Delivering cellular therapies: lessons learned from ex vivo culture and clinical applications of hematopoietic cells

Advances in stem cell biology and cellular therapy have led to promising treatments in a range of incurable diseases. However, it is unclear whether primitive stem cells can be delivered to damage tissue for regeneration of functional mature cells or stem cells must be stimulated to differentiate into mature cells in vitro and these cells delivered to patients. A range of other questions remains to be determined including how to formulate cellular products for in vivo delivery and how to undertake pharmacological testing of cellular products. Insights into these questions can be obtained from hematopoietic stem cells (HSC) which have been used for the past 50 years in bone marrow transplantation for regeneration of blood cells in patients undergoing high dose chemotherapy to treat cancer. The differentiation of HSC into mature blood cells is controlled by proteins called hematopoietic growth factors and these factors have been used to generate cellular products in vitro for clinical applications. This chapter will review some of the results of cellular therapies performed with HSC and the lessons that can be learned from these studies.     

Cancer gene-therapy: clinical trials

The objective of gene therapy for the treatment of cancer is to kill tumour cells but preserve normal tissue; therefore, the ideal gene therapy agent would be targeted for specific transduction of tumour cells and have specificity in its cytotoxic action. A variety of strategies to achieve these aims have demonstrated promising results in the laboratory, including enzyme-pro-drug activating systems, correction of genetic mutations contributing to the malignant phenotype and stimulation of a T-cell-mediated anti-tumour immune response. The key to the success of all these strategies is an effective vector that can direct appropriate expression of the therapeutic gene. Viruses have many properties that can be adapted to achieve this therapeutic endpoint; furthermore, they can be engineered to replicate selectively in cancer cells and lyse them. The challenge now is to translate these features into effective therapies that can supplement or supplant existing treatments.     

CD1d ligands: the good, the bad, and the ugly

The MHC class I-like CD1d glycoprotein is a member of the CD1 family of Ag-presenting molecules and is responsible for the selection of NKT cells. A number of ligands that can be presented by CD1d to NKT or other CD1d-restricted T cells have been identified. These include glycolipids from a marine sponge, bacterial glycolipids, normal endogenous glycolipids, tumor-derived phospholipids and glycolipids, and nonlipidic molecules. The presentation of many of these molecules can have immunopotentiating effects, such as serving as an adjuvant against malaria or resulting in a more rapid clearance of certain virus infections. They can also be protective in autoimmune diseases or cancer or can be deleterious. This review will highlight these ligands in a discussion of their potential use against (and role in the pathogenesis of) these diseases.     

Mechanisms and rate equations for dissociating systems.

The results presented in the previous paper (Boeker, E.A. (1978), Biochemistry 17 (preceding paper in this issue) indicate that the dissociation of the decamer of arginine decarboxylase of Escherichia coli B is enhanced by Na+ and retarded by H+. In this system, substances which increase the rate of dissociation can be treated kinetically either as substrates or activators, and substances which retard dissociation can be treated as products or inhibitors. In addition, the events needed for dissociation can occur in an ordered or a random sequence, and the dissociation itself, from a decamer to five dimers, can be a sequential or a concerted process. In order to provide a framework for the experimental results, mechanisms for the dissociation of arginine decarboxylase that take all of these factors into account are described. In addition, it is shown that the usual methods of steady-state kinetics can be applied to these systems when true initial rates are measured; rate equations are presented for each mechanism. The results can be used for any dissociating of three or more subunits and will describe the dissociation of a dimer under certain conditions.     

Growth Inhibition Test for Identification of Mycoplasma Species Utilizing Dried Antiserum-Impregnated Paper Discs

The growth inhibition test for identifying Mycoplasma species has been modified by drying antibody-impregnated paper discs at 5 C. When stored at -20 C, these discs have been found to retain their inhibitory activity for longer than 7 months. Since these discs can be stored for long period of time, significant advantages over present methods result. When, for example, discs are arranged on a ring, a single test can be used for the identification of an unknown human species. Valuable antisera can be distributed to other laboratories on paper discs in much less volume than can fluid antiserum. Considerable savings of time result from prior preparation of many discs that can then be stored and used over a long period of time. The growth-inhibiting antibody is stable, and the activity is not enhanced by a heat-labile accessory factor from fresh guinea pig serum which increases the antibody titer in the metabolic inhibition test.     

