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MicroRNAs (miRNAs) are increasingly recognized for their role in infection by bacterial pathogens, although the effect of each individual miRNA remains largely unknown. Here, we used a comparative genome-wide microscopy-based functional screening approach to identify miRNAs controlling infection by two bacterial pathogens-Salmonella enterica serovar Typhimurium and Shigella flexneri. Despite the similarities between these pathogens, we found infections to be controlled by largely non-overlapping subsets of miRNAs, seemingly reflecting different requirements prompted by their distinct intracellular lifestyles. By characterizing a small subset of miRNAs chosen among the strongest inhibitors of Shigella infection, we discovered that miR-3668, miR-4732-5p and miR-6073 exert a selective effect on Shigella infection by impairing bacterial actin-based motility by downregulating N-WASP. Additionally, by identifying let-7i-3p miRNA as a strong inhibitor of Salmonella replication and performing in-depth analysis of its mechanisms of action, we showed that this miRNA specifically inhibits Salmonella infection via modulation of endolysosomal trafficking and the vacuolar environment by targeting the host RGS2 protein. These findings illustrate two paradigms underlying miRNA-mediated regulation of bacterial infection, acting as part of the host response to infection, or as part of bacterial strategies to modulate the host environment and favour pathogenesis.

SARS-CoV-2 entry requires sequential cleavage of the spike glycoprotein at the S1/S2 and the S2' cleavage sites to mediate membrane fusion. SARS-CoV-2 has a polybasic insertion (PRRAR) at the S1/S2 cleavage site that can be cleaved by furin. Using lentiviral pseudotypes and a cell-culture-adapted SARS-CoV-2 virus with an S1/S2 deletion, we show that the polybasic insertion endows SARS-CoV-2 with a selective advantage in lung cells and primary human airway epithelial cells, but impairs replication in Vero E6, a cell line used for passaging SARS-CoV-2. Using engineered spike variants and live virus competition assays and by measuring growth kinetics, we find that the selective advantage in lung and primary human airway epithelial cells depends on the expression of the cell surface protease TMPRSS2, which enables endosome-independent virus entry by a route that avoids antiviral IFITM proteins. SARS-CoV-2 virus lacking the S1/S2 furin cleavage site was shed to lower titres from infected ferrets and was not transmitted to cohoused sentinel animals, unlike wild-type virus. Analysis of 100,000 SARS-CoV-2 sequences derived from patients and 24 human postmortem tissues showed low frequencies of naturally occurring mutants that harbour deletions at the polybasic site. Taken together, our findings reveal that the furin cleavage site is an important determinant of SARS-CoV-2 transmission.

There is an impelling need to develop new therapeutics for myocardial infarction and heart failure. A novel and exciting therapeutic possibility is to achieve cardiac regeneration through the stimulation of the endogenous capacity of cardiomyocytes to proliferate. Proof-of-concept evidence of microRNA-induced cardiac regeneration is available in both small and large animals using viral vectors. However, a clinically more applicable strategy is the development of lipid-mediated nanotechnologies for the administration of RNA therapeutics as synthetic molecules. The recent success of the Stable Nucleic Acid Lipid Particle (SNALP) platform for the generation of nanosized, efficient and non-inflammatory lipid nanoparticles paves the way to the development of injectable nanoformulations of microRNAs through cardiac catheterisation.

Loss of skeletal muscle mass and force is of critical importance in numerous pathologies, like age-related sarcopenia or cancer. It has been shown that the Akt-mTORC1 pathway is critical for stimulating adult muscle mass and function, however, it is unknown if mTORC1 is the only mediator downstream of Akt and which intracellular processes are required for functional muscle growth. Here, we show that loss of Raptor reduces muscle hypertrophy after Akt activation and completely prevents increases in muscle force. Interestingly, the residual hypertrophy after Raptor deletion can be completely prevented by administration of the mTORC1 inhibitor rapamycin. Using a quantitative proteomics approach we find that loss of Raptor affects the increases in mitochondrial proteins, while rapamycin mainly affects ribosomal proteins. Taken together, these results suggest that mTORC1 is the key mediator of Akt-dependent muscle growth and its regulation of the mitochondrial proteome is critical for increasing muscle force.

Summary Currently, all methods for converting non-neuronal cells into neurons involve injury to the brain; however, whether neuronal transdifferentiation can occur long after the period of insult remains largely unknown. Here, we use the transcription factor NEUROD1, previously shown to convert reactive glial cells to neurons in the cortex, to determine whether astrocyte-to-neuron transdifferentiation can occur under physiological conditions. We utilized adeno-associated virus 9 (AAV9), which crosses the blood-brain barrier without injury, to deliver NEUROD1 to astrocytes through an intravascular route. Interestingly, we found that a small, but significant number of non-reactive astrocytes converted to neurons in the striatum, but not the cortex. Moreover, astrocytes cultured to minimize their proliferative potential also exhibited limited neuronal transdifferentiation with NEUROD1 expression. Our results show that a single transcription factor can induce astrocyte-to-neuron conversion under physiological conditions, potentially facilitating future clinical approaches long after the acute injury phase., Highlights • Intravascular AAV9 efficiently targets astrocytes in the cortex and striatum • NEUROD1 can convert a small, but significant number of astrocytes to neurons in vivo • NEUROD1 induces limited neuronal transdifferentiation in vitro • Injury-related factors may be important in neuronal conversion strategies, In this article, Hsieh and colleagues use AAV9 viral infection to selectively target and overexpress NEUROD1 in astrocytes in the absence of injury to the CNS. The authors show that NEUROD1 is capable of converting a small, but significant number of astrocytes to neurons in vivo in the absence of reactive gliosis.

Hereditary hearing loss (HHL) is an extremely heterogeneous disorder with autosomal dominant, recessive, and X-linked forms. Here, we described an Italian pedigree affected by HHL but also prostate hyperplasia and increased ratio of the free/total PSA levels, with the unusual and extremely rare Y-linked pattern of inheritance. Using exome sequencing we found a missense variant (r.206A>T leading to p.Asp69Val) in the TBL1Y gene. TBL1Y is homologous of TBL1X, whose partial deletion has described to be involved in X-linked hearing loss. Here, we demonstrate that it has a restricted expression in adult human cochlea and prostate and the variant identified induces a lower protein stability caused by misfolded mutated protein that impairs its cellular function. These findings indicate that TBL1Y could be considered a novel candidate for HHL.

