Publications by authors named "Cicera R Lazzarotto"

12 Publications

  • Page 1 of 1

Enhanced Homology-directed Repair for Highly Efficient Gene Editing in Hematopoietic Stem/Progenitor Cells.

Blood 2021 Feb 23. Epub 2021 Feb 23.

National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States.

Lentivector gene therapy for X-linked chronic granulomatous disease (X-CGD) has proven to be a viable approach, but random vector integration and subnormal protein production from exogenous promoters in transduced cells remain concerning for long-term safety and efficacy. A previous genome editing-based approach using SpCas9 and an oligodeoxynucleotide donor to repair genetic mutations demonstrated the capability to restore physiological protein expression, but lacked sufficient efficiency in quiescent CD34+ hematopoietic cells for clinical translation. Here, we show transient inhibition of p53-binding protein 1 (53BP1) significantly increased (2.3-fold) long-term homology directed repair (HDR) to achieve highly efficient (80% gp91phox+ cells compared to healthy donor control) long-term correction of X-CGD CD34+ cells.
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http://dx.doi.org/10.1182/blood.2020008503DOI Listing
February 2021

BCL11A enhancer-edited hematopoietic stem cells persist in rhesus monkeys without toxicity.

J Clin Invest 2020 12;130(12):6677-6687

Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA.

Gene editing of the erythroid-specific BCL11A enhancer in hematopoietic stem and progenitor cells (HSPCs) from patients with sickle cell disease (SCD) induces fetal hemoglobin (HbF) without detectable toxicity, as assessed by mouse xenotransplant. Here, we evaluated autologous engraftment and HbF induction potential of erythroid-specific BCL11A enhancer-edited HSPCs in 4 nonhuman primates. We used a single guide RNA (sgRNA) with identical human and rhesus target sequences to disrupt a GATA1 binding site at the BCL11A +58 erythroid enhancer. Cas9 protein and sgRNA ribonucleoprotein complex (RNP) was electroporated into rhesus HSPCs, followed by autologous infusion after myeloablation. We found that gene edits persisted in peripheral blood (PB) and bone marrow (BM) for up to 101 weeks similarly for BCL11A enhancer- or control locus-targeted (AAVS1-targeted) cells. Biallelic BCL11A enhancer editing resulted in robust γ-globin induction, with the highest levels observed during stress erythropoiesis. Indels were evenly distributed across PB and BM lineages. Off-target edits were not observed. Nonhomologous end-joining repair alleles were enriched in engrafting HSCs. In summary, we found that edited HSCs can persist for at least 101 weeks after transplant and biallelic-edited HSCs provide substantial HbF levels in PB red blood cells, together supporting further clinical translation of this approach.
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http://dx.doi.org/10.1172/JCI140189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7685754PMC
December 2020

CHANGE-seq reveals genetic and epigenetic effects on CRISPR-Cas9 genome-wide activity.

Nat Biotechnol 2020 11 15;38(11):1317-1327. Epub 2020 Jun 15.

Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA.

Current methods can illuminate the genome-wide activity of CRISPR-Cas9 nucleases, but are not easily scalable to the throughput needed to fully understand the principles that govern Cas9 specificity. Here we describe 'circularization for high-throughput analysis of nuclease genome-wide effects by sequencing' (CHANGE-seq), a scalable, automatable tagmentation-based method for measuring the genome-wide activity of Cas9 in vitro. We applied CHANGE-seq to 110 single guide RNA targets across 13 therapeutically relevant loci in human primary T cells and identified 201,934 off-target sites, enabling the training of a machine learning model to predict off-target activity. Comparing matched genome-wide off-target, chromatin modification and accessibility, and transcriptional data, we found that cellular off-target activity was two to four times more likely to occur near active promoters, enhancers and transcribed regions. Finally, CHANGE-seq analysis of six targets across eight individual genomes revealed that human single-nucleotide variation had significant effects on activity at ~15.2% of off-target sites analyzed. CHANGE-seq is a simplified, sensitive and scalable approach to understanding the specificity of genome editors.
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http://dx.doi.org/10.1038/s41587-020-0555-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7652380PMC
November 2020

Efficient correction of a deleterious point mutation in primary horse fibroblasts with CRISPR-Cas9.

Sci Rep 2020 05 4;10(1):7411. Epub 2020 May 4.

Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas, USA.

