Additional file 1: Table S1. of Comparing gene expression data from formalin-fixed, paraffin embedded tissues and qPCR with that from snap-frozen tissue and microarrays for modeling outcomes of patients with ovarian carcinoma

Gene list. Table S2. Pathway list and genes in the pathway. Table S3. Scale and center data used for qPCR. Table S4. Genes unexpressed in at least one TaqMan assay. (DOCX 54 kb

Correction: Identification of a serum-induced transcriptional signature associated with metastatic cervical cancer

<p>Correction: Identification of a serum-induced transcriptional signature associated with metastatic cervical cancer</p

Additional file 1 of A statistical approach for identifying differential distributions in single-cell RNA-seq experiments

Supplement. Sensitivity analyses of MAP estimation method, further methodological details, and additional results. (PDF 553 kb

Identification of a serum-induced transcriptional signature associated with metastatic cervical cancer

<div><p>Objective</p><p>Tumor cells that escape local tissue control can convert inflammatory cells from tumor suppressors to tumor promoters. Moreover, soluble immune-modulating factors secreted from the tumor environment can be difficult to identify in patient serum due to their low abundance. We used an alternative strategy to infer a metastatic signature induced by sera of cervical cancer patients.</p><p>Methods</p><p>Sera from patients with local and metastatic cervical cancer were used to induce a disease-specific transcriptional signature in cultured, healthy peripheral blood mononuclear cells (PBMCs). An empirical Bayesian method, EBarrays, was used to identify differentially expressed (DE) genes with a target false discovery rate of <5%. Ingenuity Pathway Analysis (IPA) software was used to detect the top molecular and cellular functions associated with the DE genes. IPA and <i>in silco</i> analysis was used to pinpoint candidate upstream regulators, including cancer-related microRNAs (miRNAs).</p><p>Results</p><p>We identified enriched pathways in the metastatic cervical group related to immune surveillance functions, such as downregulation of engulfment, accumulation, and phagocytosis of hematopoietic cells. The predicted top upstream genes were IL-10 and immunoglobulins. <i>In silco</i> analysis identified miRNAs predicted to drive the transcriptional signature. Two of the 4 miRNAs (miR-23a-3p and miR-944) were validated in a cohort of women with local and metastatic cervical cancer.</p><p>Conclusions</p><p>This study supports the use of a cell-based assay that uses PBMC “reporters” to predict biologically relevant factors in patient serum. Further, disease-specific transcriptional signatures induced by patient sera have the potential to differentiate patients with local versus metastatic disease.</p></div

Top upstream regulators of dataset genes in metastatic cervical cancer.

<p>Top upstream regulators of dataset genes in metastatic cervical cancer.</p

miRNA expression levels in serum from cervical cancer patients with local or metastatic disease.

<p>Expression levels of four candidate miRNAs were determined via Taqman-based qPCR using RNA extracted from the serum of patients with local (n = 25) or metastatic (n = 24) cervical cancer. Serum expression levels of miR-23b-3p were significantly lower in the metastatic group (B; *p<0.05), while miR-944 expression was significantly higher in serum from patients with metastatic disease (D; **p<0.01). Serum expression levels of miR-23a-3p (A) and miR-193b-5p (C) were not significantly different between the local and metastatic groups.</p

Most significantly up- and downregulated genes in metastatic cancer from reporter assay.

<p>Most significantly up- and downregulated genes in metastatic cancer from reporter assay.</p

Subject characteristics for reporter assay.

<p>Subject characteristics for reporter assay.</p

Top biological functions in the metastatic cervical cancer group.

<p>Top biological functions in the metastatic cervical cancer group.</p

Cell morphology during the early stages following a drop in temperature.

<p><b>(A)</b> Morphology of wild-type (WT) and <i>SREB</i>∆ at 37°C and at 6, 24, and 48-hrs after a drop in temperature at 22°C. When compared to WT, <i>SREB</i>∆ cells exhibited a delay in the filamentous growth (germ tube and hyphal formation). At 22°C, <i>SREB</i>∆ filaments were abnormal in morphology. Scale bar equals 10 μm. <b>(B)</b> Percentage of WT and <i>SREB</i>∆ cells with yeast morphology, germ tube development, and hyphal growth at 37°C and 22°C. Results were averaged from 2 independent experiments (> 200 cells counted in duplicate). <b>(C)</b> Percent of WT and <i>SREB</i>∆ cells that are viable at 37°C and 22°C. Results were averaged from 2 independent experiments (> 200 cells counted in duplicate)</p