Heart failure is preceded by ventricular remodeling, changes in left ventricular mass, and myocardial volume after alterations in loading conditions. Concentric hypertrophy arises after pressure overload, involves wall thickening, and forms a substrate for diastolic dysfunction. Eccentric hypertrophy develops in volume overload conditions and leads wall thinning, chamber dilation, and reduced ejection fraction. The molecular events underlying these distinct forms of cardiac remodeling are poorly understood. Here, we demonstrate that miR-148a expression changes dynamically in distinct subtypes of heart failure: while it is elevated in concentric hypertrophy, it decreased in dilated cardiomyopathy. In line, antagomir-mediated silencing of miR-148a caused wall thinning, chamber dilation, increased left ventricle volume, and reduced ejection fraction. Additionally, adeno-associated viral delivery of miR-148a protected the mouse heart from pressure-overload-induced systolic dysfunction by preventing the transition of concentric hypertrophic remodeling toward dilation. Mechanistically, miR-148a targets the cytokine co-receptor glycoprotein 130 (gp130) and connects cardiomyocyte responsiveness to extracellular cytokines by modulating the Stat3 signaling. These findings show the ability of miR-148a to prevent the transition of pressure-overload induced concentric hypertrophic remodeling toward eccentric hypertrophy and dilated cardiomyopathy and provide evidence for the existence of separate molecular programs inducing distinct forms of myocardial remodeling., Raso et al. show that miR-148a is elevated in concentric hypertrophy and decreased in dilated cardiomyopathy. Adeno-associated viral delivery of miR-148a protects the mouse heart from cardiac dilation. Mechanistically, miR-148a regulates the sensitivity of the heart to extracellular cytokines.

Summary Over the last several years, mesenchymal stromal cells (MSCs) have been isolated from different tissues following a variety of different procedures. Here, we comparatively assess the ex vivo and in vivo properties of MSCs isolated from either adipose tissue or bone marrow by different purification protocols. After MSC transplantation into a mouse model of hindlimb ischemia, clinical and histological analysis revealed that bone marrow MSCs purified on adhesive substrates exerted the best therapeutic activity, preserving tissue viability and promoting formation of new arterioles without directly transdifferentiating into vascular cells. In keeping with these observations, these cells abundantly expressed cytokines involved in vessel maturation and cell retention. These findings indicate that the choice of MSC source and purification protocol is critical in determining the therapeutic potential of these cells and warrant the standardization of an optimal MSC isolation procedure in order to select the best conditions to move forward to more effective clinical experimentation., Graphical Abstract, Highlights • MSCs were isolated from various tissues according to different protocols • All MSCs provided a therapeutic benefit in a hindlimb ischemia model • Adhesive MSCs from bone marrow were the most effective in preserving tissue viability • These cells promoted massive vascularization in a paracrine fashion, Zacchigna and colleagues compared the ex vivo and in vivo properties of mesenchymal stromal cells (MSCs) isolated from either adipose tissue or bone marrow by different protocols. Adhesive MSCs from bone marrow exerted the best therapeutic activity in a hindlimb ischemia model, preserving viability and inducing angiogenesis in a paracrine manner. The optimization of a standard MSC isolation procedure is required to improve clinical results.

International audience; Deciphering the fundamental mechanisms controlling cardiac specification is critical for our understanding of how heart formation is initiated during embryonic development and for applying stem cell biology to regenerative medicine and disease modeling. Using systematic and unbiased functional screening approaches, we discovered that the Id family of helix–loop–helix proteins is both necessary and sufficient to direct cardiac mesoderm formation in frog embryos and human embryonic stem cells. Mechanistically, Id proteins specify cardiac cell fate by repressing two inhibitors of cardiogenic mesoderm formation—Tcf3 and Foxa2—and activating inducers Evx1, Grrp1, and Mesp1. Most importantly, CRISPR/Cas9-mediated ablation of the entire Id (Id1–4) family in mouse embryos leads to failure of anterior cardiac progenitor specification and the development of heartless embryos. Thus, Id proteins play a central and evolutionarily conserved role during heart formation and provide a novel means to efficiently produce cardiovascular progenitors for regenerative medicine and drug discovery applications.

Unacylated ghrelin (UnAG) may lower skeletal muscle oxidative stress, inflammation, and insulin resistance in lean and obese rodents. UnAG-induced autophagy activation may contribute to these effects, likely involving removal of dysfunctional mitochondria (mitophagy) and redox state maintenance. In chronic kidney disease (CKD) oxidative stress, inflammation and insulin resistance may negatively influence patient outcome by worsening nutritional state through muscle mass loss. Here we show in a 5/6 nephrectomy (Nx) CKD rat model that 4 d s.c. UnAG administration (200 µg twice a day) normalizes CKD-induced loss of gastrocnemius muscle mass and a cluster of high tissue mitochondrial reactive oxygen species generation, high proinflammatory cytokines, and low insulin signaling activation. Consistent with these results, human uremic serum enhanced mitochondrial reactive oxygen species generation and lowered insulin signaling activation in C2C12 myotubes while concomitant UnAG incubation completely prevented these effects. Importantly, UnAG enhanced muscle mitophagy in vivo and silencing RNA-mediated autophagy protein 5 silencing blocked UnAG activities in myotubes. UnAG therefore normalizes CKD-induced skeletal muscle oxidative stress, inflammation, and low insulin signaling as well as muscle loss. UnAG effects are mediated by autophagy activation at the mitochondrial level. UnAG administration and mitophagy activation are novel potential therapeutic strategies for skeletal muscle metabolic abnormalities and their negative clinical impact in CKD.-Gortan Cappellari, G., Semolic, A., Ruozi, G., Vinci, P., Guarnieri, G., Bortolotti, F., Barbetta, D., Zanetti, M., Giacca, M., Barazzoni, R. Unacylated ghrelin normalizes skeletal muscle oxidative stress and prevents muscle catabolism by enhancing tissue mitophagy in experimental chronic kidney disease.

Ex vivo gene transfer to the graft before transplantation is an attractive option for circumventing systemic side effects of chronic antirejection therapy. Gene delivery of the immunomodulatory protein cytotoxic T-lymphocyte-associated protein 4-immunoglobulin (CTLA4-Ig) prevented chronic kidney rejection in a rat model of allotransplantation without the need for systemic immunosuppression. Here we generated adeno-associated virus type 2 (AAV2) and AAV9 vectors encoding for LEA29Y, an optimized version of CTLA4-Ig. Both LEA29Y vectors were equally efficient for reducing T-cell proliferation in vitro. Serotype 9 was chosen for in vivo experiments owing to a lower frequency of preformed antibodies against the AAV9 capsid in 16 non-human primate tested sera. AAV9-LEA29Y was able to transduce the kidney of non-human primates in an autotransplantation model. Expression of LEA29Y mRNA by renal cells translated into the production of the corresponding protein, which was confined to the graft but not detected in serum. Results in non-human primates represent a step forward in maintaining the portability of this strategy into clinics.

Background— Cardiac hypertrophy and subsequent heart failure triggered by chronic hypertension represent major challenges for cardiovascular research. Beyond neurohormonal and myocyte signaling pathways, growing evidence suggests inflammatory signaling pathways as therapeutically targetable contributors to this process. We recently reported that microRNA-155 is a key mediator of cardiac inflammation and injury in infectious myocarditis. Here, we investigated the impact of microRNA-155 manipulation in hypertensive heart disease. Methods and Results— Genetic loss or pharmacological inhibition of the leukocyte-expressed microRNA-155 in mice markedly reduced cardiac inflammation, hypertrophy, and dysfunction on pressure overload. These alterations were macrophage dependent because in vivo cardiomyocyte-specific microRNA-155 manipulation did not affect cardiac hypertrophy or dysfunction, whereas bone marrow transplantation from wild-type mice into microRNA-155 knockout animals rescued the hypertrophic response of the cardiomyocytes and vice versa. In vitro, media from microRNA-155 knockout macrophages blocked the hypertrophic growth of stimulated cardiomyocytes, confirming that macrophages influence myocyte growth in a microRNA-155 -dependent paracrine manner. These effects were at least partly mediated by the direct microRNA-155 target suppressor of cytokine signaling 1 (Socs1) because Socs1 knockdown in microRNA-155 knockout macrophages largely restored their hypertrophy-stimulating potency. Conclusions— Our findings reveal that microRNA-155 expression in macrophages promotes cardiac inflammation, hypertrophy, and failure in response to pressure overload. These data support the causative significance of inflammatory signaling in hypertrophic heart disease and demonstrate the feasibility of therapeutic microRNA targeting of inflammation in heart failure.

Clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) 9 genomic editing has revolutionized the generation of mutant animals by simplifying the creation of null alleles in virtually any organism. However, most current approaches with this method require zygote injection, making it difficult to assess the adult, tissue-specific functions of genes that are widely expressed or which cause embryonic lethality when mutated. Here, we describe the generation of cardiac-specific Cas9 transgenic mice, which express high levels of Cas9 in the heart, but display no overt defects. In proof-of-concept experiments, we used Adeno-Associated Virus 9 (AAV9) to deliver single-guide RNA (sgRNA) that targets the Myh6 locus exclusively in cardiomyocytes. Intraperitoneal injection of postnatal cardiac-Cas9 transgenic mice with AAV9 encoding sgRNA against Myh6 resulted in robust editing of the Myh6 locus. These mice displayed severe cardiomyopathy and loss of cardiac function, with elevation of several markers of heart failure, confirming the effectiveness of this method of adult cardiac gene deletion. Mice with cardiac-specific expression of Cas9 provide a tool that will allow rapid and accurate deletion of genes following a single injection of AAV9-sgRNAs, thereby circumventing embryonic lethality. This method will be useful for disease modeling and provides a means of rapidly editing genes of interest in the heart.

Diabetes is a cause of cardiac dysfunction, reduced myocardial perfusion, and ultimately heart failure. Nerve growth factor (NGF) exerts protective effects on the cardiovascular system. This study investigated whether NGF gene transfer can prevent diabetic cardiomyopathy in mice. We worked with mice with streptozotocin-induced type 1 diabetes and with nondiabetic control mice. After having established that diabetes reduces cardiac NGF mRNA expression, we tested NGF gene therapies with adeno-associated viral vectors (AAVs) for the capacity to protect the diabetic mouse heart. To this aim, after 2 weeks of diabetes, cardiac expression of human NGF or β-Gal (control) genes was induced by either intramyocardial injection of AAV serotype 2 (AAV2) or systemic delivery of AAV serotype 9 (AAV9). Nondiabetic mice were given AAV2–β-Gal or AAV9–β-Gal. We found that the diabetic mice receiving NGF gene transfer via either AAV2 or AAV9 were spared the progressive deterioration of cardiac function and left ventricular chamber dilatation observed in β-Gal–injected diabetic mice. Moreover, they were additionally protected from myocardial microvascular rarefaction, hypoperfusion, increased deposition of interstitial fibrosis, and increased apoptosis of endothelial cells and cardiomyocytes, which afflicted the β-Gal–injected diabetic control mice. Our data suggest therapeutic potential of NGF for the prevention of cardiomyopathy in diabetic subjects.

Vascular endothelial growth factor A (VEGF-A) induces strong angiogenesis and it has been widely used in proangiogenic gene therapy studies. However, little is known about long-term effects of VEGF-A expression in skeletal muscle. Here the long- term effects of adeno-associated virus (AAV) encoding human VEGF-A(165) (AAV-VEGF-A) gene transfer in normal and ischemic rabbit hindlimb skeletal muscles were studied. AAV-LacZ was used as a control. In one-year follow-up, a remarkable increase in skeletal muscle perfusion compared with AAV-LacZ was observed measured with Doppler and contrast pulse sequence ultrasound. Angiogenesis was also seen in histology as enlarged and sprouting capillaries. In addition to favorable angiogenic effects, aberrant vascular structures with CD31 positive cell layers were seen inside muscle fibers after AAV-VEGF-A gene transfer. Importantly, we found increased amounts of extracellular matrix with a high number of macrophages and fibrosis in AAV-VEGF-A transduced muscles. No changes in skeletal muscle morphology were detected in AAV-LacZ transduced muscles. Our results indicate that local AAV-VEGF-A gene transfer efficiently promotes long-term angiogenesis in large animal model. However, non-regulated expression of VEGF-A causes unfavorable changes in muscle morphology, which suggests the need for regulation of the transgene expression in long-term AAV-mediated VEGF-A gene transfer applications.

The different protein isoforms generated from the vascular endothelial growth factor-A (VEGF-A) gene, an essential regulator of blood vessel formation, differ in biochemical property and functional activity. Despite the relevance of VEGF-A for both normal and pathologic angiogenesis, our understanding of the molecular mechanisms governing alternative splicing of its pre-mRNA is still in its infancy.

Ang-1 (angiopoietin-1) improves the ineffective angiogenesis and impaired wound healing in diabetes; however, the mechanism underlying this positive effect is still far from being completely understood. In the present study, we investigated whether rAAV (recombinant adeno-associated virus)–Ang-1 gene transfer could improve wound repair in genetically diabetic mice ( db +/ db +) and the mechanism(s) by which it causes new vessel formation. An incisional skin-wound model in diabetic and normoglycaemic mice was used. After the incision, animals received rAAV–LacZ or rAAV–Ang-1 in the wound edge. After 7 and 14 days, wounds were used to (i) confirm Ang-1 gene transfer, (ii) assess histologically the healing process, (iii) evaluate wound-breaking strength, and (iv) study new vessel formation by PECAM-1 (platelet/endothelial cell adhesion molecule-1) immunostaining. Finally, we investigated VEGF (vascular endothelial growth factor) mRNA and protein levels, eNOS (endothelial NO synthase) expression and VEGFR-1 and VEGFR-2 (VEGF receptor-1 and -2 respectively) immunostaining. The efficiency of Ang-1 gene transfer was confirmed by increased mRNA and protein expression of the protein. rAAV–Ang-1 significantly improved the healing process, stimulating re-epithelization and collagen maturation, increasing breaking strength and significantly augmenting the number of new vessels, as indicated by PECAM-1 immunostaining. However, Ang-1 gene transfer did not modify the decrease in VEGF mRNA and protein expression in diabetic mice; in contrast, Ang-1 increased eNOS expression and augmented nitrate wound content and VEGFR-2 immunostaining and protein expression. Ang-1 gene transfer did not change vascular permeability. Similar results were obtained in normoglycaemic animals. In conclusion, our results provide strong evidence that Ang-1 gene transfer improves the delayed wound repair in diabetes by inducing angiogenesis in a VEGF-independent manner. Abbreviations: AAV, adeno-associated virus; Ang, angiopoietin; CMV, cytomegalovirus; COMP, cartilage oligomeric matrix protein; EC, endothelial cell; eNOS, endothelial NO synthase; EPC, endothelial progenitor cell; GFP, green fluorescent protein; HEK-293 cells, human embryonic kidney cells; HRP, horseradish peroxidase; MVD, microvessel density; NO2−/NO3−, nitrate/nitrite; PECAM-1, platelet/EC adhesion molecule-1; PlGF, placental growth factor; rAAV, recombinant AAV; RT-PCR, real-time PCR; TBS, Tris-buffered saline; VEGF, vascular endothelial growth factor; VEGFR, VEGF receptor

To date, a complete understanding of the molecular events leading to DNA replication origin activation in mammalian cells still remains elusive. In this work, we report the results of a high resolution chromatin immunoprecipitation study to detect proteins interacting with the human Lamin B2 replication origin. In addition to the pre-RC component ORC4 and to the transcription factors USF and HOXC13, we found that 2 components of the AP-1 transcription factor, c-Fos and c-Jun, are also associated with the origin DNA during the late G1 phase of the cell cycle and that these factors interact with ORC4. Both DNA replication and AP-1 factor binding to the origin region were perturbed by cell treatment with merbarone, a topoisomerase II inhibitor, suggesting that DNA topology is essential for determining origin function.

