The CRISPR-Cas9 system provides a versatile toolkit for genome engineering that can introduce various DNA lesions at specific genomic locations. However, a better understanding of the nature of these ...lesions and the repair pathways engaged is critical to realizing the full potential of this technology. Here we characterize the different lesions arising from each Cas9 variant and the resulting repair pathway engagement. We demonstrate that the presence and polarity of the overhang structure is a critical determinant of double-strand break repair pathway choice. Similarly, single nicks deriving from different Cas9 variants differentially activate repair: D10A but not N863A-induced nicks are repaired by homologous recombination. Finally, we demonstrate that homologous recombination is required for repairing lesions using double-stranded, but not single-stranded DNA as a template. This detailed characterization of repair pathway choice in response to CRISPR-Cas9 enables a more deterministic approach for designing research and therapeutic genome engineering strategies.
The capacity to repair different types of DNA damage varies among individuals, making them more or less susceptible to the detrimental health consequences of damage exposures. Current methods for ...measuring DNA repair capacity (DRC) are relatively labor intensive, often indirect, and usually limited to a single repair pathway. Here, we describe a fluorescence-based multiplex flow-cytometric host cell reactivation assay (FM-HCR) that measures the ability of human cells to repair plasmid reporters, each bearing a different type of DNA damage or different doses of the same type of DNA damage. FM-HCR simultaneously measures repair capacity in any four of the following pathways: nucleotide excision repair, mismatch repair, base excision repair, nonhomologous end joining, homologous recombination, and methylguanine methyltransferase. We show that FM-HCR can measure interindividual DRC differences in a panel of 24 cell lines derived from genetically diverse, apparently healthy individuals, and we show that FM-HCR may be used to identify inhibitors or enhancers of DRC. We further develop a next-generation sequencing-based HCR assay (HCR-Seq) that detects rare transcriptional mutagenesis events due to lesion bypass by RNA polymerase, providing an added dimension to DRC measurements. FM-HCR and HCR-Seq provide powerful tools for exploring relationships among global DRC, disease susceptibility, and optimal treatment.
Alkylating agents are ubiquitous in our internal and external environments, causing DNA damage that contributes to mutations and cell death that can result in aging, tissue degeneration and cancer. ...Repair of methylated DNA bases occurs primarily through the base excision repair (BER) pathway, a multi-enzyme pathway initiated by the alkyladenine DNA glycosylase (Aag, also known as Mpg). Previous work demonstrated that mice treated with the alkylating agent methyl methanesulfonate (MMS) undergo cerebellar degeneration in an Aag-dependent manner, whereby increased BER initiation by Aag causes increased tissue damage that is dependent on activation of poly (ADP-ribose) polymerase 1 (Parp1). Here, we dissect the molecular mechanism of cerebellar granule neuron (CGN) sensitivity to MMS using primary ex vivo neuronal cultures. We first established a high-throughput fluorescent imaging method to assess primary neuron sensitivity to treatment with DNA damaging agents. Next, we verified that the alkylation sensitivity of CGNs is an intrinsic phenotype that accurately recapitulates the in vivo dependency of alkylation-induced CGN cell death on Aag and Parp1 activity. Finally, we show that MMS-induced CGN toxicity is independent of all the cellular events that have previously been associated with Parp-mediated toxicity, including mitochondrial depolarization, AIF translocation, calcium fluxes, and NAD+ consumption. We therefore believe that further investigation is needed to adequately describe all varieties of Parp-mediated cell death.
Inefficient knock-in of transgene cargos limits the potential of cell-based medicines. In this study, we used a CRISPR nuclease that targets a site within an exon of an essential gene and designed a ...cargo template so that correct knock-in would retain essential gene function while also integrating the transgene(s) of interest. Cells with non-productive insertions and deletions would undergo negative selection. This technology, called SLEEK (SeLection by Essential-gene Exon Knock-in), achieved knock-in efficiencies of more than 90% in clinically relevant cell types without impacting long-term viability or expansion. SLEEK knock-in rates in T cells are more efficient than state-of-the-art TRAC knock-in with AAV6 and surpass more than 90% efficiency even with non-viral DNA cargos. As a clinical application, natural killer cells generated from induced pluripotent stem cells containing SLEEK knock-in of CD16 and mbIL-15 show substantially improved tumor killing and persistence in vivo.
