Engineering Genetic Systems for Treating Mitochondrial Diseases

Mitochondria are intracellular energy generators involved in various cellular processes. Therefore, mitochondrial dysfunction often leads to multiple serious diseases, including neurodegenerative and cardiovascular diseases. A better understanding of the underlying mitochondrial dysfunctions of the molecular mechanism will provide important hints on how to mitigate the symptoms of mitochondrial diseases and eventually cure them. In this review, we first summarize the key parts of the genetic processes that control the physiology and functions of mitochondria and discuss how alterations of the processes cause mitochondrial diseases. We then list up the relevant core genetic components involved in these processes and explore the mutations of the components that link to the diseases. Lastly, we discuss recent attempts to apply multiple genetic methods to alleviate and further reverse the adverse effects of the core component mutations on the physiology and functions of mitochondria.

Stability of Retroviral Vectors Against Ultracentrifugation Is Determined by the Viral Internal Core and Envelope Proteins Used for Pseudotyping

Retroviral and lentiviral vectors are mostly pseudotyped and often purified and concentrated via ultracentrifugation. In this study, we quantified and compared the stabilities of retroviral [murine leukemia virus (MLV)-based] and lentiviral [human immunodeficiency virus (HIV)-1-based] vectors pseudotyped with relatively mechanically stable envelope proteins, vesicular stomatitis virus glycoproteins (VSVGs), and the influenza virus WSN strain envelope proteins against ultracentrifugation. Lentiviral genomic and functional particles were more stable than the corresponding retroviral particles against ultracentrifugation when pseudotyped with VSVGs. However, both retroviral and lentiviral particles were unstable when pseudotyped with the influenza virus WSN strain envelope proteins. Therefore, the stabilities of pseudotyped retroviral and lentiviral vectors against ultracentrifugation process are a function of not only the type of envelope proteins, but also the type of viral internal core (MLV or HIV-1 core). In addition, the fraction of functional viral particles among genomic viral particles greatly varied at times during packaging, depending on the type of envelope proteins used for pseudotyping and the viral internal core.

Effects of Pre-Existing Liver Disease on Acute Pain Management Using Patient-Controlled Analgesia Fentanyl With Parecoxib After Major Liver Resection: A Retrospective, Pragmatic Study

BACKGROUND

The aim of this study was to compare the outcomes of pain management with the use of patient-controlled analgesia (PCA) fentanyl with IV parecoxib between patients with healthy liver with patients with diseased liver undergoing major liver resection.

METHODS

Patients with healthy liver undergoing partial hepatectomy as liver donors for liver transplantation (group 1) and patients with liver cirrhosis (Child's criteria A) undergoing major liver resection for hepatoma (group 2) were identified retrospectively. Both groups routinely received post-operative IV PCA fentanyl and a single dose of parecoxib 40 mg. They were followed up for 3 days or until PCA fentanyl was discontinued post-operatively. Daily Visual Analog Scale, PCA fentanyl usage, rescue attempts, and common drug side effects were collected and analyzed with the use of SPSS version 20.

RESULTS

One hundred one patients were included in the study: 54 in group 1, and 47 in group 2. There were no statistical differences between the two groups in terms of the daily and total fentanyl usage, VAS resting, and incidence of itchiness. The rate of rescue analgesia on post-operative day (POD) 1 was lower in group 2, with a value of P = .045. VAS dynamics were better on POD 1 and 2 for group 2, with P = .05 and P = .012, respectively.

CONCLUSIONS

We found that combining a single dose of IV parecoxib 40 mg with PCA fentanyl is an easy and effective method of acute pain control after major liver resection. We propose the careful usage of post-operative fentanyl and parecoxib in patients with diseased liver, given the difference in effect as compared with healthy liver.

