Principles of model building: an experimentation-aided approach to development of models for signaling networks

Living cells continuously probe their environment and respond to a multitude of external cues. The information about the environment is carried by signaling cascades that act as "internal transducing and computing modules," coupled into complex and interconnected networks. A comprehensive understanding of how cells make decisions therefore necessitates a sound theoretical framework, which can be achieved through mathematical modeling of the signaling networks. In this chapter, we conceptually describe the typical workflow involved in building mathematical models that are motivated by and are developed in a tight integration with experimental analysis. In particular, we delineate the steps involved in a generic, iterative experimentation-driven model-building process, both through informal discussion and using a recently published study as an example. Experiments guide the initial development of mathematical models, including choice of appropriate template model and parameter revision. The model can then be used to generate and test hypotheses quickly and inexpensively, aiding in judicious design of future experiments. These experiments, in turn, are used to update the model. The model developed at the end of this exercise not only predicts functional behavior of the system under study but also provides insight into the biophysical underpinnings of signaling networks.

Total synthesis and stereochemical assignment of burkholdac B, a depsipeptide HDAC inhibitor

Three diastereomers of burkholdac B were prepared by total synthesis, enabling the full stereochemical assignment of the natural product. It is proposed that burkholdac B is identical to thailandepsin A independently isolated by Cheng from the same strain of Burkholderia thailandensis . Burkholdac B is the most potent among depsipeptide histone deacetylase inhibitors in growth inhibition of the MCF7 breast cancer cell line with an IC(50) of 60 pM.

Diagnosis of HIV-1 infection in infants using dried blood spots in Tamil Nadu, South India

INTRODUCTION

Diagnosis of HIV infection in infants is difficult due to the presence of maternal antibodies; only nucleic acid assays are very helpful in early detection. Filter papers are especially useful for blood collection in resource-poor settings with limited access to diagnostic facilities. MATERIALS #ENTITYSTARTX00026;

METHODS

DBS samples were collected from the infants born to HIV seropositive mothers who had received single dose nevirapine at onset of labor. The samples were directly spotted onto the Whatman 903 cards from heel, big toe or finger prick depending on the age of the infants. A total of 766 infant samples were collected on dried blood spots (DBS) and transported to the Department of Experimental Medicine (DEM), Chennai, for testing from different government hospitals of rural and urban parts of Tamil Nadu, South India. According to National AIDS Control Organization's (NACO) protocol DNA was extracted from all these DBS and PCR was performed using the Roche kit version 1.5.

RESULTS

Fifteen infants were found to be HIV positive and 751 were HIV negative; all these 15 positive infants and 49 negative infants who were in the age group between 10 and 18 months were repeated with another DBS and compared with whole blood. The DBS results were concordant with the whole blood method and the sensitivity and specificity were 100%.

The histone deacetylase inhibitors vorinostat and romidepsin downmodulate IL-10 expression in cutaneous T-cell lymphoma cells

BACKGROUND AND PURPOSE

Vorinostat and romidepsin are histone deacetylase inhibitors (HDI), approved for the treatment of cutaneous T-cell lymphoma (CTCL). However, the mechanism(s) by which these drugs exert their anti-cancer effects are not fully understood. Since CTCL is associated with immune dysregulation, we investigated whether these HDI modulated cytokine expression in CTCL cells.

EXPERIMENTAL APPROACH

CTCL cell lines and primary CTCL cells were treated in vitro with vorinostat or romidepsin, or with STAT3 pathway inhibitors. Cell cycle parameters and apoptosis were analysed by propidium iodide and annexin V/propidium iodide staining respectively. Cytokine expression was analysed using QRT-PCR and elisa assays. STAT3 expression/phosphorylation and transcriptional activity were analysed using immunoblotting and transfection/reporter assays respectively.

KEY RESULTS

Vorinostat and romidepsin strongly down-regulated expression of the immunosuppressive cytokine, interleukin (IL)-10, frequently overexpressed in CTCL, at both the RNA and protein level in CTCL cell lines and at the RNA level in primary CTCL cells. Vorinostat and romidepsin also increased expression of IFNG RNA and decreased expression of IL-2 and IL-4 RNA, although to a lesser extent compared to IL-10. Transient exposure to vorinostat was sufficient to suppress IL-10 secretion but was not sufficient to irreversibly commit cells to undergo cell death. STAT3 pathway inhibitors decreased production of IL-10 and vorinostat/romidepsin partially decreased STAT3-dependent transcription without effects on STAT3 expression or phosphorylation.

CONCLUSIONS AND IMPLICATIONS

These results demonstrate that HDI modulate cytokine expression in CTCL cells, potentially via effects on STAT3. Immunomodulation may contribute to the clinical activity of HDI in this disease.

Diagnosis of HIV-1 infection in infants using dried blood spots in Tamil Nadu, South India

INTRODUCTION

Diagnosis of HIV infection in infants is difficult due to the presence of maternal antibodies; only nucleic acid assays are very helpful in early detection. Filter papers are especially useful for blood collection in resource-poor settings with limited access to diagnostic facilities. MATERIALS #ENTITYSTARTX00026;

METHODS

DBS samples were collected from the infants born to HIV seropositive mothers who had received single dose nevirapine at onset of labor. The samples were directly spotted onto the Whatman 903 cards from heel, big toe or finger prick depending on the age of the infants. A total of 766 infant samples were collected on dried blood spots (DBS) and transported to the Department of Experimental Medicine (DEM), Chennai, for testing from different government hospitals of rural and urban parts of Tamil Nadu, South India. According to National AIDS Control Organization's (NACO) protocol DNA was extracted from all these DBS and PCR was performed using the Roche kit version 1.5.