Why do we need quality-assured diagnostic tests for sexually transmitted infections?

The bacterial sexually transmitted infections (STIs) syphilis, gonorrhoea and chlamydia can all be cured with a single dose of antibiotic. Unfortunately, however, these infections often remain undiagnosed as many infected individuals have few if any symptoms. Diagnostic tests with high sensitivity and specificity are available for all three infections but, owing to their expense and the lack of laboratory capacity, most people in developing countries do not have access to these tests. There is a great need for simple, cheap diagnostic tests for STIs that can be performed at the point of care, enabling treatment to be given immediately. It is hoped that recent advances in our understanding of the pathogenesis of these infections, and the availability of the complete genome sequences for each causative organism, will lead to the development of improved point-of-care tests that will reduce the burden of these diseases in developing countries.     

Reconstruction of NOESY maps. A requirement for a reliable conformational analysis of biomolecules using 2D NMR

The modelling of the conformation of a biomolecule in solution is based mainly on the internuclear distances deduced from measurements of nuclear Overhauser effects (nOe) in NOESY correlation maps. The distances are then used as restraints in the energy minimization procedure, which leads to one or several optimized conformations. A general and safe technique for validating these structures with respect to the experimental data is here proposed: from the internuclear distances, the relaxation matrix can be computed under the assumption of a unique rotational correlation time. By stepwise integration of these relaxation equations, the NOESY maps can be accurately reconstructed for any mixing time. Because multi-spin effects are correctly taken into account, any difference between the experimental and theoretical maps can be easily interpreted in terms of conformation, and possible inconsistencies due to conformational averaging can be pointed out. The technique is illustrated for a bacterial lipopeptide, mycosubtilin, the spectrum of which is completely assigned.     

A cell-permeable, activity-based probe for protein and lipid kinases

Protein and lipid kinases are two important classes of biomedically relevant enzymes. The expression and activity of many kinases are known to be dysregulated in a variety of diseases, and proteomic tools that can assess the presence and activity of these enzymes are likely to be useful for their evaluation. Because many of the mechanisms by which protein kinases can become unregulated involve post-translational modifications or changes in protein localization, they can only be detected by examining protein activity, sometimes within the context of the living cell. Wortmannin is a steroid-derived fungal metabolite that covalently inhibits both protein and lipid kinases. Here we describe the synthesis of three wortmannin derivatives, biotin-wortmannin, BODIPY-wortmannin, and tetramethylrhodamine-wortmannin. We demonstrate that these reagents exhibit reactivity similarly as wortmannin and react with members of the phosphatidylinositol 3-kinase and PI3-kinase related kinase families in cellular lysates. Moreover, in some cases these reagents can differentiate between the active and inactive forms of the enzyme, indicating that they are activity-based probes. The reagents also exhibit complementary properties. The biotin-wortmannin reagent is effective in the isolation of labeled proteins; all three can be used for protein labeling, and BODIPY-wortmannin is cell-permeable and can be used to label proteins within cells.     

Mechanism and yields in enzyme catalysed equilibrium and kinetically controlled synthesis of β-lactam antibiotics,peptides and other condensation products

Hydrolases can be used to catalyse the synthesis of condensation products such as β-lactam antibiotics, peptides, oligosaccharides and glycerides. In biotechnological processes, synthesis to achieve maximum yields may be carried out either as an equilibrium controlled or kinetically controlled reaction. Only in the later case is the yield of condensation product influenced by the properties of the enzyme that act as a transferase in this reaction. With the same amount of enzyme the maximum yield is also obtained much more rapidly than in the equilibrium controlled process. Hydrolases with high ratios of transferase to hydrolase activity are favourable for use. Recent results on the mechanisms of enzyme catalysed condensations allow a rational analysis of how yield controlling factors (pH, temperature, ionic strength, enzyme and substrate properties) may be changed to obtain optimum yields. This can be used to evaluate whether these biotechnological processes can compete with the chemical methods currently used for the synthesis of these products. It can also be used to plan rational protein engineering of the enzymes that in kinetically controlled synthesis of the condensation products may give yields that can compete favourably with the existing chemical processes to produce these compounds.     