The Neuregulin/ErbB system plays an important role in the peripheral nervous system, under both normal and pathological conditions. We previously demonstrated that expression of soluble ecto-ErbB4, the released extracellular fragment of the ErbB4 receptor, stimulated glial cell migration in vitro. In this study we examined the possibility of manipulating this system in vivo in order to improve injured peripheral nerve regeneration. Transected rat median nerves of adult female Wistar rats were repaired with a 10-mm-long graft made by muscle-in-vein combined nerve guide previously transduced with either the adeno-associated viral (AAV) vector AAV2-LacZ or AAV2-ecto-ErbB4. Autologous nerve grafts were used as control. Both stereological and functional analyses were performed to assess nerve regeneration. Data show that delivery of soluble ecto-ErbB4 by gene transfer in the muscle-in-vein combined nerve guide has a positive effect on fiber maturation, suggesting that it could represent a potential tool for improving peripheral nerve regeneration.

Through an elegant combination of transgenic techniques, a study by Tian et al. recently published in Science Translational Medicine1 shows that a cluster of five microRNAs (miRNAs), miR-302/367, controls cardiac myocyte proliferation during embryonic and neonatal life. More notably, reactivation of these miRNAs following myocardial infarction promotes re-entry of adult cardiomyocytes into the cell cycle and induces cardiac regeneration. The authors found that these miRNAs interfere with the recently described Hippo pathway that regulates proliferation of various cell types, including cardiomyocytes. More specifically, miR-302/367 directly reduces the expression of three inhibitory proteins in this pathway, leading to the activation of the Yap1 transcription factor, a master regulator of cardiac proliferation. The notion that miRNAs control cardiomyocyte proliferation is not entirely novel. Over the past few years, there has been a flood of exciting evidence that the miRNA network plays an essential role in regulating the extent of cardiomyocyte replication during development and that it might be harnessed in adult hearts to promote repair after myocardial damage. The sudden—and still, for the most part, not understood—arrest of cardiomyocyte proliferation immediately after birth correlates with increased levels of a large set of miRNAs, some of which are causally involved in this event. These include the six members of the miR-15 family2 and miR-29a,3 which target essential components of the cell cycle and checkpoint machineries; inhibition of miR-15 expands the proliferative potential of cardiomyocytes during fetal and early postnatal life and stimulates regeneration after myocardial infarction.4,5 By contrast, several miRNAs act in an opposite manner, by stimulating cardiomyocyte proliferation. A genomic-scale, high-throughput screen performed in my laboratory has shown that at least 40 miRNAs encoded by the human genome are capable of stimulating proliferation of neonatal cardiomyocytes.6 Among these miRNAs are miR-199a-3p, miR-590–3p, and two large families of miRNAs that previous work had shown to be essential in the regulation of embryonic cell proliferation: the miR-17/92 and the miR-302/367 clusters.7 Members of both families are highly expressed in embryonic stem cells and are essential to maintain the undifferentiated state.8 Transgenic overexpression of both the miR-17/92 cluster9 and the miR-302/367 cluster, as shown by Tian et al.,1 induces significant expansion of the cardiomyocyte pool during embryonic life, whereas their knockout leads to hypoplasia and cardiac dysfunction. More notably, in both cases reactivation of cardiomyocyte proliferation in adult mice is capable of increasing the usually ineffectual attempt at cardiac regeneration that is observed after myocardial infarction. The results of the new study strengthen and significantly expand a paradigm shift that has been occurring in the cardiovascular field over the last few years, namely that cardiac regeneration after damage can be achieved by stimulating the proliferation of already existing cardiomyocytes rather than having to rely on the implantation of exogenous cells. The notion that cardiomyocytes, or at least a subset of these, are endowed with an intrinsic capacity to proliferate during the adult life is consistent with earlier observations that a limited regenerative attempt normally occurs after infarction,10 that almost 50% of the myocardium is recycled during a lifetime,11 and that cardiac cell turnover physiologically occurs at a magnitude of ~1% cells per year.12 Expanding the endogenous cardiomyocyte proliferation capacity by genetic drugs thus appears to represent an exciting and more sustainable approach to achieve cardiac regeneration compared to ex vivo expansion and implantation of stem cell–derived cardiomyocytes. In this respect, it is worth recalling that cardiac regeneration in zebrafish, which occurs through the partial dedifferentiation and proliferation of preexisting cardiomyocytes,13,14 is also regulated by the miRNA network. In particular, recent evidence shows that miR-99/100 and Let-7a/c are downregulated during the regeneration process in zebrafish and that their forced inhibition is also effective in promoting regeneration in the mouse heart.15 Another merit of the article by Tian et al. is the description of a molecular mechanism for the miR-302/367 proliferative action based on its effect on the Hippo pathway. Originally discovered by genetic screens in the Drosophila eye, this pathway is a broad and essential regulator of cell proliferation and organ size. In mammalian cells, the main effector of the pathway is the transcriptional coactivator Yap. The kinase Mst1/2 (Hippo in Drosophila) interacts with WW45 to phosphorylate and activate the Lats1/2 and Mob1 complex, which in turn phosphorylates and inactivates Yap. In a crescendo of findings over the past few years, different investigators have shown that embryonic knockout of Mst1, WW45, and Lats causes cardiac hyperplasia, whereas overexpression of Mst1 and Lats, or knockout of Yap, leads to hypoplasia and cardiac dilation (reviewed in ref. 16). The pathway also appears to be active during postnatal life: in transgenic mice that overexpress a constitutively active Yap mutant, myocardial infarction is repaired with reduced fibrosis and increased myocardial tissue formation;17 consistent with this, Hippo deficiency enhances cardiomyocyte generation.18 Thus, the Hippo pathway stands as a master regulator of cardiac cell proliferation during both embryogenesis and postnatal life. The new study strengthens this conclusion by showing that at least one of the mechanisms of action of the miR-302/367 cluster is through repression of the kinases Mst1 and Lats2/Mob1b. Whether other miRNAs with the capacity to stimulate cardiomyocyte proliferation also act through the Hippo pathway remains a very interesting question that deserves further investigation. A most striking finding by Tian et al. is the demonstration that cardiac regeneration after myocardial infarction could be achieved by the administration, once a day, of synthetic miRNA mimics in a neutral lipid formulation. This finding is truly groundbreaking because, in the field of small-RNA therapeutics, it was thought that miRNA mimics would find little therapeutic usefulness because of their short half-life. This misconception arises because miRNA mimics, in contrast to miRNA inhibitors, must maintain their native chemical structure so as to be properly recognized by the RNA interference machinery, and thus could not be chemically modified to increase stability. The finding that the miR302b/c mimics are effective following systemic administration paves the way to a number of other mimic applications within and beyond the cardiovascular field, without the need to rely on viral vectors for intracellular miRNA expression. Will the miR302b/c mimics themselves become a real drug for patients with myocardial infarction? This is difficult to predict at this moment, but the biological activity of this miRNA cluster in inducing massive dedifferentiation toward an embryonic stem cell phenotype,19 and thus its deleterious effects when expressed for prolonged periods, would suggest caution. Should other miRNAs be identified that are equally effective in acting through the Hippo pathway but less prone to induce massive cell dedifferentiation, these would probably be better suited to development into human therapeutics. Despite this caveat, Tian et al. provide formidable proof-of-concept evidence that organ regeneration in vivo can be attained by exogenously delivered small-RNA drugs—certainly a welcome possibility, given the current critical burden of degenerative diseases.