Recent advances in developing molecular tools for targeted genome engineering of mammalian cells

Various biological molecules naturally existing in diversified species including fungi, bacteria, and bacteriophage have functionalities for DNA binding and processing. The biological molecules have been recently actively engineered for use in customized genome editing of mammalian cells as the molecule-encoding DNA sequence information and the underlying mechanisms how the molecules work are unveiled. Excitingly, multiple novel methods based on the newly constructed artificial molecular tools have enabled modifications of specific endogenous genetic elements in the genome context at efficiencies that are much higher than that of the conventional homologous recombination based methods. This minireview introduces the most recently spotlighted molecular genome engineering tools with their key features and ongoing modifications for better performance. Such ongoing efforts have mainly focused on the removal of the inherent DNA sequence recognition rigidity from the original molecular platforms, the addition of newly tailored targeting functions into the engineered molecules, and the enhancement of their targeting specificity. Effective targeted genome engineering of mammalian cells will enable not only sophisticated genetic studies in the context of the genome, but also widely-applicable universal therapeutics based on the pinpointing and correction of the disease-causing genetic elements within the genome in the near future. [BMB Reports 2015; 48(1): 6-12]

Population-based review of tetralogy of Fallot with absent pulmonary valve: is prenatal diagnosis really associated with a poor prognosis?

OBJECTIVES

Tetralogy of Fallot with absent pulmonary valve syndrome (TETAPV) is reported in obstetric literature to have an extremely poor prognosis. We sought to determine the clinical outcome associated with TETAPV and whether prenatal diagnosis confers a poor prognosis.

METHODS

All cases of TETAPV diagnosed in British Columbia between 1980 and 2009 were reviewed and grouped according to time of diagnosis, either prenatal or postnatal. The groups were compared with respect to mortality, respiratory problems, number of interventions and functional capacity at last follow-up.

RESULTS

Eight and 11 patients were included in the prenatally and postnatally diagnosed groups, with overall long-term survival of 71% and 82%, respectively. There was no significant difference in mortality, frequency of preoperative intubation, number of interventions or functional capacity between groups.

CONCLUSION

From a population-based retrospective analysis of TETAPV cases identified over three decades it is concluded that the prognosis for TETAPV is better than that previously reported in the obstetric literature. This information should be used to guide prenatal counseling.

Retroviral integration profiles: their determinants and implications for gene therapy

Retroviruses have often been used for gene therapy because of their capacity for the long-term expression of transgenes via stable integration into the host genome. However, retroviral integration can also result in the transformation of normal cells into cancer cells, as demonstrated by the incidence of leukemia in a recent retroviral gene therapy trial in Europe. This unfortunate outcome has led to the rapid initiation of studies examining various biological and pathological aspects of retroviral integration. This review summarizes recent findings from these studies, including the global integration patterns of various types of retroviruses, viral and cellular determinants of integration, implications of integration for gene therapy and retrovirus-mediated infectious diseases, and strategies to shift integration to safe host genomic loci. A more comprehensive and mechanistic understanding of retroviral integration processes will eventually make it possible to generate safer retroviral vector platforms in the near future.

Retroviral infection of hES cells produces random-like integration patterns

Retroviral integration provides us with a powerful tool to realize prolonged gene expressions that are often critical to gene therapy. However, the perturbation of gene regulations in host cells by viral genome integration can lead to detrimental effects, yielding cancer. The oncogenic potential of retroviruses is linked to the preference of retroviruses to integrate into genomic regions that are enriched in gene regulatory elements. To better navigate the double-edged sword of retroviral integration we need to understand how retroviruses select their favored genomic loci during infections. In this study I showed that in addition to host proteins that tether retroviral pre-integration complexes to specific genomic regions, the epigenetic architecture of host genome might strongly affect retroviral integration patterns. Specifically, retroviruses showed their characteristic integration preference in differentiated somatic cells. In contrast, retroviral infections of hES cells, which are known to display decondensed chromatin, produced random-like integration patterns lacking of strong preference for regulatory-element-rich genomic regions. Better identification of the cellular and viral factors that determine retroviral integration patterns will facilitate the design of retroviral vectors for safer use in gene therapy.

Resistive switching memory properties of layer-by-layer assembled enzyme multilayers

The properties of enzymes, which can cause reversible changes in currents through redox reactions in solution, are of fundamental and practical importance in bio-electrochemical applications. These redox properties of enzymes are often associated with their charge-trap sites. Here, we demonstrate that reversible changes in resistance in dried lysozyme (LYS) films can be generated by an externally applied voltage as a result of charge trap/release. Based on such changes, LYS can be used as resistive switching active material for nonvolatile memory devices. In this study, cationic LYS and anionic poly(styrene sulfonate) (PSS) layers were alternately deposited onto Pt-coated silicon substrates using a layer-by-layer assembly method. Then, top electrodes were deposited onto the top of LYS/PSS multilayers to complete the fabrication of the memory-like device. The LYS/PSS multilayer devices exhibited typical resistive switching characteristics with an ON/OFF current ratio above 10(2), a fast switching speed of 100 ns and stable performance. Furthermore, the insertion of insulating polyelectrolytes (PEs) between the respective LYS layers significantly enhanced the memory performance of the devices showing a high ON/OFF current ratio of ~10(6) and low levels of power consumption.

