Targets for neuroprotection in Parkinson's disease

Current therapies for Parkinson's disease significantly improve the quality of life for patients suffering from this neurodegenerative disease, yet none of the current therapies has been convincingly shown to slow or prevent the progression of disease. Much has been learned about the pathophysiology of Parkinson's disease in recent years, and these discoveries offer a variety of potential targets for protective therapy. Mechanisms implicated in the disease process include oxidative stress, mitochondrial dysfunction, protein aggregation and misfolding, inflammation, excitotoxicity, and apoptosis. At the same time, the involvement of these diverse processes makes modeling the disease and evaluation of potential treatments difficult. In addition, available clinical tools are limited in their ability to monitor the progression of the disease. In this review, we summarize the different pathogenic mechanisms implicated in Parkinson's disease and neuroprotective strategies targeting these mechanisms currently under clinical study or under preclinical development, with a view towards strategies that seem most promising.     

Advancements in melanoma cancer metastasis models

Metastatic melanoma is a complex and deadly disease. Due to its complexity, the development of novel therapeutic strategies to inhibit metastatic melanoma remains an outstanding challenge. Our ability to study metastasis is advanced with the development of in vitro and in vivo models that better mimic the different steps of the metastatic cascade beginning from primary tumor initiation to final metastatic seeding. In this review, we provide a comprehensive summary of in vitro models, in vivo models, and in silico platforms to study the individual steps of melanoma metastasis. Furthermore, we highlight the advantages and limitations of each model and discuss the challenges of how to improve current models to enhance translation for melanoma cancer patients and future therapies.     

Chemogenomics approaches to novel target discovery

Chemogenomics involves the combination of a compound's effect on biological targets together with modern genomics technologies. The merger of these two methodologies is creating a new way to screen for compound-target interactions, as well as map chemical and biological space in a parallel fashion. The challenge associated with mining complex databases has initiated the development of many novel in silico tools to profile and analyze data in a systematic way. The ability to analyze the combinatorial effects of chemical libraries on biological systems will aid the discovery of new therapeutic entities. Chemogenomics provides a tool for the rapid validation of novel targeted therapeutics, where a specific molecular target is modulated by a small molecule. Along with targeted therapies comes the ability to discovery pathway nodes where a single molecular target might be an essential component of more than one disease. Several disease areas will benefit directly from the chemogenomics approach, the most advanced being cancer. A genetic loss-of-function screen can be modulated in the presence of a compound to search for genes or pathways involved in the compound's activity. Several recent papers highlight how chemogenomics is changing with RNA interference-based screening and shaping the discovery of new targeted therapies. Together, chemical and RNA interference-based screens open the door for a new way to discovery disease-associated genes and novel targeted therapies.     

Harnessing genetically engineered mouse models for preclinical testing

Recent studies cast doubt on the value of traditionally used models as tools for testing therapies for human cancer. Although the standard practice of xenografting tumors into immunocompromised mice generates reproducible tumors, drug testing in these models has low predictive power when compared to the clinical responses in Phase II trials. The use of tumor-bearing genetically engineered mouse models holds promise for improving preclinical testing. These models recapitulate specific molecular pathways in tumor initiation or progression and provide a biological system in which to study the disease process for assessing efficacy of new therapies and proof-of-principle for testing molecularly targeted drugs. In this review, we discuss the advantages and limitations of genetically engineered mice and plausible solutions for adapting these valuable tumors for wider use in preclinical testing by transplantation into na?ve recipients. We also provide examples of comparative molecular analysis of mammary tumors from MMTV-Polyoma Middle-T antigen and MMTV-wnt1 models as tools for finding clinical correlates, validating existing models and guiding the development of new genetically engineered mouse models for cancer.     

