Acute renal allograft rejection is an important complication in kidney transplantation. Accurate diagnosis of rejection events is necessary for timely response and treatment. We illustrate the usefulness and biological relevance of selected multivariate approaches to detect rejection from genomic and proteomic signals. The data was used to study gene expression changes using whole genome microarray analysis of peripheral blood from subjects with acute rejection (n=20) and non-rejecting controls (n=20) to obtain insight into the molecular and biological causation of acute renal allograft rejection when combined with proteomics (iTRAQ) data for the same patients/time-points.
Novel multivariate methods for integration of genomics and proteomics data: applications in a kidney transplant rejection study.
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Renal failure is characterized by important biological changes resulting in profound pleomorphic physiological effects termed uremia, whose molecular causation is not well understood. The data was used to study gene expression changes in uremia using whole genome microarray analysis of peripheral blood from subjects with end-stage renal failure (n=63) and healthy controls (n=20) to obtain insight into the molecular and biological causation of this syndrome.
Alteration of human blood cell transcriptome in uremia.
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Acute cardiac allograft rejection is a serious complication of heart transplantation. Investigating molecular processes in whole blood via microarrays is a promising avenue of research in transplantation, particularly due to the non-invasive nature of blood sampling. However, whole blood is a complex tissue and the consequent heterogeneity in composition amongst samples is ignored in traditional microarray analysis. This complicates the biological interpretation of microarray data. Here we have applied a statistical deconvolution approach, cell-specific significance analysis of microarrays (csSAM), to whole blood samples from subjects either undergoing acute heart allograft rejection (AR) or not (NR). We identified eight differentially expressed probe-sets significantly correlated to monocytes (mapping to 6 genes, all down-regulated in ARs versus NRs) at a false discovery rate (FDR) <= 15%. None of the genes identified are present in a biomarker panel of acute heart rejection previously published by our group and discovered in the same data.
White blood cell differentials enrich whole blood expression data in the context of acute cardiac allograft rejection.
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To identify a panel of Seninel Lymph Node (SLN) genes to aid in risk stratification of patients with tumor-positive SLN, total SLN RNA from 97 SLN-positive melanoma patients were chosen from the Sunbelt Melanoma Trial. Microarray experiments were performed to screen SLN genes in recurrence (=39) versus non-recurrence (=58) group. We identified 20 differentially expressed SLN genes in the recurrence vs. the non-recurrence group.
Sentinel Lymph Node Genes to Predict Prognosis in Node-Positive Melanoma Patients.
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Exosomes are small membraneous vesicles secreted into body fluids by tumors. Tumor exosomes contain intact and functional mRNAs, small RNAs (including miRNAs), and proteins that can alter the cellular environment to favor tumor growth. Further exploration into the molecular profiling of exosomes may increase our understanding of their roles in melanoma progression in vivo, and may have potential application in biomarker studies. In the present study, we used mRNA array profiling to identify thousands of exosomal mRNAs associated with melanoma progression and metastasis. Similarly, miRNA array profiling identified specific miRNAs, such as hsa-miR-31, -185, and -34b, involved in melanoma invasion. Our results indicate that melanoma-derived exosomes have unique gene expression signatures and miRNA profiles that may have important functions in melanoma metastasis and progression.
Identifying mRNA, microRNA and protein profiles of melanoma exosomes.
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We profiled gene expression at the maternal-fetal interface during the second trimester of pregnancy (13-22 wks) in trisomy 13 (T13; Patau syndrome, n = 4), trisomy 18 (T18; Edwards syndrome, n = 4), trisomy 21 (T21; Down syndrome, n = 8), and in euploid pregnancies (n = 4). FISH confirmed the ploidy of the samples. Global transcriptional profiling identified differentially expressed transcripts ( 2-fold) in T21 (n = 160), T18 (n = 80), and T13 (n = 125). The majority were upregulated. Unexpectedly, most of the misexpressed genes were not located on the relevant trisomic chromosome, suggesting genome-wide dysregulation. A much smaller proportion of the differentially expressed transcripts were encoded on the aneuploid chromosome, also implicating gene dosage (1-5). In T21, <10% of the genes were transcribed from that chromosome, all but one from the Down syndrome critical region (21q21-22), which is postulated to play an important role in the clinical phenotype. For T13 and T18, a higher proportion of the overexpressed genes were located on the trisomic chromosome. In T13, 15% of the upregulated genes were on the affected chromosome; 15 resided on the long arm, 13q11-14. In T18, the percentage increased to 24, 15 of which were also located on the long arm (18q11-22). Our data suggested that the placental (and possibly fetal) phenotypes that are associated with T13, T18 and T21 are driven by the combined effects of genome-wide phenomena and increased gene dosage from critical regions of the triploid chromosome.