Precise correction of the CD40LG gene in T cells and hematopoietic stem/progenitor cells (HSPC) holds promise for treating X‐linked hyper‐IgM Syndrome (HIGM1), but its actual therapeutic potential ...remains elusive. Here, we developed a one‐size‐fits‐all editing strategy for effective T‐cell correction, selection, and depletion and investigated the therapeutic potential of T‐cell and HSPC therapies in the HIGM1 mouse model. Edited patients’ derived CD4 T cells restored physiologically regulated CD40L expression and contact‐dependent B‐cell helper function. Adoptive transfer of wild‐type T cells into conditioned HIGM1 mice rescued antigen‐specific IgG responses and protected mice from a disease‐relevant pathogen. We then obtained ~ 25% CD40LG editing in long‐term repopulating human HSPC. Transplanting such proportion of wild‐type HSPC in HIGM1 mice rescued immune functions similarly to T‐cell therapy. Overall, our findings suggest that autologous edited T cells can provide immediate and substantial benefits to HIGM1 patients and position T‐cell ahead of HSPC gene therapy because of easier translation, lower safety concerns and potentially comparable clinical benefits.
Synopsis
Here we report a comprehensive set of preclinical studies, performed both in vitro on X‐linked hyper‐IgM syndrome (HIGM1) patient‐derived cells and in vivo in HIGM1 mice, which uncovers crucial guiding principles towards clinical translation of CD40LG targeted gene correction in T cells or hematopoietic stem cells (HSC) for the treatment of HIGM1.
Efficient targeted integration of a corrective cDNA within the first intron of CD40LG in both T cells and HSC restored regulated CD40L expression with full functionality.
Coupling the corrective cDNA to a clinically compatible selector allows enriching, tracking, depleting edited CD4+ T cells and fully rescuing the physiological CD40L surface expression.
Adoptive transfer of functional CD4+ T cells or transplantation of a fraction of functional HSC, modelling editing efficiencies achieved in human HSC, reveals similar therapeutic potential in HIGM1 mice.
The corrective potential of T cell therapy depends on the engrafted T cell dose and may bypass the requirement for conditioning regimen when cells are sourced from antigen‐primed donors.
Here we report a comprehensive set of preclinical studies, performed both in vitro on X‐linked hyper‐IgM syndrome (HIGM1) patient‐derived cells and in vivo in HIGM1 mice, which uncovers crucial guiding principles towards clinical translation of CD40LG targeted gene correction in T cells or hematopoietic stem cells (HSC) for the treatment of HIGM1.
Regulated necrosis has emerged as a major cell death mechanism in response to different forms of physiological and pharmacological stress. The AlkB homolog 7 (ALKBH7) protein is required for ...regulated cellular necrosis in response to chemotherapeutic alkylating agents but its role within a whole organism is unknown. Here, we show that ALKBH7 modulates alkylation-induced cellular death through a tissue and sex-specific mechanism. At the whole-animal level, we find that ALKBH7 deficiency confers increased resistance to MMS-induced toxicity in male but not female mice. Moreover, ALKBH7-deficient mice exhibit protection against alkylation-mediated cytotoxicity in retinal photoreceptor and cerebellar granule cells, two cell types that undergo necrotic death through the initiation of the base excision repair pathway and hyperactivation of the PARP1/ARTD1 enzyme. Notably, the protection against alkylation-induced cerebellar degeneration is specific to ALKBH7-deficient male but not female mice. Our results uncover an in vivo role for ALKBH7 in mediating a sexually dimorphic tissue response to alkylation damage that could influence individual responses to chemotherapies based upon alkylating agents.
We have previously shown that CRISPR/Cas9 mediates high levels of gene editing in adult human CD34+ hematopoietic stem and progenitor cells (HSPCs). We now demonstrated that high levels of gene ...editing can also be achieved in HSPCs using Cpf1. In addition to NHEJ-mediated gene editing, we explored targeted integration at the ß-hemoglobin gene (HBB) with Cas9, toward gene correction for sickle cell disease (SCD). For targeted integration strategies at HBB, we designed AAV6 DNA donor repair templates flanked by either DNA sequences homologous to the cut site in the genomic location of the SCD mutation or DNA sequences non-homologous to the human genome. To evaluate targeted integration in HSPCs, adult mobilized peripheral blood (mPB) CD34+ cells were electroporated with Cas9 ribonucleoprotein (RNP) and were then transduced with AAV6 containing DNA repair templates with or without homology arms. We analyzed targeted integration at the HBB target site by digital droplet PCR (ddPCR) analysis 7 days after transduction of mPB CD34+ cells. The ddPCR results show ~30% targeted integration in HBB in mPB CD34+ cells with no impact on cell viability. DNA sequencing analysis supported the ddPCR results indicating that perfect homology directed repair-driven integration of the DNA donor template was the preferential repair mechanism. Less than 1% of targeted integration was detected by ddPCR in mPB CD34+ cells transduced with AAV6 DNA repair template that lacked homology arms, suggesting that the mechanism of integration is homology repair dependent. These integrations were maintained in the Glycophorin A+ erythroid progeny of genome-edited mPB CD34+ cells, paving the way toward gene correction for SCD. The combination of CRISPR nucleases (Cpf1, Cas9) and AAV6 DNA repair templates form a powerful genome editing platform that enables broader applications for the treatment of hematologic diseases beyond hemoglobinopathies.
