Differences in vector-genome processing and illegitimate integration of non-integrating lentiviral vectors

A variety of mutations in lentiviral vector expression systems have been shown to generate a non-integrating phenotype. We studied a novel 12 base-pair U3-long terminal repeats (LTR) integrase (IN) attachment site deletion (U3-LTR att site) mutant and found similar physical titers to the previously reported IN catalytic core mutant IN/D116N. Both mutations led to a greater than two log reduction in vector integration; with IN/D116N providing lower illegitimate integration frequency, whereas the U3-LTR att site mutant provided a higher level of transgene expression. The improved expression of the U3-LTR att site mutant could not be explained solely based on an observed modest increase in integration frequency. In evaluating processing, we noted significant differences in unintegrated vector forms, with the U3-LTR att site mutant leading to a predominance of 1-LTR circles. The mutations also differed in the manner of illegitimate integration. The U3-LTR att site mutant vector demonstrated IN-mediated integration at the intact U5-LTR att site and non-IN-mediated integration at the mutated U3-LTR att site. Finally, we combined a variety of mutations and modifications and assessed transgene expression and integration frequency to show that combining modifications can improve the potential clinical utility of non-integrating lentiviral vectors

Low energy electron interactions with resveratrol and resorcinol: anion states and likely dissociation pathways

We report a computational study of the anion states of the resveratrol (RV) and resorcinol (RS) molecules, also investigating dissociative electron attachment (DEA) pathways. RV has well known beneficial effects in human health, and its antioxidant activity was previously associated with DEA reactions producing H$_2$. Our calculations indicate a valence bound state ($\pi^*_1$) and four resonances ($\pi^*_2$ to $\pi^*_5$) for that system. While the computed thermodynamical thresholds are compatible with DEA reactions producing H$_2$ at 0~eV, the well known mechanism involving vibrational Feshbach resonances built on a dipole bound state should not be present in RV. Our results suggest that the shallow $\pi^*_1$ valence bound state is expected to account for H$_2$ elimination, probably involving $\pi_1^*$/$\sigma_{\text{OH}}^*$ couplings along the vibration dynamics. The RS molecule is also an oxidant and a subunit of RV. Since two close-lying hydroxyl groups are found in the RS moiety, the H$_2$-elimination reaction in RV should take place at the RS site. Our calculations point out a correspondence between the anion states of RV and RS, and even between the thresholds. Nevertheless, the absence of bound anion states in RS, indicated by our calculations, is expected to suppress the H$_2$-formation channel at 0~eV. One is lead to conclude that the ethene and phenol subunits in RV stabilize the $\pi^*_1$ state, thus switching on the DEA mechanism producing H$_2$.Comment: 29 pages, 13 figure

Yeast Bloodstream Infections in the COVID-19 Patient: A Multicenter Italian Study (FiCoV Study)

Fungemia is a co-infection contributing to the worsening of the critically ill COVID-19 patient. The multicenter Italian observational study FiCoV aims to estimate the frequency of yeast bloodstream infections (BSIs), to describe the factors associated with yeast BSIs in COVID-19 patients hospitalized in 10 hospitals, and to analyze the antifungal susceptibility profiles of the yeasts isolated from blood cultures. The study included all hospitalized adult COVID-19 patients with a yeast BSI; anonymous data was collected from each patient and data about antifungal susceptibility was collected. Yeast BSI occurred in 1.06% of patients, from 0.14% to 3.39% among the 10 participating centers. Patients were mainly admitted to intensive or sub-intensive care units (68.6%), over 60 years of age (73%), with a mean and median time from the hospitalization to fungemia of 29 and 22 days, respectively. Regarding risk factors for fungemia, most patients received corticosteroid therapy during hospitalization (61.8%) and had a comorbidity (25.3% diabetes, 11.5% chronic respiratory disorder, 9.5% cancer, 6% haematological malignancies, 1.4% organ transplantation). Antifungal therapy was administered to 75.6% of patients, mostly echinocandins (64.5%). The fatality rate observed in COVID-19 patients with yeast BSI was significantly higher than that of COVID-19 patients without yeast BSI (45.5% versus 30.5%). Candida parapsilosis (49.8%) and C. albicans (35.2%) were the most fungal species isolated; 72% of C. parapsilosis strains were fluconazole-resistant (range 0–93.2% among the centers). The FiCoV study highlights a high prevalence of Candida BSIs in critically ill COVID-19 patients, especially hospitalized in an intensive care unit, a high fatality rate associated with the fungal co-infection, and the worrying spread of azole-resistant C. parapsilosis

Sequential dissociation of ionized benzonitrile: New pathways to reactive interstellar ions and neutrals

Since benzonitrile’s discovery in the interstellar medium (ISM) in 2018, several studies have explored the strongest unimolecular dissociations of its radical cation (C6H5CN•+). However, sequential dissociation processes, which become important when ionization occurs with significant excess energy transfer, have received almost no attention to date. The present metastable dissociative ionization experiments reveal 14 different dissociations, of which 11 have never been observed before. Nine of these new reactions involve the dissociation of a fragment ion. A notable result shows that C4H2 •+ production (the second most intense fragment ion in conventional mass spectra without metastable dissociation analysis) derives from sequential dissociation via C6H4 •+ , as well as from the previously reported unimolecular dissociation of C6H5CN •+ . Furthermore, our experiments demonstrate new pathways that produce astrochemically important neutrals including HCN/CNH and CN• , as well as revealing CH• and C3H• production from ionized benzonitrile for the first time. In addition to the metastable dissociation experiments, we applied density functional theory to calculate two sequential dissociation routes and report the results of our detailed analysis of the peak shapes in a conventional mass spectrum of benzonitrile. The latter enabled the dominant ion to be identified in peaks with nearest-integer m/z values that match two conceivable ions. The present identification of C6H2N+ production using this approach allows its presence in the ISM to be inferred for the first time. This paper extends our understanding of how the dissociative ionization of benzonitrile can contribute to the abundances of radicals and other reactive species in interstellar environments