The association between the ratio of visceral fat to thigh muscle area and metabolic syndrome: the Korean Sarcopenic Obesity Study (KSOS)

OBJECTIVE

A relationship between visceral fat accumulation and metabolic syndrome (MetS) has been established. However, the effect of a relative increase in visceral fat and a decrease in muscle mass on metabolic disorders has not been investigated. The aim of the present study was to examine the association between the ratio of visceral fat to thigh muscle area (VMR) and MetS in Korean adults. STUDY SUBJECT/MEASUREMENTS: A total of 264 age-and gender-matched subjects recruited from the Korean Sarcopenic Obesity Study (KSOS), an ongoing prospective observational cohort study, were categorized into four groups based on their body mass index (BMI) and VMR. We measured visceral fat area and thigh muscle area using computed tomography.

RESULTS

Subjects with MetS showed a significantly higher VMR than those without MetS. In both obese and nonobese groups, the subjects with a higher VMR had a higher prevalence of MetS than those in the lower VMR groups. VMR was significantly related to components of the metabolic syndrome, especially in women, and was positively correlated with a number of MetS components in both men and women. In multiple logistic regression analysis, the odds ratio for MetS was 6·72 (highest vs lowest quartile, 95% confidence interval, 1·60-28·14) after an adjustment of potential confounders, including BMI and waist-to-hip ratio.

CONCLUSION

VMR is significantly increased in subjects with MetS and independently associated with MetS. These results suggest that the VMR may be a potential indicator for MetS risk in Korean adults.

Combinatorial latency reactivation for HIV-1 subtypes and variants

The eradication of HIV-1 will likely require novel clinical approaches to purge the reservoir of latently infected cells from a patient. We hypothesize that this therapy should target a wide range of latent integration sites, act effectively against viral variants that have acquired mutations in their promoter regions, and function across multiple HIV-1 subtypes. By using primary CD4(+) and Jurkat cell-based in vitro HIV-1 latency models, we observe that single-agent latency reactivation therapy is ineffective against most HIV-1 subtypes. However, we demonstrate that the combination of two clinically promising drugs-namely, prostratin and suberoylanilide hydroxamic acid (SAHA)-overcomes the limitations of single-agent approaches and can act synergistically for many HIV-1 subtypes, including A, B, C, D, and F. Finally, by identifying the proviral integration position of latent Jurkat cell clones, we demonstrate that this drug combination does not significantly enhance the expression of endogenous genes nearest to the proviral integration site, indicating that its effects may be selective.

Do Commonly Used Oral Antihypertensives Alter Fetal or Neonatal Heart Rate Characteristics? A Systematic Review

OBJECTIVE

To examine fetal (FHR) and neonatal heart rate patterns following use of common oral antihypertensives in pregnancy.

METHODS

A systematic review of randomized controlled trials (RCTs), observational studies (N >/= 6 women), and animal studies. Data were abstracted (two reviewers) to determine relative risk (RR) (or risk difference (RD) for low event rates) and 95% CI.

RESULTS

Eighteen RCTs (1858 women), one controlled observational study (N = 22), and seven case series (N = 117) were reviewed. Most hypertension was pregnancy-induced (N = 14 studies). The FHR was assessed by cardiotocogram (CTG) (N = 17 studies (visual interpretation); 1 study (computerized CTG), or umbilical artery velocimetry (N = 4). Four studies examined neonatal heart rate. In placebo-controlled RCTs (N = 192 women), adverse FHR effects did not differ between groups [9/101 (drugs) vs. 7/91 (placebo); RD 0.02, 95% CI (- 0.06, 0.11); chi2 = 1.02]. In six drug vs. drug RCTs (295 women), adverse FHR effects did not differ between groups [29/144 (methyldopa) vs. 42/151 (other drugs); RR 0.72, 95% CI (0.49, 1.07); chi2 = 0.69]. In one labetalol vs. placebo trial, neonatal bradycardia did not differ between groups [4/70 (labetalol) vs. 4/74 (placebo); OR 1.06, 95% CI (0.26, 4.39)], while in three drug vs. drug RCTs, neonatal bradycardia was not observed (0/24 vs. 0/26).