Phenotypic selection during animal domestication has resulted in unwanted incorporation of deleterious mutations. In horses, the autosomal recessive condition known as Glycogen Branching Enzyme Deficiency (GBED) is the result of one of these deleterious mutations (102C > A), in the first exon of the GBE1 gene (GBE1). With recent advances in genome editing, this type of genetic mutation can be precisely repaired. In this study, we used the RNA-guided nuclease CRISPR-Cas9 (clustered regularly-interspaced short palindromic repeats/CRISPR-associated protein 9) to correct the GBE1 mutation in a primary fibroblast cell line derived from a high genetic merit heterozygous stallion. To correct this mutation by homologous recombination (HR), we designed a series of single guide RNAs (sgRNAs) flanking the mutation and provided different single-stranded donor DNA templates. The distance between the Cas9-mediated double-stranded break (DSB) to the mutation site, rather than DSB efficiency, was the primary determinant for successful HR. This framework can be used for targeting other harmful diseases in animal populations.
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http://dx.doi.org/10.1038/s41598-020-62723-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7198616PMC
May 2020

Genome editing of HBG1 and HBG2 to induce fetal hemoglobin.

Blood Adv 2019 11;3(21):3379-3392

Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN.

Induction of fetal hemoglobin (HbF) via clustered regularly interspaced short palindromic repeats/Cas9-mediated disruption of DNA regulatory elements that repress γ-globin gene (HBG1 and HBG2) expression is a promising therapeutic strategy for sickle cell disease (SCD) and β-thalassemia, although the optimal technical approaches and limiting toxicities are not yet fully defined. We disrupted an HBG1/HBG2 gene promoter motif that is bound by the transcriptional repressor BCL11A. Electroporation of Cas9 single guide RNA ribonucleoprotein complex into normal and SCD donor CD34+ hematopoietic stem and progenitor cells resulted in high frequencies of on-target mutations and the induction of HbF to potentially therapeutic levels in erythroid progeny generated in vitro and in vivo after transplantation of hematopoietic stem and progenitor cells into nonobese diabetic/severe combined immunodeficiency/Il2rγ-/-/KitW41/W41 immunodeficient mice. On-target editing did not impair CD34+ cell regeneration or differentiation into erythroid, T, B, or myeloid cell lineages at 16 to 17 weeks after xenotransplantation. No off-target mutations were detected by targeted sequencing of candidate sites identified by circularization for in vitro reporting of cleavage effects by sequencing (CIRCLE-seq), an in vitro genome-scale method for detecting Cas9 activity. Engineered Cas9 containing 3 nuclear localization sequences edited human hematopoietic stem and progenitor cells more efficiently and consistently than conventional Cas9 with 2 nuclear localization sequences. Our studies provide novel and essential preclinical evidence supporting the safety, feasibility, and efficacy of a mechanism-based approach to induce HbF for treating hemoglobinopathies.
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http://dx.doi.org/10.1182/bloodadvances.2019000820DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6855127PMC
November 2019

Highly efficient therapeutic gene editing of human hematopoietic stem cells.

Nat Med 2019 05 25;25(5):776-783. Epub 2019 Mar 25.

Division of Hematology/Oncology, Boston Children's Hospital , Boston, MA, USA.

Re-expression of the paralogous γ-globin genes (HBG1/2) could be a universal strategy to ameliorate the severe β-globin disorders sickle cell disease (SCD) and β-thalassemia by induction of fetal hemoglobin (HbF, αγ). Previously, we and others have shown that core sequences at the BCL11A erythroid enhancer are required for repression of HbF in adult-stage erythroid cells but are dispensable in non-erythroid cells. CRISPR-Cas9-mediated gene modification has demonstrated variable efficiency, specificity, and persistence in hematopoietic stem cells (HSCs). Here, we demonstrate that Cas9:sgRNA ribonucleoprotein (RNP)-mediated cleavage within a GATA1 binding site at the +58 BCL11A erythroid enhancer results in highly penetrant disruption of this motif, reduction of BCL11A expression, and induction of fetal γ-globin. We optimize conditions for selection-free on-target editing in patient-derived HSCs as a nearly complete reaction lacking detectable genotoxicity or deleterious impact on stem cell function. HSCs preferentially undergo non-homologous compared with microhomology-mediated end joining repair. Erythroid progeny of edited engrafting SCD HSCs express therapeutic levels of HbF and resist sickling, while those from patients with β-thalassemia show restored globin chain balance. Non-homologous end joining repair-based BCL11A enhancer editing approaching complete allelic disruption in HSCs is a practicable therapeutic strategy to produce durable HbF induction.
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http://dx.doi.org/10.1038/s41591-019-0401-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6512986PMC
May 2019

Defining CRISPR-Cas9 genome-wide nuclease activities with CIRCLE-seq.