RESULTS

Fifteen infants were found to be HIV positive and 751 were HIV negative; all these 15 positive infants and 49 negative infants who were in the age group between 10 and 18 months were repeated with another DBS and compared with whole blood. The DBS results were concordant with the whole blood method and the sensitivity and specificity were 100%.

Signaling diversity of PKA achieved via a Ca2+-cAMP-PKA oscillatory circuit

Many protein kinases are key nodal signaling molecules that regulate a wide range of cellular functions. These functions may require complex spatiotemporal regulation of kinase activities. Here, we show that protein kinase A (PKA), Ca(2+) and cyclic AMP (cAMP) oscillate in sync in insulin-secreting MIN6 beta cells, forming a highly integrated oscillatory circuit. We found that PKA activity was essential for this oscillatory circuit and was capable of not only initiating the signaling oscillations but also modulating their frequency, thereby diversifying the spatiotemporal control of downstream signaling. Our findings suggest that exquisite temporal control of kinase activity, mediated via signaling circuits resulting from cross-regulation of signaling pathways, can encode diverse inputs into temporal parameters such as oscillation frequency, which in turn contribute to proper regulation of complex cellular functions in a context-dependent manner.

The nested structure of cancer symptoms. Implications for analyzing co-occurrence and managing symptoms

OBJECTIVE

Although many cancer patients experience multiple concurrent symptoms, most studies have either focused on the analysis of single symptoms, or have used methods such as factor analysis that make a priori assumptions about how the data is structured. This article addresses both limitations by first visually exploring the data to identify patterns in the co-occurrence of multiple symptoms, and then using those insights to select and develop quantitative measures to analyze and validate the results.

METHODS

We used networks to visualize how 665 cancer patients reported 18 symptoms, and then quantitatively analyzed the observed patterns using degree of symptom overlap between patients, degree of symptom clustering using network modularity, clustering of symptoms based on agglomerative hierarchical clustering, and degree of nestedness of the symptoms based on the most frequently co-occurring symptoms for different sizes of symptom sets. These results were validated by assessing the statistical significance of the quantitative measures through comparison with random networks of the same size and distribution.

RESULTS

The cancer symptoms tended to co-occur in a nested structure, where there was a small set of symptoms that co-occurred in many patients, and progressively larger sets of symptoms that co-occurred among a few patients.

CONCLUSIONS

These results suggest that cancer symptoms co-occur in a nested pattern as opposed to distinct clusters, thereby demonstrating the value of exploratory network analyses to reveal complex relationships between patients and symptoms. The research also extends methods for exploring symptom co-occurrence, including methods for quantifying the degree of symptom overlap and for examining nested co-occurrence in co-occurrence data. Finally, the analysis also suggested implications for the design of systems that assist in symptom assessment and management. The main limitation of the study was that only one dataset was considered, and future studies should attempt to replicate the results in new data.

TPC2 is a novel NAADP-sensitive Ca2+ release channel, operating as a dual sensor of luminal pH and Ca2+

Nicotinic acid adenine dinucleotide phosphate (NAADP) is a molecule capable of initiating the release of intracellular Ca(2+) required for many essential cellular processes. Recent evidence links two-pore channels (TPCs) with NAADP-induced release of Ca(2+) from lysosome-like acidic organelles; however, there has been no direct demonstration that TPCs can act as NAADP-sensitive Ca(2+) release channels. Controversial evidence also proposes ryanodine receptors as the primary target of NAADP. We show that TPC2, the major lysosomal targeted isoform, is a cation channel with selectivity for Ca(2+) that will enable it to act as a Ca(2+) release channel in the cellular environment. NAADP opens TPC2 channels in a concentration-dependent manner, binding to high affinity activation and low affinity inhibition sites. At the core of this process is the luminal environment of the channel. The sensitivity of TPC2 to NAADP is steeply dependent on the luminal [Ca(2+)] allowing extremely low levels of NAADP to open the channel. In parallel, luminal pH controls NAADP affinity for TPC2 by switching from reversible activation of TPC2 at low pH to irreversible activation at neutral pH. Further evidence earmarking TPCs as the likely pathway for NAADP-induced intracellular Ca(2+) release is obtained from the use of Ned-19, the selective blocker of cellular NAADP-induced Ca(2+) release. Ned-19 antagonizes NAADP-activation of TPC2 in a non-competitive manner at 1 μM but potentiates NAADP activation at nanomolar concentrations. This single-channel study provides a long awaited molecular basis for the peculiar mechanistic features of NAADP signaling and a framework for understanding how NAADP can mediate key physiological events.

Macrolactamization versus macrolactonization: total synthesis of FK228, the depsipeptide histone deacetylase inhibitor

The cyclic depsipeptide FK228 is the only natural product histone deacetylase (HDAC) inhibitor that has advanced to clinical trials as an anticancer agent. While currently obtained by fermentation, total synthesis is an attractive alternative that will facilitate the preparation of unnatural analogues. The previous total syntheses of FK228 featured macrocylization by ester bond formation from a seco-hydroxy acid. Such routes are operationally jeopardized by the steric hindrance of the carboxylic acid and the sensitivity of the allylic alcohol toward elimination. We report a strategically different approach whereby the ester bond is formed intermolecularly at an early stage and macrocyclization is efficiently achieved by amide bond formation.