Metabolomics of the Tumor Microenvironment in Pediatric Acute Lymphoblastic Leukemia

Stefano Tiziani, Yunyi Kang, Ricky Harjanto, Joshua Axelrod, Giovanni Paternostro, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of AmericaCarlo Piermarocchi, Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, United States of AmericaWilliam Roberts, Rady Children’s Hospital, Department of Pediatrics, University of California San Diego, San Diego, California, United States of AmericaStefano Tiziani, Department of Nutritional Sciences, Dell Pediatric Research Institute, University of Texas at Austin, Austin, Texas, United States of AmericaThe tumor microenvironment is emerging as an important therapeutic target. Most studies, however, are focused on the protein components, and relatively little is known of how the microenvironmental metabolome might influence tumor survival. In this study, we examined the metabolic profiles of paired bone marrow (BM) and peripheral blood (PB) samples from 10 children with acute lymphoblastic leukemia (ALL). BM and PB samples from the same patient were collected at the time of diagnosis and after 29 days of induction therapy, at which point all patients were in remission. We employed two analytical platforms, high-resolution magnetic resonance spectroscopy and gas chromatography-mass spectrometry, to identify and quantify 102 metabolites in the BM and PB. Standard ALL therapy, which includes l-asparaginase, completely removed circulating asparagine, but not glutamine. Statistical analyses of metabolite correlations and network reconstructions showed that the untreated BM microenvironment was characterized by a significant network-level signature: a cluster of highly correlated lipids and metabolites involved in lipid metabolism (p less than 0.006). In contrast, the strongest correlations in the BM upon remission were observed among amino acid metabolites and derivatives (p less than 9.2×10-10). This study provides evidence that metabolic characterization of the cancer niche could generate new hypotheses for the development of cancer therapies.This work was funded by the National Science Foundation (Grant No. 0829891). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Nutritional SciencesDell Pediatric Research InstituteEmail: [email protected] (GP), Email: [email protected] (ST

Multi-species network inference improves gene regulatory network reconstruction for early embryonic development in Drosophila

Gene regulatory network inference uses genome-wide transcriptome measurements in response to genetic, environmental or dynamic perturbations to predict causal regulatory influences between genes. We hypothesized that evolution also acts as a suitable network perturbation and that integration of data from multiple closely related species can lead to improved reconstruction of gene regulatory networks. To test this hypothesis, we predicted networks from temporal gene expression data for 3,610 genes measured during early embryonic development in six Drosophila species and compared predicted networks to gold standard networks of ChIP-chip and ChIP-seq interactions for developmental transcription factors in five species. We found that (i) the performance of single-species networks was independent of the species where the gold standard was measured; (ii) differences between predicted networks reflected the known phylogeny and differences in biology between the species; (iii) an integrative consensus network which minimized the total number of edge gains and losses with respect to all single-species networks performed better than any individual network. Our results show that in an evolutionarily conserved system, integration of data from comparable experiments in multiple species improves the inference of gene regulatory networks. They provide a basis for future studies on the numerous multi-species gene expression datasets for other biological processes available in the literature.Comment: 10 pages text + 3 figures + 1 table + 2 supplementary figures + 3 supplementary table

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Characterisation of the conditioned media produced by the visceral endoderm-like cell lines : towards a defined medium for the osteogenic differentiation of embryonic stem cells

