Additional file 1: Table S1. of A phase I dose-escalation study of PEP02 (irinotecan liposome injection) in combination with 5-fluorouracil and leucovorin in advanced solid tumors

Tumor type, dose level, DLT, best response and single nucleotide polymorphisms of UGT1A1*28 and UGT1A1*6. (DOCX 18 kb

Gene Expression Profiling of Dendritic Cells in Different Physiological Stages under <em>Cordyceps sinensis</em> Treatment

<div><p><em>Cordyceps sinensis</em> (CS) has been commonly used as herbal medicine and a health supplement in China for over two thousand years. Although previous studies have demonstrated that CS has benefits in immunoregulation and anti-inflammation, the precise mechanism by which CS affects immunomodulation is still unclear. In this study, we exploited duplicate sets of loop-design microarray experiments to examine two different batches of CS and analyze the effects of CS on dendritic cells (DCs), in different physiology stages: naïve stage and inflammatory stage. Immature DCs were treated with CS, lipopolysaccharide (LPS), or LPS plus CS (LPS/CS) for two days, and the gene expression profiles were examined using cDNA microarrays. The results of two loop-design microarray experiments showed good intersection rates. The expression level of common genes found in both loop-design microarray experiments was consistent, and the correlation coefficients (Rs), were higher than 0.96. Through intersection analysis of microarray results, we identified 295 intersecting significantly differentially expressed (SDE) genes of the three different treatments (CS, LPS, and LPS/CS), which participated mainly in the adjustment of immune response and the regulation of cell proliferation and death. Genes regulated uniquely by CS treatment were significantly involved in the regulation of focal adhesion pathway, ECM-receptor interaction pathway, and hematopoietic cell lineage pathway. Unique LPS regulated genes were significantly involved in the regulation of Toll-like receptor signaling pathway, systemic lupus erythematosus pathway, and complement and coagulation cascades pathway. Unique LPS/CS regulated genes were significantly involved in the regulation of oxidative phosphorylation pathway. These results could provide useful information in further study of the pharmacological mechanisms of CS. This study also demonstrates that with a rigorous experimental design, the biological effects of a complex compound can be reliably studied by a complex system like cDNA microarray.</p> </div

Correlation of gene expression ratios between cDNA microarray and qRT-PCR.

<p>A total of 36 microarray samples were validated by qRT-PCR (6 representative genes in different treatments (CS, LPS, and LPS/CS) of duplicate microarrays (Loop1 and Loop2)). Data from both microarray and PCR were normalized by setting the expression level of untreated control.</p

Design of microarray experiment adopting duplicate sets of loop-design microarray experiments.

<p>Each experiment contained ten hybridizations and five experimental conditions, two controls and three treatments. Each mRNA sample was a combination of the mRNA of three donors, performed for biological replication in the loop-design microarray experiment. In addition, we utilized duplicate samples in each experiment for technical replication as well as internal control, estimate technological error and enhance the reliability of data.</p

Microarray analysis using intersection analysis and gene clustering.

<p>(A) Assesses the genes uniquely regulated by CS, LPS, and LPS/CS through an intersectional method. The SDE genes obtained in both loop experiments were divided into 7 groups. The different regulation genes of A1, A2, A3, A4, A5, A6, and A7 groups were 295, 31, 20, 80, 59, 95, and 47 genes, respectively. (B) The expression of common genes under treatment with CS, LPS, or LPS/CS( A1 group genes) was analyzed by gene clustering (hierarchical model).</p

Functional enrichment analysis of A5 group genes by GO-terms and KEGG pathway (<i>P</i><0.05).

#<p>Category: B.P. (biological process); C.C. (cellular component); M.F. (molecular function).</p

Linear regression of the expression level of common genes found in both sets of loop microarray experiments.

<p>The Numbers of common genes found in both loop microarray experiments under treatment with CS, LPS, or LPS/CS are 405, 490, and 453 respectively. Loop1 and loop2 log₂ ratio denotes the expression ratio between control and treatments (CS, LPS, or LPS/CS) regarding duplicate sets of loop microarray experiments. The correlation coefficients (Rs) in the three lists of common genes are 0.96, 0.97, and 0.97, respectively.</p

The number of significantly differentially expressed genes and the intersection rate in two biological replication experiments treated with CS, LPS, and LPS/CS.

#<p>Intersection rate was calculated by the following equation: common genes/((Loop1 genes+Loop2 genes)/2).</p

Functional enrichment analysis of A7 group genes by GO-terms and KEGG pathway (<i>P</i><0.05).

#<p>Category: B.P. (biological process); C.C. (cellular component); M.F. (molecular function).</p