HIV-1 integration into the host cell genome occurs in the outer shell of the nucleus in close correspondence with the nuclear pore, in which a series of cellular genes are preferentially targeted by the virus. Infection by human immunodeficiency virus type 1 (HIV-1) requires the integration of the viral genome into host DNA, and the virus is known to integrate preferentially into a subset of transcriptionally active genes. Mauro Giacca and colleagues report here that nuclear location influences target gene selection. They show that hotspots preferentially targeted by the virus are more commonly found in the outer shell of the nucleus proximal to the nuclear pore rather than centrally, implying that perhaps because of the short half-life of HIV-1 integrase, the virus interacts with the first open chromatin regions it encounters on its route into the nucleus. Long-standing evidence indicates that human immunodeficiency virus type 1 (HIV-1) preferentially integrates into a subset of transcriptionally active genes of the host cell genome1,2,3,4. However, the reason why the virus selects only certain genes among all transcriptionally active regions in a target cell remains largely unknown. Here we show that HIV-1 integration occurs in the outer shell of the nucleus in close correspondence with the nuclear pore. This region contains a series of cellular genes, which are preferentially targeted by the virus, and characterized by the presence of active transcription chromatin marks before viral infection. In contrast, the virus strongly disfavours the heterochromatic regions in the nuclear lamin-associated domains5 and other transcriptionally active regions located centrally in the nucleus. Functional viral integrase and the presence of the cellular Nup153 and LEDGF/p75 integration cofactors are indispensable for the peripheral integration of the virus. Once integrated at the nuclear pore, the HIV-1 DNA makes contact with various nucleoporins; this association takes part in the transcriptional regulation of the viral genome. These results indicate that nuclear topography is an essential determinant of the HIV-1 life cycle.

Although in the last decades the molecular underpinnings of the cell cycle have been unraveled, the acquired knowledge has been rarely translated into practical applications. Here, we investigate the feasibility and safety of triggering proliferation in vivo by temporary suppression of the cyclin-dependent kinase inhibitor, p21. Adeno-associated virus (AAV)-mediated, acute knockdown of p21 in intact skeletal muscles elicited proliferation of multiple, otherwise quiescent cell types, notably including satellite cells. Compared with controls, p21-suppressed muscles exhibited a striking two- to threefold expansion in cellularity and increased fiber numbers by 10 days post-transduction, with no detectable inflammation. These changes partially persisted for at least 60 days, indicating that the muscles had undergone lasting modifications. Furthermore, morphological hyperplasia was accompanied by 20% increases in maximum strength and resistance to fatigue. To assess the safety of transiently suppressing p21, cells subjected to p21 knockdown in vitro were analyzed for γ-H2AX accumulation, DNA fragmentation, cytogenetic abnormalities, ploidy, and mutations. Moreover, the differentiation competence of p21-suppressed myoblasts was investigated. These assays confirmed that transient suppression of p21 causes no genetic damage and does not impair differentiation. Our results establish the basis for further exploring the manipulation of the cell cycle as a strategy in regenerative medicine.

Lineage commitment of Th cells is associated with the establishment of specific transcriptional programs of cytokines. However, how Th cell differentiation affects the program of DNA replication has not been addressed. To gain insight into interplays between differentiation-induced transcription regulation and initiation of DNA replication, we took advantage of an in vitro differentiation system of naive T cells, in which one can manipulate their differentiation into Th1 or Th2 cells. We searched for replication origins in the murine IL-4/IL-13 locus and compared their profiles in the two Th cell lineages which were derived in vitro from the same precursor T cells. We identified a replication origin (oriIL-13) downstream from exon 4 of IL-13 and showed that this origin functions in both Th2 and Th1 cells. A distant regulatory element called CNS-1 (conserved noncoding sequence 1) in the IL-4/IL-13 intergenic region coincides with a Th2-specific DNase I-hypersensitive site and is required for efficient, coordinated expression of Th2 cytokines. Replication initiation from oriIL-13 is significantly reduced in Th1 and Th2 cells derived from CNS-1-deficient mice. However, the replication timing of this locus is consistently early during S phase in both Th1 and Th2 cells under either the wild-type or CNS-1 deletion background. Thus, the conserved noncoding element in the intergenic region regulates replication initiation from a distant replication origin in a manner independent from its effect on lineage-specific transcription but not the replication timing of the segment surrounding this origin.

The regulation of transcription of the human immunodeficiency virus (HIV) is a complex event of significant pathological relevance, which recapitulates general concepts of cellular transcription with some peculiarities. The viral promoter is embedded in a chromatin structure that exerts powerful repression on transcription; activation of gene expression relies on the combined activity of a series of cellular factors that respond to different external stimuli, and on the function of a single viral regulatory protein, the Tat transactivator. Transcriptional activation is consequent to both chromatin remodeling and to the recruitment of elongation-competent RNA polymerase II complexes onto the integrated promoter, two events that require the coordinate, but transient, assembly of different protein complexes. Application of optical imaging techniques now allows us to appreciate the spatial and temporal evolvement of these reactions in vivo. The picture that is emerging is not only descriptive, but also relevant to the understanding of the regulation of the process. In particular, it appears that the confinement of biomolecules within specific subcellular compartments represents a way to control and coordinate the assembly of functional complexes that regulate viral gene expression.

The human immunodeficiency virus (HIV-1) (transactivator of transcription (Tat)) protein is a pleiotropic factor that induces a broad range of biological effects in numerous cell types. At the HIV promoter, Tat is a powerful transactivator of gene expression, which acts by both inducing chromatin remodeling and by recruiting elongation-competent transcriptional complexes onto the viral LTR. Besides these transcriptional activities, Tat is released outside the cells and interacts with different cell membrane-associated receptors. Finally, extracellular Tat can be internalized by cells through an active endocytosis process. Here we discuss some of the molecular mechanisms involved in intracellular and extracellular Tat function.