Nat Protoc 2018 11;13(11):2615-2642

Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.

Circularization for in vitro reporting of cleavage effects by sequencing (CIRCLE-seq) is a sensitive and unbiased method for defining the genome-wide activity (on-target and off-target) of CRISPR-Cas9 nucleases by selective sequencing of nuclease-cleaved genomic DNA (gDNA). Here, we describe a detailed experimental and analytical protocol for CIRCLE-seq. The principle of our method is to generate a library of circularized gDNA with minimized numbers of free ends. Highly purified gDNA circles are treated with CRISPR-Cas9 ribonucleoprotein complexes, and nuclease-linearized DNA fragments are then ligated to adapters for high-throughput sequencing. The primary advantages of CIRCLE-seq as compared with other in vitro methods for defining genome-wide genome editing activity are (i) high enrichment for sequencing nuclease-cleaved gDNA/low background, enabling sensitive detection with low sequencing depth requirements; and (ii) the fact that paired-end reads can contain complete information on individual nuclease cleavage sites, enabling use of CIRCLE-seq in species without high-quality reference genomes. The entire protocol can be completed in 2 weeks, including time for gRNA cloning, sequence verification, in vitro transcription, library preparation, and sequencing.
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http://dx.doi.org/10.1038/s41596-018-0055-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6512799PMC
November 2018

Genetic Inactivation of CD33 in Hematopoietic Stem Cells to Enable CAR T Cell Immunotherapy for Acute Myeloid Leukemia.

Cell 2018 05 31;173(6):1439-1453.e19. Epub 2018 May 31.

Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA. Electronic address:

The absence of cancer-restricted surface markers is a major impediment to antigen-specific immunotherapy using chimeric antigen receptor (CAR) T cells. For example, targeting the canonical myeloid marker CD33 in acute myeloid leukemia (AML) results in toxicity from destruction of normal myeloid cells. We hypothesized that a leukemia-specific antigen could be created by deleting CD33 from normal hematopoietic stem and progenitor cells (HSPCs), thereby generating a hematopoietic system resistant to CD33-targeted therapy and enabling specific targeting of AML with CAR T cells. We generated CD33-deficient human HSPCs and demonstrated normal engraftment and differentiation in immunodeficient mice. Autologous CD33 KO HSPC transplantation in rhesus macaques demonstrated long-term multilineage engraftment of gene-edited cells with normal myeloid function. CD33-deficient cells were impervious to CD33-targeting CAR T cells, allowing for efficient elimination of leukemia without myelotoxicity. These studies illuminate a novel approach to antigen-specific immunotherapy by genetically engineering the host to avoid on-target, off-tumor toxicity.
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http://dx.doi.org/10.1016/j.cell.2018.05.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6003425PMC
May 2018

Susceptibility of Brazilian isolates of Trypanosoma evansi to suramin sodium: test in experimentally infected mice.

Exp Parasitol 2013 Jul 4;134(3):309-12. Epub 2013 Apr 4.

Department of Microbiology and Parasitology, Universidade Federal de Santa Maria, Santa Maria, Brazil.

This study aimed to evaluate the susceptibility of Brazilian isolates of Trypanosoma evansi to suramin sodium. For this purpose, three isolates of T. evansi (LPV-2005, LPV-2009 and LPV-2010) and seventy mice were used, with the animals divided in 10 groups (A, B, C, D, E, F, G, H, I and J) with seven animals each group. Mice of groups A, B, and C were infected with LPV-2005; Groups D, E and F with LPV-2009 and the groups G, H and I with LPV-2010. The group J was composed by healthy mice or uninfected. The parasitemia was monitored daily through blood smear, and the treatment of all groups was performed three days post-infection (PI), when all mice showed increased parasitemia. Groups A, D and G represented the positives controls, while groups B, E and H received a single dose of suramin sodium at 10 mgkg(-1) intramuscularly. Groups C, F and I were treated with three doses of suramin sodium at 10 mgkg(-1), respecting an interval of 24 h between each dose. Negative blood smears from all animals were obtained 24 h after treatment (AT), status maintained until the end of the experiment (50 days PI). The specific PCR for T. evansi was carried out from blood, showing negative results AT. Therefore, this study showed that a single dose of suramin sodium at 10 mgkg(-1) has the same efficacy of three doses, as recommended by the therapeutic literature. Furthermore, we observed that Brazilian isolates did not show resistance to the drug.
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http://dx.doi.org/10.1016/j.exppara.2013.03.027DOI Listing
July 2013

Biochemistry detection of acetylcholinesterase activity in Trypanosoma evansi and possible functional correlations.