Clinical Proteomics: From Biomarker Discovery and Cell Signaling Profiles to Individualized Personal Therapy

The discovery of new highly sensitive and specific biomarkers for early disease detection and risk stratification coupled with the development of personalized “designer” therapies holds the key to future treatment of complex diseases such as cancer. Mounting evidence confirms that the low molecular weight (LMW) range of the circulatory proteome contains a rich source of information that may be able to detect early stage disease and stratify risk. Current mass spectrometry (MS) platforms can generate a rapid and high resolution portrait of the LMW proteome. Emerging novel nanotechnology strategies to amplify and harvest these LMW biomarkers in vivo or ex vivo will greatly enhance our ability to discover and characterize molecules for early disease detection, subclassification and prognostic capability of current proteomics modalities. Ultimately genetic mutations giving rise to disease are played out and manifested on a protein level, involving derangements in protein function and information flow within diseased cells and the interconnected tissue microenvironment. Newly developed highly sensitive, specific and linearly dynamic reverse phase protein microarray systems are now able to generate circuit maps of information flow through phosphoprotein networks of pure populations of microdissected tumor cells obtained from patient biopsies. We postulate that this type of enabling technology will provide the foundation for the development of individualized combinatorial therapies of molecular inhibitors to target tumor-specific deranged pathways regulating key biologic processes including proliferation, differentiation, apoptosis, immunity and metastasis. Hence future therapies will be tailored to the specific deranged molecular circuitry of an individual patient’s disease. The successful transition of these groundbreaking proteomic technologies from research tools to integrated clinical diagnostic platforms will require ongoing continued development, and optimization with rigorous standardization development and quality control procedures.     

The systematic production of cells for cell therapies

Stem cells have emerged as the starting material of choice for bioprocesses to produce cells and tissues to treat degenerative, genetic, and immunological disease. Translating the biological properties and potential of stem cells into therapies will require overcoming significant cell-manufacturing and regulatory challenges. Bioprocess engineering fundamentals, including bioreactor design and process control, need to be combined with cellular systems biology principles to guide the development of next-generation technologies capable of producing cell-based products in a safe, robust, and cost-effective manner. The step-wise implementation of these bioengineering strategies will enhance cell therapy product quality and safety, expediting clinical development.     

Biomarkers in T-cell therapy clinical trials

T-cell therapy represents an emerging and promising modality for the treatment of disease. Data from recent clinical trials of genetically modified T cells, most notably chimeric antigen receptor (CAR) T cells, have yielded dramatic clinical results and highlighted the potential for this approach to mediate anti-tumor activity. Continued progress in the development of such T-cell therapies will require the identification of the relevant biomarker strategies to support and guide clinical development of the candidate products. In this review, we review and discuss (i) principles for development and use of biomarkers in clinical research, (ii) the rationale and a strategy for the integration of biomarker data at all stages of the product development process, from preclinical studies through product manufacture and during the clinical trial and (iii) the different classes of biomarkers that are relevant to T-cell therapy trials. Throughout this review, we discuss how biomarkers can play a central role in the development of novel T-cell therapeutic agents and highlight how appropriately designed biomarker studies can provide critical insights to this process. Finally, we discuss future directions and challenges for the appropriate development of biomarkers to evaluate product bioactivity and treatment efficacy.     

Genetic therapies for cardiovascular diseases

Recent advances in understanding the molecular and cellular basis of cardiovascular diseases, together with the availability of tools for genetic manipulation of the cardiovascular system, offer possibilities for new treatments. Gene therapies have demonstrated potential usefulness for treating complex cardiovascular diseases, such as hypertension, atherosclerosis and myocardial ischemia, in various animal models. Some of these experimental therapies are now undergoing clinical evaluation in patients with cardiovascular disease. However, the successful transition of these therapies into mainstream clinical practice awaits further improvements to vector platforms and delivery tools and the documentation of clinical feasibility, safety and efficacy through multi-center randomized trials.     

New targets of high-density lipoprotein therapy

PURPOSE OF REVIEW: Increasing attention has focused on the development of therapeutic strategies to promote the biologic activity of HDL particles, which possess a number of functional properties that contribute to their role in cardioprotection. Currently available therapies raise levels of HDL-cholesterol by relatively modest amounts. This review describes experimental strategies that promote HDL activity. RECENT FINDINGS: The functional quality of HDL may be more important than the absolute level of HDL-cholesterol found in the systemic circulation. This is supported by the observation that small rises in HDL-cholesterol with current therapies is associated with clinical benefit. This has major implications for the development of new therapies. A number of therapeutic strategies have been developed that promote reverse cholesterol transport, inhibit inflammatory events in the vessel wall, and modify remodeling of HDL particles within the systemic circulation. SUMMARY: A number of emerging therapies appear to promote the biologic activity of HDL. These agents can be administered as acute infusions in the setting of acute ischemic syndromes or as oral therapy for chronic prevention of cardiovascular disease.     