Gene therapy approaches using recombinant adeno-associated virus serotype 2 (rAAV2) and serotype 8 (rAAV8) have achieved significant clinical benefits. The generation of rAAV Reference Standard Materials (RSM) is key to providing points of reference for particle titer, vector genome titer, and infectious titer for gene transfer vectors. Following the example of the rAAV2RSM, here we have generated and characterized a novel RSM based on rAAV serotype 8. The rAAV8RSM was produced using transient transfection, and the purification was based on density gradient ultracentrifugation. The rAAV8RSM was distributed for characterization along with standard assay protocols to 16 laboratories worldwide. Mean titers and 95% confidence intervals were determined for capsid particles (mean, 5.50×1011 pt/ml; CI, 4.26×1011 to 6.75×1011 pt/ml), vector genomes (mean, 5.75×1011 vg/ml; CI, 3.05×1011 to 1.09×1012 vg/ml), and infectious units (mean, 1.26×109 IU/ml; CI, 6.46×108 to 2.51×109 IU/ml). Notably, there was a significant degree of variation between institutions for each assay despite the relatively tight correlation of assay results within an institution. This outcome emphasizes the need to use RSMs to calibrate the titers of rAAV vectors in preclinical and clinical studies at a time when the field is maturing rapidly. The rAAV8RSM has been deposited at the American Type Culture Collection (VR-1816) and is available to the scientific community. © Mary Ann Liebert, Inc. 2014

Increasing evidence suggests an important role for miRNAs in the molecular interplay between bacterial pathogens and host cells. Here we perform a fluorescence microscopy-based screen using a library of miRNA mimics and demonstrate that miRNAs modulate Salmonella infection. Several members of the miR-15 miRNA family were among the 17 miRNAs that more efficiently inhibit Salmonella infection. We discovered that these miRNAs are downregulated during Salmonella infection, through the inhibition of the transcription factor E2F1. Analysis of miR-15 family targets revealed that derepression of cyclin D1 and the consequent promotion of G1/S transition are crucial for Salmonella intracellular proliferation. In addition, Salmonella induces G2/M cell cycle arrest in infected cells, further promoting its replication. Overall, these findings uncover a mechanism whereby Salmonella renders host cells more susceptible to infection by controlling cell cycle progression through the active modulation of host cell miRNAs.

Null mutations in the UGT1A1 gene result in Crigler–Najjar syndrome type I (CNSI), characterized by severe hyperbilirubinemia and constant risk of developing neurological damage. Phototherapy treatment lowers plasma bilirubin levels, but its efficacy is limited and liver transplantation is required. To find alternative therapies, we applied AAV liver- specific gene therapy to a lethal mouse model of CNSI. We demonstrated that a single neonatal hUGT1A1 gene transfer was successful and the therapeutic effect lasted up to 17 months postinjection. The therapeutic effect was mediated by the presence of transcriptionally active double-stranded episomes. We also compared the efficacy of two different gene therapy approaches: liver versus skeletal muscle transgene expression. We observed that 5–8% of normal liver expression and activity levels were sufficient to significantly reduce bilirubin levels and maintain lifelong low plasma bilirubin concentration (3.1±1.5 mg/dl). In contrast, skeletal muscle was not able to efficiently lower bilirubin (6.4±2.0 mg/dl), despite 20–30% of hUgt1a1 expression levels, compared with normal liver. We propose that this remarkable difference in gene therapy efficacy could be related to the absence of the Mrp2 and Mrp3 transporters of conjugated bilirubin in muscle. Taken together, our data support the concept that liver is the best organ for efficient and long-term CNSI gene therapy, and suggest that the use of extra- hepatic tissues should be coupled to the presence of bilirubin transporters.

Current antiretroviral therapies fail to cure HIV-1 (human immunodeficiency virus type 1) infection because HIV-1 persists as a transcriptionally inactive provirus in resting memory CD4(+) T cells. Multiple molecular events are known to regulate HIV-1 gene expression, yet the mechanisms governing the establishment and maintenance of latency remain incompletely understood. Here we summarize different molecular aspects of viral latency, from its establishment in resting CD4(+) T cells to the mechanisms involved in the reactivation of latent viral reservoirs. We focus on the relevance of chromatin structure and nuclear architecture in determining the transcriptional fate of integrated HIV-1 genomes, in light of recent findings indicating that proximity to specific subnuclear neighborhoods regulates HIV-1 gene expression.

The tyrosine kinase receptor vascular endothelial growth factor receptor 2 (VEGFR2) is a key regulator of angiogenesis. Here we show that VEGFR2 is acetylated in endothelial cells both at four lysine residues forming a dense cluster in the kinase insert domain and at a single lysine located in the receptor activation loop. These modifications are under dynamic control of the acetyltransferase p300 and two deacetylases HDAC5 and HDAC6. We demonstrate that VEGFR2 acetylation essentially regulates receptor phosphorylation. In particular, VEGFR2 acetylation significantly alters the kinetics of receptor phosphorylation after ligand binding, allowing receptor phosphorylation and intracellular signaling upon prolonged stimulation with VEGF. Molecular dynamics simulations indicate that acetylation of the lysine in the activation loop contributes to the transition to an open active state, in which tyrosine phosphorylation is favored by better exposure of the kinase target residues. These findings indicate that post-translational modification by acetylation is a critical mechanism that directly affects VEGFR2 function.

International audience; Heart failure is a leading cause of mortality and morbidity in the developed world, partly because mammals lack the ability to regenerate heart tissue. Whether this is due to evolutionary loss of regenerative mechanisms present in other organisms or to an inability to activate such mechanisms is currently unclear. Here we decipher mechanisms underlying heart regeneration in adult zebrafish and show that the molecular regulators of this response are conserved in mammals. We identified miR-99/100 and Let-7a/c and their protein targets smarca5 and fntb as critical regulators of cardiomyocyte dedifferentiation and heart regeneration in zebrafish. Although human and murine adult cardiomyocytes fail to elicit an endogenous regenerative response after myocardial infarction, we show that in vivo manipulation of this molecular machinery in mice results in cardiomyocyte dedifferentiation and improved heart functionality after injury. These data provide a proof of concept for identifying and activating conserved molecular programs to regenerate the damaged heart.

Productive HIV-1 infection requires viral cDNA integration into the host genome, an event catalyzed by HIV-1 integrase. In this issue of Cell Host & Microbe, Demeulemeester et al. (2014) report the existence of natural integrase polymorphisms that retarget viral integration away from gene-dense regions and are associated with rapid disease progression.

