Thesis (B.A.)--Boston University. University Professors Program Senior theses. / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / 2031-01-01

5 Abstract Aims Determination of gene expression of HBG1 gamma globin in myelodysplastic syndrome (MDS) patients in CD34+ pluripotent hæmatopoietic cells and connection of HBG1 gene expression with various subtypes of MDS. Furthermore, detection of single nucleotide polymorphisms rs 4671393 and rs 11886868 in these patients and in healthy Czech population donors and to determine whether a connection exists between the occurrence of the above polymorphisms and HBG1 gene over-expression, as demonstrated in some hæmatological disorders. Samples The source of genetic material to identify gene expression were 80 HBG1 RNA samples isolated from the pluripotent hematopoietic CD34+ cells of MDS patients. As a sample of healthy controls, 6 samples of commercially purchased CD 34+ cells from the Lonza com- pany were used. The source of genetic material for the detection of polymorphisms were 140 DNA samples isolated from purified granulocytes of MDS patients and 49 samples of DNA isolated from peripheral blood granulocytes from healthy Czech population donors. Methods Real-Time PCR was used to determine HBG1 gene expression and detection of single nu- cleotide polymorphisms. Taqman Gene Expression Assay was used to determine the level of expression and the results were evaluated using the comparative ΔΔCT method....

Submitted by Simone Fortunato (simone.fortunato@conveniado.bahia.fiocruz.br) on 2017-10-04T13:49:03Z No. of bitstreams: 1 2017 Rifkath_19 de setembro colorido.pdf: 1577388 bytes, checksum: db9deae3ad793c3fb4c568df25016401 (MD5) / Approved for entry into archive by Uillis de Assis Santos (uillis.assis@ufba.br) on 2017-10-04T14:02:02Z (GMT) No. of bitstreams: 1 2017 Rifkath_19 de setembro colorido.pdf: 1577388 bytes, checksum: db9deae3ad793c3fb4c568df25016401 (MD5) / Made available in DSpace on 2017-10-04T14:02:02Z (GMT). No. of bitstreams: 1 2017 Rifkath_19 de setembro colorido.pdf: 1577388 bytes, checksum: db9deae3ad793c3fb4c568df25016401 (MD5) / RESUMO INTRODUÇÃO: Os níveis séricos de bilirrubina encontram-se frequentemente aumentados em pacientes com anemia falciforme, já acometidos por hemólise exacerbada, favorecendo a agravação do quadro clinico e a ocorrência de litíases biliares. OBJETIVO: O objetivo foi analisar a influência do polimorfismo A(TA)nTAA no promotor do gene UGT1A1 (rs8175347) e de dois polimorfismos no gene BCL11A (rs1427407 e rs7606173), sobre alguns parâmetros laboratoriais e sobre a resposta à hidroxiureia em pacientes pediátricos com anemia falciforme. MATERIAL E MÉTODOS: Amostras de sangue total e soro foram utilizadas para a realização das análises hematológicas e bioquímicas. O DNA foi extraído a partir de amostras de sangue periférico, e os fragmentos contendo os polimorfismos foram amplificados por PCR seguida de sequenciamento com primers específicos. RESULTADOS: Foram estudados 97 pacientes, com idade variando entre dois e 17 anos (7,433±4,075). Para o polimorfismo em UGT1A1, foram encontrados de cinco até oito repetições (TA) e as frequências do alelo selvagem (TA)6 e do alelo mutante (TA)7 foram respectivamente de 0,60 e 0,34. Quarenta pacientes (41,24%) eram homozigotos para o alelo (TA)6, 33 heterozigotos (TA)6/7, e 13 homozigotos (TA)7/7. Os níveis de bilirrubina total e indireta foram significativamente maiores nos pacientes com sete ou mais repetições (TA), p=0,0038 e p=0,0022, respectivamente, em comparação aos homozigotos (TA)6/6 ou heterozigotos (TA)5/6 ou (TA)5/7. Foi encontrada uma correlação negativa significativa entre os níveis de hemoglobina fetal e os níveis de bilirrubina total (r=-0,3782, p=0,0001) e de bilirrubina indireta (r=-0,3761, p=0,0015), sendo que para os indivíduos (TA)7/7 e (TA)7/8, essa correlação deixou de ser válida (p>0,05), tanto para a bilirrubina total quanto para a bilirrubina indireta. Ademais, os níveis maiores de bilirrubina nos indivíduos (TA)7/7 e (TA)7/8 não estavam associados com o aumento dos níveis de marcadores de hemólise. A frequência do