Mutation in erythroid specific transcription factor KLF1 causes Hereditary Spherocytosis in the Nan hemolytic anemia mouse model

KLF1 regulates definitive erythropoiesis of red blood cells by facilitating transcription through high affinity binding to CACCC elements within its erythroid specific target genes including those encoding erythrocyte membrane skeleton (EMS) proteins. Deficiencies of EMS proteins in humans lead to the hemolytic anemia Hereditary Spherocytosis (HS) which includes a subpopulation with no known genetic defect. Here we report that a mutation, E339D, in the second zinc finger domain of KLF1 is responsible for HS in the mouse model Nan. The causative nature of this mutation was verified with an allelic test cross between Nan/+ and heterozygous Klf1(+/-) knockout mice. Homology modeling predicted Nan KLF1 binds CACCC elements more tightly, suggesting that Nan KLF1 is a competitive inhibitor of wild-type KLF1. This is the first association of a KLF1 mutation with a disease state in adult mammals and also presents the possibility of being another causative gene for HS in humans

Revisiting CN − Formation Mechanisms in Electron Collisions with Benzonitrile

Radiation‐induced processes in the aromatic cyano compound benzonitrile have attracted renewed interest since its detection in the interstellar medium in 2018, and recent studies have elucidated dissociative ionization pathways leading to species such as CN• and HCN, which can play important roles in interstellar chemistry. This work explores negative ion formation from benzonitrile upon electron attachment with mass spectrometry experiments and the most extensive theoretical study to date of the underlying negative ion states and their respective dissociative relaxation pathways. The measurements confirm the previously reported CN− formation at a collision energy of 3.0 eV as well as formation of the dehydrogenated parent anion and phenyl anion and CN− formation in the 7–10 eV energy range. Threshold energies for these dissociation channels are reported at the G4(MP2) level of theory for the first time. Furthermore, by using both scattering calculations and bound state techniques, CN− formation at around 3.0 eV may proceed from a 2B1, π4* shape resonance through nonadiabatic coupling with the σ*, C CN state. In the 7–10 eV range, complete active space plus second‐order perturbation (CASPT2) calculations suggest strong contributions from core excited π4* and σ* resonances

Abrogated cryptic activation of lentiviral transfer vectors

Despite significant improvements in lentivirus (LV) vector-based gene therapy there are still several safety risks using LV vectors including the potential formation of replication-competent LV particles. To address this shortcoming, we constructed a novel and safer gene transfer system using modified SIN-based LV gene transfer vectors. Central to our approach is a conditional deletion of the Ψ packaging signal after integration in the target genome. Here we demonstrate that after transduction of target cells, conventional SIN-based LV transfer vectors can still be mobilized. However mobilization is rendered undetectable if transductions are followed by a Cre/loxP-mediated excision of Ψ. Thus conditional elimination of the packaging signal may represent another advance in increasing the safety of LV vectors for gene therapeutic treatment of chronic diseases

Replication competent retrovirus testing (RCR) in the National Gene Vector Biorepository: No evidence of RCR in 1,595 post-treatment peripheral blood samples obtained from 60 clinical trials

The clinical impact of any therapy requires the product be safe and effective. Gammaretroviral vectors pose several unique risks, including inadvertent exposure to replication competent retrovirus (RCR) that can arise during vector manufacture. The US FDA has required patient monitoring for RCR, and the National Gene Vector Biorepository is an NIH resource that has assisted eligible investigators in meeting this requirement. To date, we have found no evidence of RCR in 338 pre-treatment and 1,595 post-treatment blood samples from 737 patients associated with 60 clinical trials. Most samples (75%) were obtained within 1 year of treatment, and samples as far out as 9 years after treatment were analyzed. The majority of trials (93%) were cancer immunotherapy, and 90% of the trials used vector products produced with the PG13 packaging cell line. The data presented here provide further evidence that current manufacturing methods generate RCR-free products and support the overall safety profile of retroviral gene therapy

Platelet-targeted gene therapy with human factor VIII establishes haemostasis in dogs with haemophilia A

It is essential to improve therapies for controlling excessive bleeding in patients with haemorrhagic disorders. As activated blood platelets mediate the primary response to vascular injury, we hypothesize that storage of coagulation Factor VIII within platelets may provide a locally inducible treatment to maintain haemostasis for haemophilia A. Here we show that haematopoietic stem cell gene therapy can prevent the occurrence of severe bleeding episodes in dogs with haemophilia A for at least 2.5 years after transplantation. We employ a clinically relevant strategy based on a lentiviral vector encoding the ITGA2B gene promoter, which drives platelet-specific expression of human FVIII permitting storage and release of FVIII from activated platelets. One animal receives a hybrid molecule of FVIII fused to the von Willebrand Factor propeptide-D2 domain that traffics FVIII more effectively into α-granules. The absence of inhibitory antibodies to platelet-derived FVIII indicates that this approach may have benefit in patients who reject FVIII replacement therapies. Thus, platelet FVIII may provide effective long-term control of bleeding in patients with haemophilia A. Haemophilia is a genetic bleeding disorder associated with a deficiency in the coagulation factor VIII. Here, the authors use gene therapy to achieve stable overexpression of factor VIII in platelets of dogs with haemophilia A, preventing the occurrence of severe bleeding episodes for over 2.5 years