Atherosclerosis in rheumatoid arthritis and systemic lupus erythematosus

PURPOSE OF REVIEW: Our aim was to review recent studies that address the increased risk of atherosclerosis and coronary heart disease in patients with rheumatoid arthritis and systemic lupus erythematosus. We examine the strength of this association, how inflammation mediates this increased risk and what impact therapies may have. RECENT FINDINGS: Atherosclerosis is more prevalent and accelerated in both conditions. Indeed the process may actually precede the onset of clinical inflammatory disease. Metabolic alterations include insulin resistance and the generation of proinflammatory HDL. In addition, inflammatory mechanisms central to both rheumatoid arthritis and systemic lupus erythematosus such as macrophage activation, interferon-1 and complement deficiency may contribute to atherogenesis. There is still no consensus as to the value of primary preventive strategies in these conditions. However, drugs such as hydroxychloroquine seem to modify coronary heart disease risk and may improve survival. The recently developed antitumour necrosis factor drugs may also reduce coronary heart disease risk but biomarker studies to date have been inconclusive. SUMMARY: There is an urgent need for clinical trials to examine both the lipid-lowering and inflammatory hypotheses of atherosclerosis in rheumatoid arthritis and systemic lupus erythematosus. Novel targeted therapies in development may also have a major impact on future coronary heart disease risk in these conditions.     

The rocky road to personalized medicine in acute myeloid leukaemia

Acute myeloid leukaemia (AML) is a malignant disorder of the myeloid blood lineage characterized by impaired differentiation and increased proliferation of hematopoietic precursor cells. Recent technological advances have led to an improved understanding of AML biology but also uncovered the enormous cytogenetic and molecular heterogeneity of the disease. Despite this heterogeneity, AML is mostly managed by a ‘one‐size‐fits‐all’ approach consisting of intensive, highly toxic induction and consolidation chemotherapy. These treatment protocols have remained largely unchanged for the past several decades and only lead to a cure in approximately 30–35% of cases. The advent of targeted therapies in chronic myeloid leukaemia and other malignancies has sparked hope to improve patient outcome in AML. However, the implementation of targeted agents in AML therapy has been unexpectedly cumbersome and remains a difficult task due to a variety of disease‐ and patient‐specific factors. In this review, we describe current standard and investigational therapeutic strategies with a focus on targeted agents and highlight potential tools that might facilitate the development of targeted therapies for this fatal disease. The classes of agents described in this review include constitutively activated signalling pathway inhibitors, surface receptor targets, epigenetic modifiers, drugs targeting the interaction of the hematopoietic progenitor cell with the stroma and drugs that target the apoptotic machinery. The clinical context and outcome with these agents will be examined to gain insight about their optimal utilization.     

Rational design and optimization of downstream processes of virus particles for biopharmaceutical applications: current advances

The advent of advanced therapies in the pharmaceutical industry has moved the spotlight into virus-like particles and viral vectors produced in cell culture holding great promise in a myriad of clinical targets, including cancer prophylaxis and treatment. Even though a couple of cases have reached the clinic, these products have yet to overcome a number of biological and technological challenges before broad utilization. Concerning the manufacturing processes, there is significant research focusing on the optimization of current cell culture systems and, more recently, on developing scalable downstream processes to generate material for pre-clinical and clinical trials. We review the current options for downstream processing of these complex biopharmaceuticals and underline current advances on knowledge-based toolboxes proposed for rational optimization of their processing. Rational tools developed to increase the yet scarce knowledge on the purification processes of complex biologicals are discussed as alternative to empirical, “black-boxed” based strategies classically used for process development. Innovative methodologies based on surface plasmon resonance, dynamic light scattering, scale-down high-throughput screening and mathematical modeling for supporting ion-exchange chromatography show great potential for a more efficient and cost-effective process design, optimization and equipment prototyping.     