alelo mutante T do rs1427407 foi de 0,22 e a do alelo selvagem G do rs7606173 foi 0,57. Nenhum indivíduo com o genótipo mutante TT para o rs1427407 estava sob tratamento com hidroxiureia. Em indivíduos sem uso de hidroxiureia, o maior nível de hemoglobina fetal foi associado com o genótipo mutante TT. Já para o genótipo selvagem GG do rs7606173 ocorreu aumento de hemoglobina fetal, mas não foi significativo. Quanto aos níveis de bilirrubina, os homozigotos TT para o rs1427407 e GG para o rs7606173 apresentaram níveis menores. Além disso, o efeito dos polimorfismos em BCL11A sobre a bilirrubina pareceu superar o efeito do rs8175347 no grupo (TA)7/7 e (TA)7/8. Não foi encontrada associação TT/CC, e também não foi encontrado nenhum mutante TT entre os portadores do haplótipo CAR/CAR. Conclusões: Este estudo confirmou a associação do alelo (TA)7 a níveis elevados de bilirrubina, independentemente do grau de hemólise. O alelo mutante T do rs1427407 e o alelo ancestral G do rs7606173 são associados à níveis maiores de hemoglobina fetal e menores níveis de bilirrubina, sendo o efeito maior associado ao alelo T. / ABSTRACT INTRODUCTION: Serum bilirubin levels are frequently increased in patients with sickle cell anemia, who already are affected by exacerbated hemolysis, which worsens symptoms and especially favors the occurrence of pigment gallstones. AIM: The aim of the present study was to analyze the influence of the polymorphism A(TA)nTAA in the UGT1A1 gene promoter (rs8175347) and two polymorphisms in the BCL11A gene (rs1427407 and rs7606173), on some laboratory parameters and on the response to hydroxyurea in pediatric patients with sickle cell anemia. MATERIAL AND METHODS: Whole blood and serum samples were used to perform hematological and biochemical analysis. DNA was extracted from peripheral blood samples, and fragments containing the polymorphisms were amplified by Polymerase Chain Reaction followed by sequencing with specific primers. RESULTS: We studied 97 patients, ranging in age from 2 to 17 years (7.433±4.075). For the UGT1A1 polymorphism, five to eight (TA) repeats were found and the wild-type (TA)6 and mutant allele (TA)7 frequencies were respectively 0.60 and 0.34. Forty patients (41.24%) were homozygous (TA)6/6, 33 heterozygotes (TA)6/7, and 13 homozygous (TA)7/7. Total and unconjugated bilirubin levels were significantly higher in patients with seven or more (TA) repeats, p=0.0038 and p=0.0022, respectively, compared to homozygotes (TA)6/6 or heterozygotes (TA)5/6 or (TA)5/7. A significant negative correlation was found between fetal hemoglobin levels and total bilirubin levels (r =-0.3782, p=0.0001) and unconjugated bilirubin levels (r =-0.3761, p=0.0015). This correlation was no longer valid (p> 0.05) for individuals (TA)7/7 and (TA)7/8. In addition, the higher levels of bilirubin in (TA)7/7 and (TA)7/8 individuals were not associated with increased markers of markers of hemolysis. The frequency of the mutant allele G of rs1427407 was 0.22, and for the wild-type allele G of rs7606173, the frequency was 0.57. In individuals that were not using hydroxyurea, a significant higher fetal hemoglobin level was associated with the TT mutant genotype, while a non-significant increase occurred for the wild-type genotype GG of rs7606173. Subsequently, patients homozygous for the TT genotype of rs1427407 had significant lower levels of total and unconjugated bilirubin (p=0.0102 and p=0.0108, respectively). Furthermore, the effect of the BCL11A polymorphisms on bilirubin levels appeared to outweigh the effect of rs8175347 in the group (TA)7/7 and (TA)7/8. No patient simultaneously carrying the homozygous mutant genotypes TT/CC was found; and no mutant homozygotes TT was found in patients with the CAR/CAR haplotype. CONCLUSION: This study confirmed that allele (TA)7 is associated with elevated levels of bilirubin, regardless of the rate of hemolysis. The mutant allele T of rs1427407 and the ancestral allele G of rs7606173 are associated with higher levels of fetal hemoglobin and lower levels of bilirubin, the strongest effect being associated with the T allele.