We appreciate the interest that Andersen et al. (2014) have shown in our work on neonatal cardiac regeneration. Their recent paper relates directly to resection methodology first presented by Porrello et al. (2011) and describes a failure to reproduce the observations made in that study regarding regeneration after resection. We are puzzled by the results and conclusion because in the hands of the seven different groups who authored this letter, this methodology has proved robust and reproducible and has been used in several ongoing studies across our different laboratories that are in various stages of completion (Heallen et al., [2013], as well as studies by the Lee, Takeuchi, and Nei groups that are currently under review). Importantly, several independent groups had similar observations using various types of neonatal injury (Strungs et al., 2013; Haubner et al., 2012; Naqvi et al., 2014; Jesty et al., 2012), where an increase in cardiomyocytes was also observed. Having carefully examined the study published by Andersen et al. (2014), it is our overall impression that methodological differences are likely to account for the difference in published results. Although it is difficult to draw clear conclusions about such differences without a detailed analysis of primary data, our impression is that variations in surgical technique, amount of resected myocardium, methods of quantification of resected and regenerated myocardium, and methods of assessment of myocyte proliferation form the basis of the differences seen. In particular, we used ventricular weight and surface area immediately after resection and 21 days later to assess the degree of injury and regeneration, while the Andersen group used HW/BW immediately after resection and ventricular weight 21 days later. Notably, in Figure 1E of the Andersen et al., 2014, paper, the amount of resected myocardium by ventricular weight 2 days after resection was in excess of 40%. We have not examined the effect of resection of such a large segment of the myocardium, but it is plausible that it not compatible with regeneration. We stand by the reproducibility of the initial report and we would be happy to assist Andersen et al. (2014) with various technical aspects of the neonatal apical resection method.

The use of vectors based on the small parvovirus adeno-associated virus has gained significant momentum during the past decade. Their high efficiency of transduction of postmitotic tissues in vivo, such as heart, brain, and retina, renders these vectors extremely attractive for several gene therapy applications affecting these organs. Besides functional correction of different monogenic diseases, the possibility to drive efficient and persistent transgene expression in the heart offers the possibility to develop innovative therapies for prevalent conditions, such as ischemic cardiomyopathy and heart failure. Therapeutic genes are not only restricted to protein-coding complementary DNAs but also include short hairpin RNAs and microRNA genes, thus broadening the spectrum of possible applications. In addition, several spontaneous or engineered variants in the virus capsid have recently improved vector efficiency and expanded their tropism. Apart from their therapeutic potential, adeno-associated virus vectors also represent outstanding investigational tools to explore the function of individual genes or gene combinations in vivo, thus providing information that is conceptually similar to that obtained from genetically modified animals. Finally, their single-stranded DNA genome can drive homology-directed gene repair at high efficiency. Here, we review the main molecular characteristics of adeno-associated virus vectors, with a particular view to their applications in the cardiovascular field.

We performed whole exome sequencing in individuals from a family with autosomal dominant gastropathy resembling Méné trier disease, a premalignant gastric disorder with epithelial hyperplasia and enhanced EGFR signalling. Méné trier disease is believed to be an acquired disorder, but its aetiology is unknown. In affected members, we found a missense p.V742G variant in MIB2, a gene regulating NOTCH signalling that has not been previously linked to human diseases. The variant segregated with the disease in the pedigree, affected a highly conserved amino acid residue, and was predicted to be deleterious although it was found with a low frequency in control individuals. The purified protein carrying the p.V742G variant showed reduced ubiquitination activity in vitro and white blood cells from affected individuals exhibited significant reductions of HES1 and NOTCH3 expression reflecting alteration of NOTCH signalling. Because mutations of MIB1, the homolog of MIB2, have been found in patients with left ventricle non-compaction (LVNC), we investigated members of our family with Méné trier-like disease for this cardiac abnormality. Asymptomatic left ventricular hypertrabeculation, the mildest end of the LVNC spectrum, was detected in two members carrying the MIB2 variant. Finally, we identified an additional MIB2 variant (p.V984L) affecting protein stability in an unrelated isolated case with LVNC. Expression of both MIB2 variants affected NOTCH signalling, proliferation and apoptosis in primary rat cardiomyocytes. In conclusion, we report the first example of left ventricular hypertrabeculation/LVNC with germline MIB2 variants resulting in altered NOTCH signalling that might be associated with a gastropathy clinically overlapping with Méné trier disease.

Functional recovery after peripheral nerve injury depends on both improvement of nerve regeneration and prevention of denervation-related skeletal muscle atrophy. To reach these goals, in this study we overexpressed vascular endothelial growth factor (VEGF) by means of local gene transfer with adeno-associated virus (AAV). Local gene transfer in the regenerating peripheral nerve was obtained by reconstructing a 1-cm-long rat median nerve defect using a vein segment filled with skeletal muscle fibers that have been previously injected with either AAV2-VEGF or AAV2-LacZ, and the morphofunctional outcome of nerve regeneration was assessed 3 months after surgery. Surprisingly, results showed that overexpression of VEGF in the muscle-vein-combined guide led to a worse nerve regeneration in comparison with AAV-LacZ controls. Local gene transfer in the denervated muscle was obtained by direct injection of either AAV2-VEGF or AAV2-LacZ in the flexor digitorum sublimis muscle after median nerve transection and results showed a significantly lower progression of muscle atrophy in AAV2-VEGF-treated muscles in comparison with muscles treated with AAV2-LacZ. Altogether, our results suggest that local delivery of VEGF by AAV2-VEGF-injected transplanted muscle fibers do not represent a rational approach to promote axonal regeneration along a venous nerve guide. By contrast, AAV2-VEGF direct local injection in denervated skeletal muscle significantly attenuates denervation-related atrophy, thus representing a promising strategy for improving the outcome of post-traumatic neuromuscular recovery after nerve injury and repair.Gene Therapy advance online publication, 30 May 2013; doi:10.1038/gt.2013.26.

We have previously shown that a cell cycle-dependent nucleoprotein complex assembles in vivo on a 74 bp sequence within the human DNA replication origin associated to the Lamin B2 gene. Here, we report the identification, using a one-hybrid screen in yeast, of three proteins interacting with the 74 bp sequence. All of them, namely HOXA13, HOXC10 and HOXC13, are orthologues of the Abdominal-B gene of Drosophila melanogaster and are members of the homeogene family of developmental regulators. We describe the complete open reading frame sequence of HOXC10 and HOXC13 along with the structure of the HoxC13 gene. The specificity of binding of these two proteins to the Lamin B2 origin is confirmed by both band-shift and in vitro footprinting assays. In addition, the ability of HOXC10 and HOXC13 to increase the activity of a promoter containing the 74 bp sequence, as assayed by CAT-assay experiments, demonstrates a direct interaction of these homeoproteins with the origin sequence in mammalian cells. We also show that HOXC10 expression is cell-type-dependent and positively correlates with cell proliferation.

We have comparatively evaluated the efficiency of a series of retroviral vectors transducing the gp91-phox gene, whose defects are responsible for impaired production of superoxide anion (O2-) by phagocytic cells and lead to the X-linked form of chronic granulomatous disease (X-CGD). These vectors included four constructs based on the MoMuLV backbone and expressing gp91-phox from the viral long terminal repeat (LTR) or from internal promoters, and one construct based on the myelotropic FMEV vector. Expression of the therapeutic gene from the MoMuLV LTR was unsatisfactory after transduction of the PLB985 X-CGD knockout cell line and of primary CD34+ hematopoietic progenitors from X-CGD patients. The presence of either constitutive or inducible internal promoters did not result in important improvements in the efficiency of O2- production and lowered the titers of the viral preparations. In contrast, sustained levels of superoxide generation were obtained upon transduction with the FMEV vector. To analyze the efficiency of transgene expression at the single cell level, over 150 cellular clones were generated from bulk cultures of PLB985 X-CGD cells transduced with this vector, each one representative of an individual transduction event. These clones revealed a markedly heterogeneous pattern of gp91-phox expression, ranging from complete silencing to full restoration of superoxide production. Within each clone, expression of the therapeutic gene correlated with the number of expressing cells rather than with the average levels of expression from each cell, indicating that at the single cell level, the proviral promoter is regulated by a binary, on/off mechanism. Moreover, both transduced bulk and clonal cell populations displayed a tendency to a progressive extinction of expression over time, with a mechanism involving LTR methylation. The design of novel retroviral vectors escaping silencing is highly desirable for efficient gene therapy.