Placental transcriptomes in the common aneuploidies reveal critical regions on the trisomic chromosomes and genome-wide effects.
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Placental trophoblasts are key determinants of in utero development. Mouse trophoblast stem cells (mTSCs), which were first derived over a decade ago, are a powerful cell culture model for studying their self-renewal or differentiation. Our attempts to isolate an equivalent population from the trophectoderm of human blastocysts generated colonies that quickly differentiated in vitro. This finding suggested that the human placenta has another progenitor niche. Here we show that the chorion is one such site. Initially, we immunolocalized pluripotency factors and trophoblast fate determinants in the early-gestation placenta, amnion and chorion. Immunoreactive cells were numerous in the chorion. We isolated these cells and plated them in medium containing FGF and an inhibitor of activin/nodal signaling, which is required for human embryonic SC self-renewal. Colonies of polarized cells with a limited lifespan emerged. Trypsin dissociation yielded continuously self-replicating monolayers. Colonies and monolayers formed the two major human trophoblast lineagesmultinucleate syncytiotrophoblasts and invasive cytotrophoblasts (CTBs). Transcriptional profiling experiments revealed the factors associated with the self-renewal or differentiation of human chorionic trophoblast progenitor cells (TBPCs). They included imprinted genes, NR2F1/2, HMGA2 and adhesion molecules that were required for TBPC differentiation. Together, the results of these experiments suggested that the chorion is one source of epithelial CTB progenitors. These findings explain why CTBs of fully formed chorionic villi have a modest mitotic index and identify the chorionic mesoderm as a niche for TBPCs that support placental growth.
Establishment of human trophoblast progenitor cell lines from the chorion.
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During human pregnancy, a subset of placental cytotrophoblasts (CTBs) differentiates into cells that aggressively invade the uterus and its vasculature, anchoring the progeny and rerouting maternal blood to the placenta. In preeclampsia (PE), CTB invasion is limited, reducing placental perfusion and/or creating intermittent flow. This syndrome, affecting 4-8% of pregnancies, entails maternal vascular alterations (e.g., high blood pressure, proteinuria, and edema) fetal growth restriction. The only cure is removal of the faulty placenta, i.e., delivery. Previously we showed that defective CTB differentiation contributes to the placental component of PE, but the causes were unknown. Here, CTBs isolated from PE and control placentas were cultured for 48 h, enabling differentiation/invasion. In various severe forms of PE, transcriptomics revealed common aberrations in CTB gene expression immediately after isolation that resolved in culture. The upregulated genes included SEMA3B. Adding this protein to normal CTBs inhibited invasion and re-created aspects of the phenotype of these cells in PE. Additionally, SEMA3B downregulated VEGF signaling through the PI3K/AKT and GSK3 pathways, effects that were observed in PE CTBs. We propose that, in severe PE, the in vivo environment dysregulates CTB gene expression, the autocrine actions of the upregulated molecules, including SEMA3B, impair differentiation/invasion/signaling and patient-specific factors determine the signs.
Reversal of gene dysregulation in cultured cytotrophoblasts reveals possible causes of preeclampsia.
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Acute rejection in cardiac transplant patients is still a contributing factor to limited survival of the implanted heart. Currently there are no biomarkers in clinical use that can predict, at the time of transplantation, the likelihood of post-transplantation acute rejection, which would be of great importance for personalizing immunosuppressive treatment. Within the Biomarkers in Transplantation initiative, the predictive biomarker discovery focused on data and samples collected before or during transplantation such as: clinical variables, genes and proteins from the recipient, and genes from the donor. Based on this study, the best predictive biomarker panel contains genes from the recipient whole blood and from donor endomyocardial tissue and has an estimated area under the curve of 0.90. This biomarker panel provides clinically relevant prediction power and may help personalize immunosuppressive treatment and frequency of rejection monitoring.
Predicting acute cardiac rejection from donor heart and pre-transplant recipient blood gene expression.
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