Sickle cell disease (SCD) is a severe hemoglobin disorder caused by co-inheritance of a single mutation in the β-globin gene of adult hemoglobin (HbA; α2β2). This alteration leads to the formation of sickle hemoglobin (HbS; α2βS2) and deformed, sickle-shaped red blood cells (RBCs). Sickle RBCs obstruct small blood vessels resulting in anemia, excruciating pain crises, organ damage, and stroke. For the millions of people affected by this disease, life expectancy is only 40-60 years of age. The only cure for SCD is hematopoietic stem cell (HSC, CD34+) transplantation, which requires a human leukocyte antigen (HLA)-matched donor. However, this option runs the risk of complications associated with graft versus host disease and infection. Before birth, individuals with SCD do well because their RBCs are filled with γ-globin containing fetal hemoglobin (HbF; α2γ2), which inhibits the formation of HbS. In fact, some SCD patients who co-inherit mutations that allow for high-level expression of HbF into adulthood are asymptomatic. This suggests that genetic modification of the patient’s own HSCs to permit HbF production would be a viable therapeutic alternative to HSC transplantation. Our work has focused on the use of lentiviral vectors to introduce an exogenous γ-globin gene or shRNA sequences designed to knockdown repressors of γ-globin, such as the zinc-finger transcription factor, BCL11A, to prevent silencing of the endogenous γ-globin genes allowing for persistent expression of HbF. Despite significant progress using both approaches, we have been unable to increase the level of HbF > 30%; a curative threshold for SCD patients who continue to produce HbF into adulthood. The goal of my project was to combine these approaches into a single lentiviral vector to achieve co-regulated, erythroid-specific expression and augmented levels of HbF. I successfully modified the insulated, erythroid-specific γ-globin vector (termed V5m3-400) to include microRNA (miR)-adapted shRNAs (or shmiRs) targeting BCL11A (based on miR-30 and miR-E architectures) in the first and second noncoding introns of the γ-globin genomic sequences. Inclusion of shmiRs had no appreciable effect on integrity of the integrated provirus or vector titer. Vector performance was initially tested using human K562 erythroleukemia cells expressing a flag-tagged version of BCL11A. In this cell line, BCL11A knockdown was significantly improved using miR-E-shRNAs due to a dramatic increase (up to 350-fold) in processing of mature shRNA sequences. The miR-E vectors also provided high-level expression of γ-globin. Erythroid-specific expression of the γ-globin transgene and BCL11A knockdown was confirmed in maturing erythroid cells derived from transduced CD34+ cells of a healthy donor resulting in a 50% increase in HbF levels compared with cells transduced with V5m3-400 as a control. While encouraging, I was unable to discriminate HbF derived from the vector-encoded versus endogenous γ-globin genes. To address this, I introduced a single base change in exon 2 of the γ-globin gene encoded by V5m3-400 such that threonine replaces isoleucine at amino acid 75 (I75T). This variant was successfully distinguished from endogenous γ-globin gene products by reverse phase high performance liquid chromatography (HPLC) in culture-differentiated erythroid cells. Based on these findings, I created compound γ-globin/shmiR-E vectors that include the I75T substitution (I75Tγ-globin/shmiR-E). Future studies will focus on testing this novel vector design in erythroid cells derived from transduced CD34+ cells of healthy donors and patients with SCD. I anticipate that this compound vector has the potential to maximize γ-globin expression and promote levels of HbF that are unlikely to be safely and effectively achieved by conventional globin gene addition or shRNA knockdown approaches alone.