deDreuzy:Editas Medicine: Employment. Chalishazar:Editas Medicine: Employment. Heath:Editas Medicine: Employment. Margulies:Editas Medicine: Employment. Labella:Editas Medicine: Employment. Viswanathan:Editas Medicine: Employment. Loveluck:Editas Medicine: Employment. Chang:Editas Medicine: Employment. Jayaram:Editas Medicine: Employment. Zuris:Editas Medicine: Employment. Myer:Editas Medicine: Employment, Equity Ownership. Albright:Editas Medicine: Employment. Cotta-Ramusino:Editas Medicine: Employment. Gori:Editas Medicine: Employment.
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, 2016.
Cataloged from PDF version of thesis.
Includes bibliographical references.
Methylating agents are ...ubiquitous in our internal and external environments and can cause damage to all cellular components, including our DNA. If left unrepaired, methylated DNA can cause mutations, cell death, and disease, such as cancer and neurodegeneration. The majority of DNA lesions caused by methylating agents are repaired by the base excision repair (BER) pathway, which is initiated by the lesion-specific alkyladenine glycosylase (Aag). Loss of Aag in embryonic stem (ES) cells renders them sensitive to the methylating agent MMS (methyl methanesulfonate) compared to wild-type (WT). Surprisingly, this phenotype is reversed in hematopoietic myeloid progenitors and cerebellar granule neurons (CGNs) where Aag' cells are resistant to MMS induced killing compared to WT. In this study, we investigated how Aag can cause cell-specific responses to alkylating agents. We generated new WT, Aag-/-, and Aag overexpressing (mAagTg) 129 and C57B1/6 ES cells and showed that inbred genetic background did not affect sensitivity to MMS, indicating this to be a cell-intrinsic response. Moreover, we found that cells overexpressing Aag were even more sensitive to MMS than Aag-/- cells, suggesting that ES cells endure methylation treatment best when they express Aag within an optimal range. To study Aag-dependent neural sensitivity to methylating agents, we optimized protocols for the isolation and culture of primary cerebellar granule neurons and determination of cell death after drug treatment by high-throughput imaging. CGNs isolated from WT, Aag-/-, and mAagTg mice exhibited cell sensitivity to MMS treatment that was dependent on Aag and Parp activity, thus recapitulating in vivo results and proving that CGN death is cell-intrinsic. Cell death was independent of caspases, mitochondrial depolarization, and AIF translocation. We did observe the formation of enlarged mitochondria and are investigating whether mitochondrial dynamics are causative of cell death in an Aag-dependent manner. Finally, we used in vitro hematopoietic and neuronal differentiation to monitor cell responses to MMS as a function of cellular development. Three different methods all successfully generated mature neurons based on morphology, immunochemical staining, and Aag expression. Though we successfully differentiated ES cells into cell types of interest, we are continuing to optimize methods for the assessment of alkylation sensitivity in the resulting heterogeneous populations.
by Carrie Marie Margulies.
Ph. D.
Abstract Background Heart failure in patients with preserved left ventricular systolic function (HFpEF) is a prevalent disease characterized by exercise intolerance with poorly understood ...pathophysiology. We hypothesized that recruitable contractility is impaired in HFpEF, accounting for the appearance of symptoms with exertion. Methods and Results Echocardiographic analysis of myocardial performance was performed at baseline and after a modified dobutamine protocol (max dose 16 μg/kg/min) in participants with known HFpEF and age- and gender-matched controls. The primary outcome variable was change in contractile reserve, measured as a change in ejection fraction (EF). Recruitable contractility was decreased in HFpEF participants compared with control subjects (HFpEF 0.4 ± 1.9% vs control 19.0 ± 1.4%; P < .001). During dobutamine infusion, velocities increased in control participants but remained unchanged in the HFpEF group, yielding a significant difference between groups ( P < .05) for both longitudinal displacement and velocity. Conclusions Patients with HFpEF have an impaired contractile response to adrenergic stimulation. The blunted response to adrenergic stimulation in the HFpEF group suggests that these patients may be unable to respond to periods of increased cardiac demand. This inability to increase contractility appropriately suggests abnormalities of systolic function in this disease and may contribute to exertional intolerance in HFpEF.
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, ...alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization.
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