Autoimmunity and inflammation: murine models and translational studies

Autoimmune and inflammatory diseases, including type 1 diabetes, multiple sclerosis, inflammatory bowel disease, and rheumatoid arthritis, constitute an important and growing public health burden. However, in many cases our understanding of disease biology is limited and available therapies vary greatly in their efficacy and safety. Animal models of autoimmune and inflammatory diseases have provided valuable tools to researchers investigating their aetiology, pathology, and novel therapeutic strategies. Although such models vary in the degree to which they reflect human autoimmune and inflammatory diseases and caution is required in the extrapolation of animal data to the clinical setting, therapeutic approaches first evaluated in established animal models, including collagen-induced arthritis, experimental autoimmune encephalomyelitis, and the nonobese diabetic mouse, have successfully progressed to clinical investigation and practice. Similarly, these models have proven useful in providing support for basic hypotheses regarding the underlying causes and pathology of autoimmune and inflammatory diseases. Here we review selected murine models of autoimmunity and inflammation and efforts to translate findings from these models into both basic insights into disease biology and novel therapeutic strategies.     

Integrating forward and reverse proteomics to unravel protein function

To date, proteomics approaches have aimed to either identify novel proteins or change in protein expression/modification in various organisms under normal or disease conditions. One major aspect of functional proteomics is to identify protein biological properties in a given context, however, forward proteomics approaches alone cannot complete this goal. Indeed, with the increasing successes of such proteomics-based research strategies and the subsequent increasing amounts of proteins identified with unknown molecular functions, approaches allowing for systematic analyses of protein functions are desired. In this review, we propose to depict the complementarities of forward and reverse proteomics approaches in the definite understanding of protein functions. This dual strategy requires a data integration loop which allows for systematic characterization of protein function(s). The details of the integrative process combining both in silico and experimental resources and tools are presented. Altogether, we believe that the integration of forward and reverse proteomics approaches supported by bioinformatics will provide an efficient path towards systems biology.     

Animal models for the study of lymphatic insufficiency

Lymphedema is the term commonly employed to describe the spectrum of pathological states that arise as a consequence of functional lymphatic insufficiency. These human disease entities currently lack an effective cure. Satisfactory therapeutic strategies for both primary and secondary lymphedema will require additional insight into the complex cellular mechanisms and responses that comprise both normal lymphatic function and its regional derangement in states of pathologic dysfunction. Such insights must, initially, be derived from suitable animal models of the chronic human disease process. Historically, efforts to replicate the untreated disease of human lymphedema in animals, through surgery, irradiation, and toxicology, have been fraught with difficulty. The major impediments to the creation of satisfactory animal models have included an inability to reproduce the chronic disease in a stable, reproducible format. Recently, with the promise of potentially successful growth factor-mediated therapeutic lymphangiogenesis, and with the enhanced availability of investigative tools to assess therapeutic responses to molecular therapies, there has been a resurgence of interest in the development of viable animal models of lymphatic insufficiency. Current research has led to the development of genetic and postsurgical models of lymphedema that closely simulate the human conditions of primary and secondary lymphatic insufficiency, respectively. Such models will help to refine the assessment of various therapeutic approaches and their potential applicability to human disease interventions.     

In vitro and in silico assessment of the developability of a designed monoclonal antibody library

Despite major advances in antibody discovery technologies, the successful development of monoclonal antibodies (mAbs) into effective therapeutic and diagnostic agents can often be impeded by developability liabilities, such as poor expression, low solubility, high viscosity and aggregation. Therefore, strategies to predict at the early phases of antibody development the risk of late-stage failure of antibody candidates are highly valuable. In this work, we employ the in silico solubility predictor CamSol to design a library of 17 variants of a humanized mAb predicted to span a broad range of solubility values, and we examine their developability potential with a battery of commonly used in vitro and in silico assays. Our results demonstrate the ability of CamSol to rationally enhance mAb developability, and provide a quantitative comparison of in vitro developability measurements with each other and with more resource-intensive solubility measurements, as well as with in silico predictors that offer a potentially faster and cheaper alternative. We observed a strong correlation between predicted and experimentally determined solubility values, as well as with measurements obtained using a panel of in vitro developability assays that probe non-specific interactions. These results indicate that computational methods have the potential to reduce or eliminate the need of carrying out laborious in vitro quality controls for large numbers of lead candidates. Overall, our study provides support to the emerging view that the implementation of in silico tools in antibody discovery campaigns can ensure rapid and early selection of antibodies with optimal developability potential.     