CONCLUSIONS

Available data are inadequate to conclude whether oral methyldopa, labetalol, nifedipine, or hydralazine adversely affect fetal or neonatal heart rate and pattern. Until definitive data are available, FHR changes cannot be reliably attributed to drug effect, but may be due to progression of the underlying maternal or placental disease.

Computational fitness landscape for all gene-order permutations of an RNA virus

How does the growth of a virus depend on the linear arrangement of genes in its genome? Answering this question may enhance our basic understanding of virus evolution and advance applications of viruses as live attenuated vaccines, gene-therapy vectors, or anti-tumor therapeutics. We used a mathematical model for vesicular stomatitis virus (VSV), a prototype RNA virus that encodes five genes (N-P-M-G-L), to simulate the intracellular growth of all 120 possible gene-order variants. Simulated yields of virus infection varied by 6,000-fold and were found to be most sensitive to gene-order permutations that increased levels of the L gene transcript or reduced levels of the N gene transcript, the lowest and highest expressed genes of the wild-type virus, respectively. Effects of gene order on virus growth also depended upon the host-cell environment, reflecting different resources for protein synthesis and different cell susceptibilities to infection. Moreover, by computationally deleting intergenic attenuations, which define a key mechanism of transcriptional regulation in VSV, the variation in growth associated with the 120 gene-order variants was drastically narrowed from 6,000- to 20-fold, and many variants produced higher progeny yields than wild-type. These results suggest that regulation by intergenic attenuation preceded or co-evolved with the fixation of the wild type gene order in the evolution of VSV. In summary, our models have begun to reveal how gene functions, gene regulation, and genomic organization of viruses interact with their host environments to define processes of viral growth and evolution.

Although many viruses are linked to diseases that adversely impact the health of their human, animal, and plant hosts, viruses could help promote wellness and treat disease if their “good traits” could be harnessed. Potentially useful virus traits include their abilities to stimulate a robust immune response, target specific tissues for the delivery of foreign genes, and destroy tumors. The exploitation of such traits in the engineering of virus-based vaccines, gene therapies and anti-cancer strategies is limited in part by our inability to control how viruses grow. Generally, viruses that grow poorly will be more desirable for vaccine applications, whereas viruses that grow and spread rapidly will be useful for destroying tumors. Further, gene therapies will rely on controlling the extent to which a therapeutic gene is delivered and expressed. Robust methods for controlling virus growth have yet to be discovered. However, for some viruses, such as vesicular stomatitis virus (VSV), growth can be very sensitive to the specific linear order of its five genes. Our current work is significant in combining experiments and computational models to identify which virus genes and genome positions most sensitively impact VSV growth, providing a foundation for its applications in human health.

Molecular engineering of viral gene delivery vehicles

Viruses can be engineered to efficiently deliver exogenous genes, but their natural gene delivery properties often fail to meet human therapeutic needs. Therefore, engineering viral vectors with new properties, including enhanced targeting abilities and resistance to immune responses, is a growing area of research. This review discusses protein engineering approaches to generate viral vectors with novel gene delivery capabilities. Rational design of viral vectors has yielded successful advances in vitro, and to an extent in vivo. However, there is often insufficient knowledge of viral structure-function relationships to reengineer existing functions or create new capabilities, such as virus-cell interactions, whose molecular basis is distributed throughout the primary sequence of the viral proteins. Therefore, high-throughput library and directed evolution methods offer alternative approaches to engineer viral vectors with desired properties. Parallel and integrated efforts in rational and library-based design promise to aid the translation of engineered viral vectors toward the clinic.

