Analysis of alternative splicing with microarrays: successes and challenges

Recently, DNA microarrays have emerged as potentially powerful tools for analyzing alternative splicing. We briefly review the latest results in this field and highlight the current challenges that they have revealed.     

Therapeutic vaccines for chronic diseases: successes and technical challenges

Chronic, non-communicable diseases are the major cause of death and disability worldwide and have replaced infectious diseases as the major burden of society in large parts of the world. Despite the complexity of chronic diseases, relatively few predisposing risk factors have been identified by the World Health Organization. Those include smoking, alcohol abuse, obesity, high cholesterol and high blood pressure as the cause of many of these chronic conditions. Here, we discuss several examples of vaccines that target these risk factors with the aim of preventing the associated diseases and some of the challenges they face.     

Directly observed therapy and improved tuberculosis treatment outcomes in Thailand

Background

The World Health Organization (WHO) recommends that tuberculosis (TB) patients receive directly observed therapy (DOT). Randomized controlled trials have not consistently shown that this practice improves TB treatment success rates. In Thailand, one of 22 WHO-designated high burden TB countries, patients may have TB treatment observed by a health care worker (HCW), family member, or no one. We studied whether DOT improved TB treatment outcomes in a prospective, observational cohort.

Methods and Findings

We prospectively collected epidemiologic data about TB patients treated at public and private facilities in four provinces in Thailand and the national infectious diseases hospital from 2004–2006. Public health staff recorded the type of observed therapy that patients received during the first two months of TB treatment. We limited our analysis to pulmonary TB patients never previously treated for TB and not known to have multidrug-resistant TB. We analyzed the proportion of patients still on treatment at the end of two months and with treatment success at the end of treatment according to DOT type. We used propensity score analysis to control for factors associated with DOT and treatment outcome. Of 8,031 patients eligible for analysis, 24% received HCW DOT, 59% family DOT, and 18% self-administered therapy (SAT). Smear-positive TB was diagnosed in 63%, and 21% were HIV-infected. Of patients either on treatment or that defaulted at two months, 1601/1636 (98%) patients that received HCW DOT remained on treatment at two months compared with 1096/1268 (86%) patients that received SAT (adjusted OR [aOR] 3.8; 95% confidence interval [CI] 2.4–6.0) and 3782/3987 (95%) patients that received family DOT (aOR 2.1; CI, 1.4–3.1). Of patients that had treatment success or that defaulted at the end of treatment, 1369/1477 (93%) patients that received HCW DOT completed treatment compared with 744/1074 (69%) patients that received SAT (aOR 3.3; CI, 2.4–4.5) and 3130/3529 (89%) patients that received family DOT (aOR 1.5; 1.2–1.9). The benefit of HCW DOT compared with SAT was similar, but smaller, when comparing patients with treatment success to those with death, default, or failure.

Conclusions

In Thailand, two months of DOT was associated with lower odds of default during treatment. The magnitude of benefit was greater for DOT provided by a HCW compared with a family member. Thailand should consider increasing its use of HCW DOT during TB treatment.     

Simultaneous and selective inference: Current successes and future challenges

The previous decade can be viewed as a second golden for era Multiple Comparisons research. I argue that much of the success stems from our being able to address real current needs. At the same time, this success generated a plethora of concepts for error rate and power, as well as multiplicity of methods for addressing them. These confuse the users of our methodology and pose a threat. To avoid the threat, it is our responsibility to match our theoretical goals to the goals of the users of statistics. Only then should we match the methods to the theoretical goals. Considerations related to such needs are discussed: simultaneous inference or selective inference, testing or estimation, decision making or scientific reporting. I then further argue that the vitality of our field in the future - as a research area - depends upon our ability to continue and address the real needs of statistical analyses in current problems. Two application areas offering new challenges have received less attention in our community to date are discussed. Safety analysis in clinical trials, where I offer an aggregated safety assessment methodology and functional Magnetic Resonance Imaging.     

Macromolecular crowding: qualitative and semiquantitative successes,quantitative challenges

The concept of excluded volume and the theory of effects of excluded volume on the equilibria and rates of macromolecular reactions in fluid media containing high total concentrations of macromolecules ('crowded' media) are summarized. Reports of experimental studies of crowding effects published during the last year are tabulated. Limitations of current excluded volume theory are discussed, and a determination is made of conditions under which this theory may and may not be validly applied. Recently suggested novel approaches to quantitative analysis of crowding phenomena, which may help to overcome some of the limitations of current theory, are summarized.     