Destruction of bone tissues due to related diseases and developmental defects in skeletal tissues can cause severe pain and mobility problems in daily life. One way to address the clinical needs of these bone-related diseases is to restore or replace the function of bone tissues using tissue engineering approaches. Embryonic stem cells (ESCs) have recently emerged as a potentially suitable cell source for skeletal tissue engineering applications due to their unique developmental and self renewal potential. However, despite the considerable progress made in directing ESC differentiation to therapeutically useful lineages, key challenges still remain, particularly in improving differentiation efficiency and achieving a homogeneous population of the desired cell type. The overall aim of this thesis is to work towards the generation of a defined medium for the enhanced skeletal lineage differentiation of ESCs, which could be used for 11 potential therapeutic applications. In order to accomplish this aim, the osteogenic-inducing effects of media obtained from visceral endoderm (VE)-like cell lines (HepG2 and END2 cells) were investigated and subsequently were characterised using proteomics. In embryogenesis, VE plays an important role as a source of signals which instruct adjacent cells to differentiate. Therefore, it is hypothesised that the soluble factors produced by VE-like cell lines might act as important signals during ESC differentiation. Experimental results showed that the conditioned media (CM) by the VE-like cell lines enhanced the osteogenic differentiation of murine ESCs. The proteins present in the CM were identified and certain ones were investigated for their inductive activities, as observed in the CM. It was established that fibronectin was involved in the stimulatory effect of the CM, thereby demonstrating its potential applicability in development of a defined medium.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Research on ultra-low energy consumption renovation of teaching buildings in severe cold areas under EPC mode

In order to explore the energy saving benefits and economy of ultra-low energy consumption renovation of existing buildings in cold areas under the contract energy management (EPC) mode under different renovation schemes. On the basis of the existing net present value and net present value increment, the net present value rate is proposed as the evaluation index of the transformation plan, so as to realize the comprehensive benefit evaluation of a variety of transformation schemes. The results show that the energy-saving transformation scheme of the project with an external wall of 120 mm rock wool board, a 150 mm extruded polyphenylene board on the roof, and a three-glass single Low-E argon-filled glass on the exterior window has the greatest comprehensive benefits and meets the ultra-low energy consumption standard, the energy saving rate of the envelope transformation reaches 28.07%, and the static recovery period is 5.27 years. This paper provides a design method and reference basis for the ultra-low energy transformation of existing buildings in cold areas using EPC mode

Identifying Rhodamine Dye Plume Sources in Near-Shore Oceanic Environments by Integration of Chemical and Visual Sensors

sensor

Identification of Drug Combinations Containing Imatinib for Treatment of BCR-ABL+ Leukemias

<div><p>The BCR-ABL translocation is found in chronic myeloid leukemia (CML) and in Ph+ acute lymphoblastic leukemia (ALL) patients. Although imatinib and its analogues have been used as front-line therapy to target this mutation and control the disease for over a decade, resistance to the therapy is still observed and most patients are not cured but need to continue the therapy indefinitely. It is therefore of great importance to find new therapies, possibly as drug combinations, which can overcome drug resistance. In this study, we identified eleven candidate anti-leukemic drugs that might be combined with imatinib, using three approaches: a kinase inhibitor library screen, a gene expression correlation analysis, and literature analysis. We then used an experimental search algorithm to efficiently explore the large space of possible drug and dose combinations and identified drug combinations that selectively kill a BCR-ABL+ leukemic cell line (K562) over a normal fibroblast cell line (IMR-90). Only six iterations of the algorithm were needed to identify very selective drug combinations. The efficacy of the top forty-nine combinations was further confirmed using Ph+ and Ph- ALL patient cells, including imatinib-resistant cells. Collectively, the drug combinations and methods we describe might be a first step towards more effective interventions for leukemia patients, especially those with the BCR-ABL translocation.</p></div

Scheme of our search strategy

<p>(a) anti-leukemic drugs were selected using three approaches: kinase inhibitor library screens, correlation analysis, and literature survey. (b) Dose responses of single agent and pair-wise analysis with a fixed dose of imatinib (pairs and triplets) were performed. (c) The drug combinations were optimized using iterative search algorithm (d) The optimal drug combinations were validated with primary patient cells.</p

Concentrations (µM) and levels of 11 small molecules used with imatinib in the combinatorial drug searches.

<p>Concentrations (µM) and levels of 11 small molecules used with imatinib in the combinatorial drug searches.</p