Consistent micro, macro and state-based population modelling

A population system can be modelled using a micro model focusing on the individual entities, a macro model where the entities are aggregated into compartments, or a state-based model where each possible discrete state in which the system can exist is represented. However, the concepts, building blocks, procedural mechanisms and the time handling for these approaches are very different. For the results and conclusions from studies based on micro, macro and state-based models to be consistent (contradiction-free), a number of modelling issues must be understood and appropriate modelling procedures be applied. This paper presents a uniform approach to micro, macro and state-based population modelling so that these different types of models produce consistent results and conclusions. In particular, we demonstrate the procedures (distribution, attribute and combinatorial expansions) necessary to keep these three types of models consistent. We also show that the different time handling methods usually used in micro, macro and state-based models can be regarded as different integration methods that can be applied to any of these modelling categories. The result is free choice in selecting the modelling approach and the time handling method most appropriate for the study without distorting the results and conclusions.     

Why, when, and how biochemists should use least squares.

One of the most commonly used methods for the analysis of experimental data in the biochemical literature is nonlinear least squares (regression). This group of methods are also commonly misused. The purpose of this article is to review the assumptions inherent in the use of least-squares techniques and how these assumptions govern the ways that least-squares techniques can and should be used. Since these assumptions pertain to the nature of the experimental data to be analyzed they also dictate many aspects of the data collection protocol. The examination of these assumptions includes a discussion of questions like: Why would a biochemist want to use nonlinear least-squares techniques? When is it appropriate for a biochemist to use nonlinear least-squares techniques? What confidence can be assigned to the results of a nonlinear least-squares analysis?     

Bayesian inference for identifying interaction rules in moving animal groups

The emergence of similar collective patterns from different self-propelled particle models of animal groups points to a restricted set of "universal" classes for these patterns. While universality is interesting, it is often the fine details of animal interactions that are of biological importance. Universality thus presents a challenge to inferring such interactions from macroscopic group dynamics since these can be consistent with many underlying interaction models. We present a Bayesian framework for learning animal interaction rules from fine scale recordings of animal movements in swarms. We apply these techniques to the inverse problem of inferring interaction rules from simulation models, showing that parameters can often be inferred from a small number of observations. Our methodology allows us to quantify our confidence in parameter fitting. For example, we show that attraction and alignment terms can be reliably estimated when animals are milling in a torus shape, while interaction radius cannot be reliably measured in such a situation. We assess the importance of rate of data collection and show how to test different models, such as topological and metric neighbourhood models. Taken together our results both inform the design of experiments on animal interactions and suggest how these data should be best analysed.     

Water-Dispersible Three-Dimensional LC-Nanoresonators

Nanolithography techniques enable the fabrication of complex nanodevices that can be used for biosensing purposes. However, these devices are normally supported by a substrate and their use is limited to in vitro applications. Following a top-down procedure, we designed and fabricated composite inductance-capacitance (LC) nanoresonators that can be detached from their substrate and dispersed in water. The multimaterial composition of these resonators makes it possible to differentially functionalize different parts of the device to obtain stable aqueous suspensions and multi-sensing capabilities. For the first time, we demonstrate detection of these devices in an aqueous environment, and we show that they can be sensitized to their local environment and to chemical binding of specific molecular moieties. The possibility to optically probe the nanoresonator resonance in liquid dispersions paves the way to a variety of new applications, including injection into living organisms for in vivo sensing and imaging.     

Spermicide by females: what should males do?

The female reproductive tract can be particularly aggressive towards ejaculates, often leading to the death of large numbers of sperm. It has been suggested that males can respond to these actions by investing more in sperm and donating larger ejaculates. Such counteractions may lead to arms races, which can have significant implications for the mating system. In a series of simple models we first show that arms races are not necessarily supported: in fact, sperm killing may even favour no change or reductions in sperm allocation. Second, we identify a simple mechanistic rule for sperm killing that determines whether an arms race or sperm reduction will be favoured. Which of these responses is favoured by selection depends on whether a certain number, or proportion, of sperm are killed. When a specific number is killed, larger investment in sperm is favoured and when a specific proportion is killed, no change or lower investment in sperm is favoured. Both of these mechanisms are biologically plausible.     