Exp Parasitol 2012 Dec 5;132(4):546-9. Epub 2012 Sep 5.

Department of Chemistry, Universidade Federal de Santa Maria, Brazil.

Several chemical and immunohistochemical techniques can be used for the detection of acetylcholinesterase (AChE) activity. In this experiment we aimed to detect AChE activity in Trypanosoma evansi. For this, the parasites were isolated from the blood of experimentally infected rats using a DEA-cellulose column. Enzymatic activity was determined in trypomastigote forms at 0, 0.2, 0.4, 0.8 and 1.2 mg/mL of protein concentrations by a standard biochemical protocol. At all concentrations tested, the study showed that T. evansi expresses the enzyme AChE and its activity was proportional to the concentration of protein, ranging between 0.64 and 2.70 μmol of AcSCh/h. Therefore, we concluded that it is possible to biochemically detect AChE in T. evansi, an enzyme that may be associated with vital functions of the parasite and also can be related to chemotherapy treatments, as further discussed in this article.
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http://dx.doi.org/10.1016/j.exppara.2012.08.015DOI Listing
December 2012

Susceptibility of mice to Trypanosoma evansi treated with human plasma containing different concentrations of apolipoprotein L-1.

Korean J Parasitol 2011 Dec 16;49(4):427-30. Epub 2011 Dec 16.

Department of Microbiology and Parasitology, Universidade Federal de Santa Maria, Brazil.

The aim of this study was to test the susceptibility of mice to Trypanosoma evansi treated with human plasma containing different concentrations of apolipoprotein L-1 (APOL1). For this experiment, a strain of T. evansi and human plasma (plasmas 1, 2, and 3) from 3 adult males clinically healthy were used. In vivo test used 50 mice divided in 5 groups (A to E) with 10 animals in each group. Animals of groups B to E were infected, and then treated with 0.2 ml of human plasma in the following outline: negative control (A), positive control (B), treatment with plasma 1 (C), treatment with plasma 2 (D), and treatment with plasma 3 (E). Mice treated with human plasma showed an increase in longevity of 40.9 ± 0.3 (C), 20 ± 9.0 (D) and 35.6 ± 9.3 (E) days compared to the control group (B) which was 4.3 ± 0.5 days. The number of surviving mice and free of the parasite (blood smear and PCR negative) at the end of the experiment was 90%, 0%, and 60% for groups C, D, and E, respectively. The quantification of APOL1 was performed due to the large difference in the treatments that differed in the source plasma. In plasmas 1, 2, and 3 was detected the concentration of 194, 99, and 115 mg/dl of APOL1, respectively. However, we believe that this difference in the treatment efficiency is related to the level of APOL1 in plasmas.
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http://dx.doi.org/10.3347/kjp.2011.49.4.427DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279684PMC
December 2011

Biochemical detection of adenosine deaminase in Trypanosoma evansi.

Exp Parasitol 2011 Jul 21;128(3):298-300. Epub 2011 Mar 21.

Department of Microbiology and Parasitology, Universidade Federal de Santa Maria, Brazil.

Biochemical and molecular research on parasites has increased considerably in trypanosomes in the recent years. Many of them have the purpose of identify areas, proteins and structures of the parasite which are vulnerable and could be used in therapy against the protozoan. Based on this hypothesis this study aimed to detect biochemically the enzyme adenosine deaminase (ADA) in Trypanosoma evansi, and to adapt an assay to the measurement of its activity in trypomastigotes. Firstly, the parasites were separated from the blood of mice experimentally infected with a DEAE-cellulose column. The ADA activity in trypomastigotes was evaluated at concentrations of 0.1, 0.2, 0.5, 0.6 and 0.8mg of protein by spectrophotometry. ADA activity was observed in the parasites at all concentrations tested and its activity was proportional to the concentration of protein, ranging between 0.64 and 2.24U/L in the lowest and highest concentration of protein, respectively. Therefore, it is possible to detect biochemically ADA in T. evansi, an enzyme that may be associated with vital functions of the parasite, similar to what occurs in mammals. This knowledge may be useful in the association of the chemotherapic treatment with specific inhibitors of the enzyme, in future studies.
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http://dx.doi.org/10.1016/j.exppara.2011.03.002DOI Listing
July 2011