Library selection approaches to engineering enhanced retroviral and lentiviral vectors

Retroviral and lentiviral based gene delivery vectors have been used in numerous pre-clinical studies and clinical trials due to their advantages, including stable and prolonged expression of therapeutic transgenes and minimal immune responses against the vector. Despite such advantages, however, retroviral vectors also have several limitations for gene therapy applications. For example, they can suffer from a lack of efficient or targeted gene delivery to key cell types. In addition, retroviral vector stability can be compromised by their envelope proteins. This review briefly describes how such limitations have been overcome by recently developed library selection approaches that borrow a lesson from nature: the ability of evolution to generate biomolecules with novel function. These library selection approaches are based on the construction of retroviral libraries where the sequences encoding natural viral components are partially randomized using a variety of methods in order to generate diverse libraries that can be selected to create improved or novel functions. These high throughput, library-based approaches provide a strong complement to rational engineering of viral components for the rapid development of efficient and safe retroviral and lentiviral vector systems for gene therapy.

Central venous catheter-related blood stream infections: incidence and an analysis of risk factors

Six hundred and fifty-five central venous catheters (CVC) in 496 patients in the intensive care unit of Hospital Sultanah Aminah were studied to determine the incidence and risk factors for central venous catheter-related blood stream infection (CR-BSI). CR-BSI was diagnosed in 38 catheters, giving an incidence of 9.43 CR-BSI per 1000 catheter days. The mean duration in situ was 8.4 +/- 4.9 days for infected CVCs and 6.0 +/- 3.8 days for non infected CVCs (p = 0.001). CVCs inserted in ICU had the highest infection rate (9.4%) compared to those inserted in the operating theatre (1.4%) and ward (2.8%) (p = 0.001). The highest rate of CR-BSI occurred with 4-lumen catheters (usually inserted when patients needed total parenteral nutrition) with a percentage of 15.8%. The majority of the CVCs (97.9%) were inserted via the subclavian or the internal jugular routes and there was no statistical difference in CR-BSI between them (p = 0.83). Number of attempts more than one had a higher rate of CR-BSI compared to single attempt with percentage of 7.0% vs 4.8% (p = 0.22). The top two organisms were Klebseilla pneumoniae and Pseudomonas aeruginosa. In conclusion, the incidence of CR-BSI in our ICU was 9.43 CR-BSI per 1000 catheter days. The risk factors were duration of CVC in situ, venue of insertion and use of 4 lumen catheter for total parenteral nutrition. The site of insertion, number of lumen up to 3 lumens and the number of attempts were not risk factors.

Library selection and directed evolution approaches to engineering targeted viral vectors

Gene therapy, to delivery of genetic material to a patient for therapeutic benefit, has significant promise for translating basic knowledge of disease mechanism into biomedical treatments. The clinical development of the field has been slowed, however, by the need for improvements in the properties and capabilities of gene delivery vehicles. Vehicles based on viruses offer the potential for efficient gene delivery, but because viruses did not evolve to serve human therapeutic needs, many of their properties require significant improvement, including their safety, efficiency, and capacity for targeted gene delivery. Since viruses are highly complex biological entities, engineering such properties at the molecular level can be challenging. However, there has been significant progress in developing approaches that mimic the mechanisms by which viruses arose in the first place. In particular, library-based selection, the generation of one diverse genetic library and selection for new properties, and directed evolution, based on the multiple rounds of library generation and selection for iterative improvement of function, have strong potential in engineering novel properties into these complex biomolecular assemblies. This review will discuss progress in the application of peptide display, library selection, and directed evolution technologies toward engineering vectors based on retrovirus, adeno-associated virus, and adenovirus that are capable of targeted delivery to specific cell types. In addition to creating biomedically useful products, these approaches have future potential to yield novel insights into viral structure-function relationships.

Model-based design of growth-attenuated viruses

Live-virus vaccines activate both humoral and cell-mediated immunity, require only a single boosting, and generally provide longer immune protection than killed or subunit vaccines. However, growth of live-virus vaccines must be attenuated to minimize their potential pathogenic effects, and mechanisms of attenuation by conventional serial-transfer viral adaptation are not well-understood. New methods of attenuation based on rational engineering of viral genomes may offer a potentially greater control if one can link defined genetic modifications to changes in virus growth. To begin to establish such links between genotype and growth phenotype, we developed a computer model for the intracellular growth of vesicular stomatitis virus (VSV), a well-studied, nonsegmented, negative-stranded RNA virus. Our model incorporated established regulatory mechanisms of VSV while integrating key wild-type infection steps: hijacking of host resources, transcription, translation, and replication, followed by assembly and release of progeny VSV particles. Generalization of the wild-type model to allow for genome rearrangements matched the experimentally observed attenuation ranking for recombinant VSV strains that altered the genome position of their nucleocapsid gene. Finally, our simulations captured previously reported experimental results showing how altering the positions of other VSV genes has the potential to attenuate the VSV growth while overexpressing the immunogenic VSV surface glycoprotein. Such models will facilitate the engineering of new live-virus vaccines by linking genomic manipulations to controlled changes in virus gene-expression and growth.