Therapeutic cell engineering: designing programmable synthetic genetic circuits in mammalian cells

Cell therapy approaches that employ engineered mammalian cells for on-demand production of therapeutic agents in the patient’s body are moving beyond proof-of-concept in translational medicine. The therapeutic cells can be customized to sense user-defined signals, process them, and respond in a programmable and predictable way. In this paper, we introduce the available tools and strategies employed to design therapeutic cells. Then, various approaches to control cell behaviors, including open-loop and closed-loop systems, are discussed. We also highlight therapeutic applications of engineered cells for early diagnosis and treatment of various diseases in the clinic and in experimental disease models. Finally, we consider emerging technologies such as digital devices and their potential for incorporation into future cell-based therapies.     

In silico tools for predicting peptides binding to HLA-class II molecules: more confusion than conclusion

Identification of promiscuous peptides, which bind to human leukocyte antigen, is indispensable for global vaccination. However, the development of such vaccines is impaired due to the exhaustive polymorphism in human leukocyte antigens. The use of in silico tools for mining such peptides circumvents the expensive and laborious experimental screening methods. Nevertheless, the intrepid use of such tools warrants a rational assessment with respect to experimental findings. Here, we have adopted a 'bottom up' approach, where we have used experimental data to assess the reliability of existing in silico methods. We have used a data set of 179 peptides from diverse antigens and have validated six commonly used in silico methods; ProPred, MHC2PRED, RANKPEP, SVMHC, MHCPred, and MHC-BPS. We observe that the prediction efficiency of the programs is not balanced for all the HLA-DR alleles and there is extremely high level of discrepancy in the prediction efficiency apropos of the nature of the antigen. It has not escaped our notice that the in silico methods studied here are not very proficient in identifying promiscuous peptides. This puts a much constraint on the intrepid use of such programs for human leukocyte antigen class II binding peptides. We conclude from this study that the in silico methods cannot be wholly relied for selecting crucial peptides for development of vaccines.     

High-risk, clinically localized prostate cancer: is monotherapy adequate?

High-risk, clinically localized prostate cancer represents a diverse disease entity. Patients who are considered to be at highest risk for biochemical failure after localized treatments may not be at significant risk for disea-sespecific mortality. In this review, an attempt will be made to define high-risk status and help identify patients at high risk for mortality after a diagnosis of localized prostate cancer. Subsequently, a review of monotherapy approaches as well as previously successful strategies utilizing multimodality therapy for high-risk disease will be presented. Finally, a synopsis will be given of several ongoing randomized clinical trials using the most effective systemic therapies in the adjuvant setting following thorough local treatments such as radical prostatectomy. This review will provide a glimpse into the future and describe the tools that it is hoped will improve further upon the results of surgical monotherapy for high-risk, localized prostate cancer.     

Endothelial development taking shape

Blood vessel development is a vital process during embryonic development, during tissue growth, regeneration and disease processes in the adult. In the past decade researchers have begun to unravel basic molecular mechanisms that regulate the formation of vascular lumen, sprouting angiogenesis, fusion of vessels, and pruning of the vascular plexus. The understanding of the biology of these angiogenic processes is increasingly driven through studies on vascular development at the cellular resolution. Single cell analysis in vivo, advanced genetic tools and the widespread use of powerful animal models combined with improved imaging possibilities are delivering new insights into endothelial cell form, function and behavior angiogenesis. Moreover, the combination of in silico modeling and experimentation including dynamic imaging promotes insights into higher level cooperative behavior leading to functional patterning of vascular networks. Here we summarize recent concepts and advances in the field of vascular development, focusing in detail on the endothelial cell.