Upon infection of susceptible cells, the RNA genome of the human immunodeficiency virus type 1 (HIV-1) is reverse transcribed into double-stranded DNA, which can be subsequently integrated into the cellular genome. After integration, the viral long terminal repeat (LTR) promoter is present in a nucleosome-bound conformation and is transcriptionally silent in the absence of stimulation. Activation of HIV-I gene expression is concomitant with an acetylation-dependent rearrangement of the nucleosome positioned at the viral transcription start site. Thus, similar to most cellular genes, the transcriptional state of the integrated HIV-I provirus is closely linked to histone acetylation. This enzymatic activity results from the function of histone-specific nuclear acetyltransferase (HAT) enzymes. Efficient viral transcription is strongly dependent on the virally-encoded Tat protein. The mechanism by which Tat increases the rate of transcriptional initiation has been recently demonstrated and involves the interaction of Tat with the transcriptional coactivator p300 and the closely related CREB-binding protein (CBP), having histone acetyltransferase activity

Recombinant adeno-associated vectors (AAVs) have gained momentum due to their combined characteristics of safety and efficiency. Nonetheless, the identity of the host functions intercepting the AAV transduction pathway still needs to be thoroughly understood.To address this issue on a genome-wide scale, we previously performed an unbiased RNAi high throughput screening (HTS; 18,120 human target genes) and identified 710 negative and 414 positive regulators of AAV efficiency. Based on the results obtained and with the purpose to identify factors involved in single-stranded (ss) AAV genome processing, we compared, again in an HTS format, siRNAs affecting ssAAV, but dispensable for scAAV transduction. One of the genes identified was ERI-1. While the effects of this protein were negligible on scAAV transduction, its knock down or overexpression lead to a 5 fold decrease or 2-7 fold increase of ssAAV efficiency, respectively.ERI-1 is a 3’-exoribonuclease known to degrade endogenous miRNAs and histone mRNAs. Indeed, we observed that AAV transduction negatively correlated with histone mRNA levels. Chromatin immunoprecipitation (ChIP) studies aimed at assessing the extent of chromatinization of the AAV genome revealed that the overexpression of ERI-1 determined an over 10-fold, selective reduction on ssAAV genome association with H3 and H4, while changes were negligible for scAAV DNA and for control cellular genes. Consistent with chromatin exerting a repressive role on ssAAV transduction, we also noticed that the downregulation of the main replication-dependent histone chaperone CAF-1 induced an over 20-fold increase in transduction. Increase of ssAAV2 transduction by ERI-1 also decreased the association, with the viral DNA, of proteins of the cellular DNA damage response (DDR; e.g. Nbs1 and Mre11), which our previous work had indicated as inhibitory of AAV transduction.Interestingly, DNA damage per se induced downregulation of histone gene expression. In particular, hydroxyurea, a drug markedly increasing AAV transduction, also determined histone mRNA degradation, an effect that required integrity of ERI-1.These results underline the importance of chromatin and its dynamic regulation in determining the fate of productive AAV transduction. These findings can be exploited for the development of more effective AAV-mediated gene delivery strategies.

A major advance in the study of the pathogenesis of dilated cardiomyopathy (DC) has been the identification of a familial trait in a relevant proportion of cases (more than 25\%), which indicates that, at least in these cases, a mutated gene is the cause of the disease. Familial dilated cardiomyopathy is a genetically heterogeneous disorder, most frequently with autosomal-dominant inheritance. Five different loci that cosegregate with the disease have been mapped so far; the identification of the disease genes is still in progress. The only disease gene known so far is the dystrophin gene, which causes X-linked DC. By analogy with dystrophin, it is believed that other cytoskeletal proteins could be involved in the pathogenesis of DC. Finally, in right ventricular cardiomyopathy, a peculiar form of cardiomyopathy that is frequently familial as well, several disease loci have been described. Also in this case, no disease gene has been yet identified. The advances in clinical and molecular genetics of DC have relevant clinical and therapeutic implications.

Viral DNA integration into the infected cell genome is an essential step in the HIV-1 life cycle. Hence, the viral integrase enzyme has become an important target for antiviral therapy. The integrase's activity action relies on the binding to its cellular partners, therefore the knowledge of the structural determinants is very important from a therapeutic perspective. Here we first review published computer-aided structural predictions of HIV-1 integrase in complex with its interactors. These include DNA and the human HAT protein. Next, we present a prediction of the complex between HIV-1 integrase with the human prolyl-isomerase-1 (hPin1) enzyme. Interaction with hPin1 is crucial for efficient HIV-1 infection and it increases integrase stability (Manganaro et. al 2010, Nat. Med. 16, 329). The modeling presented here, which is validated against experimental data, provides a rationale for a variety of viral protein's mutations which impair protein function and HIV-1 virus replication in vivo without significantly affecting enzymatic activity.

We report the genome-wide mapping of ORC1 binding sites in mammals, by chromatin immunoprecipitation and parallel sequencing (ChIP-seq). ORC1 binding sites in HeLa cells were validated as active DNA replication origins (ORIs) using Repli-seq, a method that allows identification of ORI-containing regions by parallel sequencing of temporally ordered replicating DNA. ORC1 sites were universally associated with transcription start sites (TSSs) of coding or noncoding RNAs (ncRNAs). Transcription levels at the ORC1 sites directly correlated with replication timing, suggesting the existence of two classes of ORIs: those associated with moderate/high transcription levels (≥1 RNA copy/cell), firing in early S and mapping to the TSSs of coding RNAs; and those associated with low transcription levels (1 and the probability of firing during S.

X-linked chronic granulomatous disease (X-CGD) is an immunodeficiency caused by mutations in the gene coding for the β subunit of cytochrome b 558 . A database (X-CGDbase) of X-CGD mutations has been compiled, and its use and resultant information are discussed in this article.

To assess the efficacy of the therapeutic use of inhibitors of ribonucleotide reductase for the treatment of human immunodeficiency virus (HIV) type 1 infection, 7 consecutive patients were enrolled in a clinical trial involving monotherapy with hydroxyurea for 8-19 weeks. During therapy, patients were evaluated for clinical status and immunologic, hematologic, and quantitative virologic parameters, including determinations of viremia and the number of provirus-containing cells by competitive polymerase chain reaction. In all patients, these parameters were not modified during the course of therapy. The number of CD4 cells remained generally unchanged or showed a tendency to further decline. No sign of improvement in HIV disease was detected in any patient. These observations indicate that monotherapy with hydroxyurea does not provide therapeutic benefit to HIV-1-infected patients.