Solidarity and justice as guiding principles in genomic research

In genomic research the ideal standard of free, informed, prior and explicit consent is sometimes difficult to apply. This has raised concern that important genomic research will be restricted. Different consent procedures have therefore been proposed. This paper explicitly examines the question how, in genomic research, the principles of solidarity and justice can be used to justify forms of diminished individual control over personal data and bio-samples. After a discussion of the notions of solidarity and justice and how they can be related to health care and genomic research, we examine how and in which situations these notions can form a strong moral basis for demanding certain financial sacrifices. Then we examine when these principles can justify consent procedures which diverge from the ideal standard. Because much genomic research is not expected to lead to immediate (clinical) benefits we also discuss the question of whether we can be obliged to make any sacrifices for future (not yet existing) patients. We conclude with the formulation of a number of conditions that have to be met before autonomy sacrifices can be reasonably demanded in genomic research.     

Genetic and individual assignment of tetraploid green sturgeon with SNP assay data

Polyploid organisms pose substantial obstacles to genetic analysis, as molecular assay data are usually difficult to evaluate in a Mendelian framework. Green sturgeon (Acipenser medirostris) is a tetraploid species and is facing significant conservation challenges, including bycatch in ocean fisheries. We present here novel molecular genetic assays and analytical methodology for green sturgeon that allow discrimination of fish from the two visually indistinguishable distinct population segments (DPSs), and also provide individual-specific genetic tags. We show how the relative fluorescence intensity data from a standard quantitative PCR assay, designed for a biallelic single nucleotide polymorphism, can be grouped into “genotype categories” using standard analytical software and post-processing manipulation. We then show how these genotype category data can be used to discriminate green sturgeon from the southern DPS, which is protected under the US Endangered Species Act, and the northern DPS, which is not. We also show how these data can be used to reliably identify individual green sturgeon, and can therefore be used in capture/recapture analyses. Both types of identification are extremely accurate even when fewer than half of the assays are successfully called. We then apply these new techniques to show that proportions of the two green sturgeon DPSs are extremely different in the two major fishery areas where they are encountered as bycatch. While these assays and methods do not provide data that can be used in pedigree-based analyses, they are an important advance in the application of genetic analysis to conservation and management of polyploid organisms.     

The generation of a single nick per plasmid molecule using restriction endonucleases with multiple recognition sites

Some restriction endonucleases generate a single-stranded nick at their recognition sequences in the presence of ethidium bromide (EtBr). This nick can then be extended to a single-stranded gap in which mutations can be introduced by a variety of techniques. To date, the templates used in these studies have largely contained a single recognition site for a given enzyme. Therefore, we have extended these studies to twelve enzymes for which multiple recognition sites exist in the template and show that, under appropriate conditions, one single-stranded nick is introduced per plasmid molecule.     

Skin explant cultures as a source of keratinocytes for cultivation

Cultivated human keratinocytes can be used successfully in the treatment of burn patients, but efforts to heal burns and other wounds can be hampered by the very small skin biopsies available for cultivation of transplantable keratinocyte sheets. A small biopsy (and correspondingly small number of enzymatically isolated keratinocytes for use in classical cultivation techniques) can lead to a low yield of multilayer sheets for clinical application or unacceptably long cultivation times. One way of addressing this is to make use of skin remnants remaining after enzymatic digestion and culture cells migrating out of these skin explants. Sufficient numbers of explant-derived keratinocytes can be obtained to facilitate additional routine cultivation of these cells. Biopsy remnants can be used to initiate explant cultures repeatedly (we were able to re-use pieces of skin 10 times and still obtain useful numbers of keratinocytes) and this “passaging” yields substantially more cells for classical cultivation than would be available from conventional methodology alone, and in a comparable timeframe. Another advantage of this method is that it does not require additional biopsies to be procured from already-compromised patients and overcomes problems associated with contamination of skin samples with resistant hospital-acquired bacterial infections common during prolonged hospitalization.