Dynamic tradeoffs in the raft-mediated entry of human immunodeficiency virus type 1 into cells

To initiate an infection human immunodeficiency virus type 1 (HIV-1) particles must first bind to receptors on the surface of their host cells, a process that eventually leads to fusion of viral and cellular membranes and release of the viral genome into the cytoplasm. Understanding the molecular mechanisms of these processes may enable the development of new anti-HIV strategies. Disagreement currently prevails on the role in virus entry of microdomains within the cellular plasma membrane known as lipid rafts. Experiments have suggested that lipid rafts, in their interactions with cellular receptors and viral particles, either promote or have minimal effect on viral entry. Here we develop a dynamic model for HIV-1 entry that enables us to identify and quantitatively assess tradeoffs that can arise from the clustering of receptors in rafts. Specifically, receptor clustering can be detrimental to the initiation of viral infection by reducing the probability that a virus particle finds its primary receptor, CD4. However, receptor clustering can also enable a virus particle, once bound, to rapidly form multivalent interactions with receptors and co-receptors that are required for virus-cell membrane fusion. We show how the resolution of such tradeoffs hinges on the level and spatial distribution of receptors and co-receptors on the cell surface, and we discuss implications of these effects for the design of therapeutics that inhibit HIV-1 entry.

Monoamniotic twins discordant for anencephaly managed conservatively with good outcomes: two case reports and a review of the literature

Monoamniotic twin pregnancy discordant for anencephaly (MATDA) is a rare occurrence with only seven prior reported cases. Selective termination has been advocated in managing discordant monoamniotic twins. We report two cases managed expectantly with good outcomes and review other previously reported cases. The first case was a primigravid woman diagnosed with MATDA at 18 weeks. She was managed expectantly until 32 + 5 weeks when a Cesarean section was performed for preterm labor. The surviving female infant weighed 1610 g. The second case was a multigravid woman who was diagnosed with MATDA at 17 + 5 weeks and was managed as an outpatient. An emergency Cesarean section was performed at 31 weeks for non-reassuring monitoring and the surviving male infant weighed 1790 g. In both cases, the survivors were discharged home in good condition. A review of these two cases and those in the literature suggests that expectant management should be considered among management options for this rare condition.

The effects of phospholipase C inhibition on insulin-stimulated glucose transport in skeletal muscle

Previous research has demonstrated that phospholipase C (PLC) is involved in insulin-stimulated glucose transport in 3T3-L1 adipocytes. The purpose of the current investigation was to determine if PLC is also involved in insulin-stimulated glucose uptake in rat skeletal muscle. To that end, we used an in vitro muscle preparation of the rat soleus muscle to test the effects of the PLC inhibitor, U73122, on glucose transport. The PLC inhibitor, U73122, led to a concentration-dependent inhibition of insulin (0.6 nmol/L)-stimulated glucose transport, whereas it had no effect on basal glucose transport. Specifically 10, 20, 50, and 150 micromol/L U73122 inhibited insulin (0.6 nmol/L)-stimulated glucose transport approximately 17%, 20%, 26%, and 38%, respectively, while an equal molar concentration of U73343 (inactive form of U73122) and/or carrier media (dimethyl sulfoxide [DMSO]) did not influence glucose uptake. A secondary aim of this investigation was to determine if increasing the concentration of insulin from a physiologic concentration (0.6 nmol/L) to a supraphysiologic concentration (6.0 nmol/L) could ameliorate the inhibitory effects of U73122. A 10-fold increase in insulin eliminated the inhibitory effects of U73122 on insulin-stimulated glucose uptake in soleus muscle. In summary, this preliminary report provides evidence to suggest that a PLC signaling mechanism modifies insulin-stimulated glucose uptake in skeletal muscle via its influence on insulin sensitivity.