiologically-based treatment. Their phenotypic heterogeneity prompted genomic approaches to identify modifiers that ultimately might be exploited therapeutically. Fetal hemoglobin (HbF) is the major modulator of the phenotype of the β hemoglobinopathies. HbF inhibits deoxyHbS polymerization and in β thalassemia compensates for the reduction of HbA. The major success of genomics has been a better understanding the genetic regulation of HbF by identifying the major quantitative trait loci for this trait. If the targets identified can lead to means of increasing HbF to therapeutic levels in sufficient numbers of sickle or β-thalassemia erythrocytes, the pathophysiology of these diseases would be reversed. The availability of new target loci, high-throughput drug screening, and recent advances in genome editing provide the opportunity for new approaches to therapeutically increasing HbF production.

Genetic studies of fetal hemoglobin in the Arab-Indian haplotype sickle cell-β0 thalassemia

Independently of its African roots, the HbS gene is also indigenous to the Middle East and India where it can be on an Arab-Indian (AI) HBB haplotype. This haplotype is associated with high levels of fetal hemoglobin (HbF) and increased HbF improves many complications of sickle cell disease [1]. Polymorphisms in BCL11A (chr 2p) and HBS1L-MYB (chr 6q) and in elements linked to HBB (chr 11p) are associated with HbF level. In AI haplotype HbS homozygotes, SNPs in BCL11A and HBS1L-MYB accounted for 8.8% of HbF variance. We studied 61 patients with HbS-b thalassemia, aged 12 years and not taking hydroxyurea at the time HbF was measured by high performance liquid chromatography (HPLC). HbS-b thalassemia was determined by the presence of the HbSF phenotype by HPLC, heterozygosity for the HbS mutation and microcytosis. The b-thalassemia mutation was not genotyped. The HbS mutation was ascertained using ARMS (amplification refractory mutation system) analysis. The AI haplotype was determined by genotyping the 50 HBG2 Xmn1 C>T restriction site (rs7482144) and a Hinc2 site 50 to HBE1 (rs3834466), and confirmed by the presence of a C>T polymorphism 68 bp 50 to HBD [2]. Single nucleotide polymorphism (SNP)s studied are shown in Table I and were detected by TaqMan assays (Applied Bio systems) or by Sanger di-deoxy sequencing. Linear regression was performed on HbF for each genetic locus, adjusting for gender. The analysis was performed using an additive genetic model whereby the total number of minor alleles present was counted for each subject. b-Thalassemia is common in Al-Ahsa. The four most prevalent mutations are: codon 39 C-T (25%); IVSII-1 G-A (22.2%); IVSI-5 G-C (13.3%); and IVSI 25 bp deletion (13.0%). a-Thalassemia has little effect on HbF in other haplotypes of sickle cell anemia [3,4]. More than 40% of AI haplotype HbS homozygotes had some form of a-thalassemia. HbS-b thalassemia patients had a mean HbF of 17.7%, a level similar to that found in HbS homozygotes and similar to those previously reported in AI haplotype HbS-b thalassemia but distinct from HbS-b thalassemia with African haplotypes. Their HbF distribution is not significantly different from that in AI haplotype HbS homozygotes (Fig. 1). There was no association of SNPs in BCL11A or the HBS1L-MYB intergenic region with HbF (Table I). The number of patients we studied was small. To have 80% power to detect associations of SNPs in BCL11A (rs766432) with HbF 140 cases would be needed; 1,640 cased are required to detect an association with rs9399137 in HBS1L-MYB. Given the results in sickle cell anemia and the AI haplotype, the effects of these SNPs on HbF in Saudi patients with HbS-b thalassemia are likely to be small. Along with interactions of cis-acting elements of the AI haplotype with trans-acting factors prevalent in the Saudi Arab population that remain to be discovered, reduced or abnormal b-globin mRNA caused by b thalassemia and stress erythropoiesis might contribute to increasing HbF expression [5]. Less b-globin mRNA might enhance the stability of g-globin RNA by reducing post-transcriptional competition for the translational machinery [6]. Sickle cell trait carriers with the AI haplotype and Saudi Arab heterozygotes with b thalassemia had nearly normal HbF levels. The absence of hemolytic anemia or suppression of HBB expression trans to the HbS gene might account for their normal HbF.