Commentary: models of sleep regulation: successes and continuing challenges

Quantitative models have been developed to describe salient aspects of human sleep regulation. The two-process model of sleep regulation and the thermoregulatory model of sleep control highlight the interaction between sleep homeostasis and circadian rhythmicity and the association between sleep and temperature regulation, respectively. These models have been successful and inspiring, but continuing progress remains dependent on rigorous testing of some of their basic assumptions. Whereas it has been established that EEG slow-wave activity is a marker of sleep homeostasis, its causal role in regulating the timing of sleep and wakefulness remains to be demonstrated conclusively. Likewise, the causal role of the temperature regulatory system in sleep timing requires further investigation. In both models, many parameters have yet to be associated with specific physiologic processes. This makes it challenging, at least within the framework of these models, to account for interindividual differences or age-related changes in such features as sleep duration and sleep timing, as well as changes in the phase angle between the sleep-wake cycle and accepted markers of the circadian pacemaker, such as the body temperature or melatonin rhythm. Although the models may describe adequately global sleep patterns and their circadian modulation, detailed modeling of the frequent short awakenings from, and the subsequent transitions back to, sleep, as well as the variation of the propensity to awaken across the ultradian non-REM-REM cycle, is not addressed. Incoporation of these aspects of sleep in mathematical models of sleep regulation may further our understanding of a key aspect of sleep regulation, that is, its timing.     

Current progress and challenges in HIV gene therapy

HIV-1 causes AIDS, a syndrome that affects millions of people globally. Existing HAART is efficient in slowing down disease progression but cannot eradicate the virus. Furthermore the severity of the side effects and the emergence of drug-resistant mutants call for better therapy. Gene therapy serves as an attractive alternative as it reconstitutes the immune system with HIV-resistant cells and could thereby provide a potential cure. The feasibility of this approach was first demonstrated with the 'Berlin patient', who was functionally cured from HIV/AIDS with undetectable HIV-1 viral load after transplantation of bone marrow harboring a naturally occurring CCR5 mutation that blocks viral entry. Here, we give an overview of the current status of HIV gene therapy and remaining challenges and obstacles.     

Theoretical models of wound healing: past successes and future challenges

The complex biology of wound healing is an area in which theoretical modelling has already made a significant impact. In this review article, the authors describe the key features of wound healing biology, divided into four components: epidermal wound healing, remodelling of the dermal extracellular matrix, wound contraction, and angiogenesis. Within each of these categories, previous modelling work is described, and the authors identify what they regard as the main challenges for future theoretical work.     

Comparison of cost effectiveness of directly observed treatment (DOT) and conventionally delivered treatment for tuberculosis: experience from rural South Africa.

OBJECTIVE: To conduct an economic evaluation of directly observed treatment (DOT) and conventionally delivered treatment for the management of new cases of tuberculosis in adults. DESIGN: Community based directly observed treatment, which has been implemented in the Hlabisa district of South Africa since 1991, was compared with a conventional approach to tuberculosis treatment widely used in Africa. Each was assessed in terms of cost, cost effectiveness, and feasibility of implementation within existing resource constraints. SETTING: Hlabisa Health District, South Africa. SUBJECTS: Adult patients with new cases of tuberculosis on smear testing; the number of cases increased from 20 per month to over 100 from 1991 to 1996. MAIN OUTCOME MEASURES: Cost of case management in 1996, cost effectiveness in terms of the cost per case cured, and bed requirements in comparison with bed availability for the 1990, 1993, and 1996 caseload. Costs are expressed in US dollars at values for 1996. RESULTS: Directly observed treatment was 2.8 times cheaper overall than conventional treatment ($740.90 compared with $2047.70) to deliver. Directly observed treatment worked out 2.4-4.2 times more cost effective, costing $890.50 per patient cured compared with either $2095.60 (best case) or $3700.40 (worst case) for conventional treatment. The 1996 caseload of tuberculosis required 47 beds to be dedicated to tuberculosis to implement directly observed treatment, whereas conventionally delivered treatment would have required 160 beds; the current number of beds for tuberculosis treatment in Hlabisa is fixed at 56. CONCLUSIONS: Because of the reduced stay in hospital, directly observed treatment is cheaper, more cost effective, and more feasible than conventional treatment in managing tuberculosis in Hlabisa, given the existing hospital bed capacity and the escalating caseload due to the HIV/AIDS epidemic. Such results may hold elsewhere, and wherever conventional tuberculosis management is practised a switch to directly observed treatment will increase hospital capacity to cope with a growing caseload.     

CHO microRNA engineering is growing up: Recent successes and future challenges

microRNAs with their ability to regulate complex pathways that control cellular behavior and phenotype have been proposed as potential targets for cell engineering in the context of optimization of biopharmaceutical production cell lines, specifically of Chinese Hamster Ovary cells. However, until recently, research was limited by a lack of genomic sequence information on this industrially important cell line. With the publication of the genomic sequence and other relevant data sets for CHO cells since 2011, the doors have been opened for an improved understanding of CHO cell physiology and for the development of the necessary tools for novel engineering strategies. In the present review we discuss both knowledge on the regulatory mechanisms of microRNAs obtained from other biological models and proof of concepts already performed on CHO cells, thus providing an outlook of potential applications of microRNA engineering in production cell lines.     

CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock

CAPRI Rounds 3, 4, and 5 are the first public test of the published RosettaDock algorithm. The targets cover a wide range of sizes and shapes. For most targets, published biological information indicated the region of the binding site on at least one docking partner. The RosettaDock algorithm produced high accuracy predictions for three targets, medium-accuracy predictions for two targets, and an acceptable prediction for one target. RosettaDock predicted all five targets with less than 450 residues to high or medium accuracy, but it predicted only one of seven targets with above 450 residues to acceptable accuracy. RosettaDock's high-accuracy predictions for small to moderately large targets reveal the predictive power and fidelity of the algorithm, especially the high-resolution refinement and scoring protocol. In addition, RosettaDock can predict complexes from at least one homology-modeled docking partner with comparable accuracy to unbound cases of similar size. Larger targets present a more intensive sampling problem, and some large targets present repulsive barriers to entering the binding site. Ongoing improvements to RosettaDock's low-resolution search may alleviate this problem. This first public test suggests that RosettaDock can be useful in a significant range of applications in biochemistry and cell biology.     

Viral-mediated gene therapy for the muscular dystrophies: successes, limitations and recent advances

Much progress has been made over the past decade elucidating the molecular basis for a variety of muscular dystrophies (MDs). Accordingly, there are examples of mouse models of MD whose disease progression has been halted in large part with the use of viral vector technology. Even so, we must acknowledge significant limitations of present vector systems that must be overcome prior to successful treatment of humans with such approaches. This review will present a variety of viral-mediated therapeutic strategies aimed at counteracting the muscle-wasting symptoms associated with muscular dystrophy. We include viral vector systems used for muscle gene transfer, with a particular emphasis on adeno-associated virus. Findings of several encouraging studies focusing on repair of the mutant dystrophin gene are also included. Lastly, we present a discussion of muscle compensatory therapeutics being considered that include pathways involved in the up-regulation of utrophin, promotion of cellular adhesion, enhancement of muscle mass, and antagonism of the inflammatory response. Considering the complexity of the muscular dystrophies, it appears likely that a multilayered approach tailored to a patient sub-group may be warranted in order to effectively contest the progression of this devastating disease.     

HIV envelope: challenges and opportunities for development of entry inhibitors

The HIV envelope proteins glycoprotein 120 (gp120) and glycoprotein 41 (gp41) play crucial roles in HIV entry, therefore they are of extreme interest in the development of novel therapeutics. Studies using diverse methods, including structural biology and mutagenesis, have resulted in a detailed model for envelope-mediated entry, which consists of multiple conformations, each a potential target for therapeutic intervention. In this review, the challenges, strategies and progress to date for developing novel entry inhibitors directed at disrupting HIV gp120 and gp41 function are discussed.     

The HIV epidemic: medical and social challenges

The sudden appearance, rapid spread, and devastating clinical impact of HIV infection in Africa, Europe and North America has created a medical problem unprecedented in the modern era. HIV is sexually transmitted, afflicts sexual and racial minorities in developed countries, and appears likely to be fatal and incurable in a majority of infected people. Its epidemiology (transmission and natural history) and clinical manifestations have been well described, but treatment of HIV remains minimally effective, creating only a short respite from progressive deterioration. In the absence of effective vaccination, HIV will continue to spread, abetted by a long period of asymptomatic carriage during which carriers are infectious. It has spread internationally to most undeveloped countries aided by fear and ignorance. The problem will resist simple technological solutions and adversely impact the lives of tens of millions of people in these areas over the next several decades. In developed countries HIV will strain medical resources and kill several million people before the end of the century. Despite the tremendous problems created by the AIDS epidemic, it has driven a remarkable expansion of virologic and immunologic understanding which promises to ultimately lead to control of not only AIDS, but a variety of other serious diseases. The following reviews of pivotal issues in AIDS research document this progress.     

Peptide receptor radionuclide therapy (PRRT) with 177Lu-DOTATATE in individuals with neck or mediastinal paraganglioma (PGL)

Paragangliomas (PGLs) are neuroendocrine tum-ors that arise embryologically from the neural crest. Sympathetic PGLs can be located in the thoracic-abdominal region while parasympathetic PGLs are mainly situated in the head and neck region. Most PGLs are sporadic, but in 30% of cases they are hereditary (associated with mutations of SDHB, SDHC, SDHD, SDHAF2, SDHA, TMEM, MAX, and VHL); they can be classified into 4 different paraganglioma syndromes: PGL1, PGL2, PGL3, and PGL4. Surgery is the treatment of choice for both sympathetic and parasympathetic PGLs. Other types of treatment include medical agents (such as gemcitabine, cisplatin, or sunitinib) and radiotherapy (external-beam radiotherapy or stereotactic surgery). Surgery and radiotherapy, however, can cause important side effects such as vascular complications and peripheral nerve damage (hypoglossal, recurrent laryngeal, glossopharyngeal, and vagus). Another possible treatment option is the use of peptide receptor radionuclide therapy (PRRT), including PRRT with 177Lu-DOTATATE. We studied 4 patients with hereditary nonmetastatic paraganglioma syndrome type 1 (PGL1), with progressive disease, in whom surgical excision was not possible. They were treated with 177Lu-DOTATATE (3-5 cycles) and all had a partial response (PR) or a stable disease (SD) to the treatment. In conclusion, a good alternative treatment when surgical or radiation therapy are contraindicated could be radiometabolic therapy with 177Lu-DOTATATE.