The most widely transfused blood component is red blood cells (RBCs), and voluntary donation is the main resource for RBC transfusion. In the UK, 7,000 units of RBCs are transfused daily but this life-saving cell therapy is completely dependent on donors and there are persistent problems associated with transfusion transmitted infections and in blood group compatibility. Furthermore, the quality, safety and efficiency of donated RBCs gradually decrease with storage time. A number of novel sources of RBCs are being explored including the production of RBCs from adult haematopoietic progenitor cells, erythroid progenitor cell lines and induced pluripotent stem cells (iPSCs). The iPSC source could essentially provide a limitless supply and a route to producing cells that are matched to the recipient. A number of protocols have been described to produce mature RBCs from human pluripotent stem cells but they are relatively inefficient and would be difficult to scale up to the levels required for clinical translation. We tested and evaluated a defined feeder- and serum-free differentiation protocol for deriving erythroid cells from hiPSCs. RBC production was not efficient, the cells that were produced did not enucleate efficiently and they expressed embryonic rather than adult globin. We hypothesised that the production of RBCs from iPSCs could be enhanced by enforced expression of erythroid-specific transcription factors (TFs). Previous studies had demonstrated that Krüppel-like factor 1 (KLF1) plays an important role in RBC development and maturation so we generated iPSC lines expressing a tamoxifen-inducible KLF1-ERT2 fusion protein. Using zinc finger nuclease technology, we targeted the expression cassette to the AAVS1 locus to ensure consistent expression levels and to avoid integration site specific effects and/or silencing. These iKLF1 iPSCs were applied to our defined RBC differentiation protocol and the activity of KLF1 was induced by adding tamoxifen. Activation of KLF1 from day 10 accelerated erythroid differentiation and maturation with an increase in the proportion of erythroblasts, a higher level of expression of erythroid genes associated with maturation and an apparently more robust morphology. However, KLF1 activation had an anti-proliferation effect resulting in significantly less cell generated overall and HPLC analysis demonstrated that KLF1-activated cells expressed higher levels of embryonic globin compared to control iPSCs-derived cells. Many of the effects that were observed when KLF1 was activated from day 10 were not observed when activated from day 18. We therefore concluded that activation of exogenous KLF1 is able to promote erythroid cell production and maturation in progenitors (day 10) but not at the later stage of erythropoiesis (day 18). We hypothesised that KLF1 might require a co-factor to regulate RBC maturation and adult globin expression at the later stage of erythropoiesis. The TF, B-cell lymphoma/leukaemia 11a (BCL11A), plays a key role in the suppression of foetal globin expression, thereby completing globin switching to adult globin. Preliminary data showed that iPSC-derived erythroid cells were able to express adult globin when transduced with a BCL11A-expressing lentiviral-vector. Based on that finding we then generated an iPSC line expressing tamoxifen-inducible BCL11AERT2 and KLF1-ERT2 fusion proteins, applied this iBK iPSC line to our differentiation protocol. Activation of both TFs from day 18 slightly increased the expression of genes associated with RBC maturation and the inclusion of BCL11A appeared to eliminate the anti-proliferation effect of KLF1. Most importantly, activation of both BCL11A and KLF1 from day 18 of the differentiation protocol increased the production of α- globin (foetal / adult globin) indicating that some definitive-like erythroid cells might be generated by activation of both TFs at the later stage of erythroid differentiation. Collectively, these findings demonstrate that enforced expression of erythroid TFs could be a useful strategy to enhance RBC maturation from iPSCs.

There has been tremendous amount of effort focused on the development and improvement of genome editing applications over the decades. Particularly, the development of programmable nucleases has revolutionized genome editing with regards to their improvements in mutagenesis efficacy and targeting feasibility. Programmable nucleases are competent for a variety of genome editing applications. There is growing interest in employing the programmable nucleases in therapeutic genome editing applications, such as correcting mutations in genetic disorders. Type II CRISPR-Cas9 bacterial adaptive immunity systems have recently been engineered as RNA-guided programmable nucleases. Native CRISPR-Cas9 nucleases have two stages of sequence-specific target DNA recognition prior to cleavage: the intrinsic binding of the Cas9 nuclease to a short DNA element (the PAM) followed by testing target site complementarity with the programmable guide RNA. The ease of reprogramming CRISPR-Cas9 nucleases for new target sequences makes them favorable genome editing platform for many applications including gene therapy. However, wild-type Cas9 nucleases have limitations: (i) The PAM element requirement restricts the targeting range of Cas9; (ii) despite the presence of two stages of target recognition, wild-type Cas9 can cleave DNA at unintended sites, which is not desired for therapeutic purposes; and (iii) there is a lack of control over the mutagenic editing product that is procuded. In this study, we developed and characterized chimeric Cas9 platforms to provide solutions to these limitations. In these platforms, the DNA-binding affinity of Cas9 protein from S. pyogenes is attenuated such that the target site binding is dependent on a fused programmable DNA-targeting-unit that recognizes a neighboring DNA-sequence. This modification extends the range of usable PAM elements and substantially improves the targeting specify of wild type Cas9. Furthermore, one of the featured chimeric Cas9 variants developed in this study has both robust nuclease activity and ability to generate predictable uniform editing products. These superior properties of the chimeric Cas9 platforms make them favorable for various genome editing applications and bring programmable nucleases one step closer to therapeutic applications.