Direct multiplexed measurement of gene expression with color-coded probe pairs

Geiss, Gary; Bumgarner, Roger E.; Birditt, Brian; Dahl, Timothy; Dowidar, Naeem; Dunaway, Dwayne; Fell, H Perry; Ferree, Sean; George, Renee D.; Grogan, Tammy; James, Jeffrey J; Maysuria, Malini; Mitton, Jeffrey D; Oliveri, Paola; Osborn, Jennifer L.; Peng, Tao; Ratcliffe, Amber; Webster, Philippa; Davidson, Eric H.; Hood, Leroy; Dimitrov, Krassen

doi:10.1038/nbt1385

Cited by 1,827 publications

(1,766 citation statements)

References 18 publications

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“…It utilizes a new technique for the expression profiling. The technical features of the nCounter platform 20,21 made this study feasible, because this system works with small amounts of RNA extracted from formalin-fixed paraffin tissue. Extraction of tissue from paraffin blocks matched to H&E slides allowed accurate sampling of areas of interest based on histomorphologic features.…”

Section: Discussionmentioning

confidence: 99%

“…10,12 In this study, we chose a different approach by using a new analysis platform, the nCounter system, to assess the expression of several hundred genes. 20,21 This platform yields good results with small quantities of RNA isolated from formalin fixed paraffin embedded tissue without a prior amplification step. This allowed us to look for differences in gene expression in matched samples of plexiform neurofibroma and malignant peripheral nerve sheath tumor isolated from within the same surgical specimens.…”

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confidence: 99%

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Expression profiling of 519 kinase genes in matched malignant peripheral nerve sheath tumor/plexiform neurofibroma samples is discriminatory and identifies mitotic regulators BUB1B, PBK and NEK2 as overexpressed with transformation

et al. 2013

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About 50% of all malignant peripheral nerve sheath tumors (MPNSTs) arise as neurofibromatosis type 1 associated lesions. In those patients malignant peripheral nerve sheath tumors are thought to arise through malignant transformation of a preexisting plexiform neurofibroma. The molecular changes associated with this transformation are still poorly understood. We sought to test the hypothesis that dysregulation of expression of kinases contributes to this malignant transformation. We analyzed expression of all 519 kinase genes in the human genome using the nanostring nCounter system. Twelve cases of malignant peripheral nerve sheath tumor arising in a background of preexisting plexiform neurofibroma were included. Both components were separately sampled. Statistical analysis compared global changes in expression levels as well as changes observed in the pairwise comparison of samples taken from the same surgical specimen. Immunohistochemical studies were performed on tissue array slides to confirm expression of selected proteins. The expression pattern of kinase genes can separate malignant peripheral nerve sheath tumors and preexisting plexiform neurofibromas. The majority of kinase genes is downregulated rather than overexpressed with malignant transformation. The patterns of expression changes are complex without simple recurring alteration. Pathway analysis demonstrates that differentially expressed kinases are enriched for kinases involved in the direct regulation of mitosis, and several of these show increased expression in malignant peripheral nerve sheath tumors. Immunohistochemical studies for the mitotic regulators BUB1B, PBK and NEK2 confirm higher expression levels at the protein level. These results suggest that the malignant transformation of plexiform neurofibroma is associated with distinct changes in the expression of kinase genes. The patterns of these changes are complex and heterogeneous. There is no single unifying alteration. Kinases involved in mitotic regulation are particularly enriched in the pool of differentially expressed kinases. Some of these are overexpressed and are therefore possible targets for kinase inhibitors.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Expression profiling of 519 kinase genes in matched malignant peripheral nerve sheath tumor/plexiform neurofibroma samples is discriminatory and identifies mitotic regulators BUB1B, PBK and NEK2 as overexpressed with transformation

et al. 2013

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“…Hybridized samples were run on the NanoString nCounter preparation station using their high‐sensitivity protocol in which excess capture and reporter probes were removed and transcript‐specific ternary complexes were immobilized on a streptavidin‐coated cartridge. The samples were scanned at maximum scan resolution capabilities using the nCounter Digital Analyzer (NanoString Technologies) 23, 24…”

Section: Methodsmentioning

confidence: 99%

T‐cell infiltration and clonality correlate with programmed cell death protein 1 and programmed death‐ligand 1 expression in patients with soft tissue sarcomas

Pollack

Yearley

et al. 2017

Cancer

212

198

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BACKGROUNDPatients with metastatic sarcomas have poor outcomes and although the disease may be amenable to immunotherapies, information regarding the immunologic profiles of soft tissue sarcoma (STS) subtypes is limited.METHODSThe authors identified patients with the common STS subtypes: leiomyosarcoma, undifferentiated pleomorphic sarcoma (UPS), synovial sarcoma (SS), well‐differentiated/dedifferentiated liposarcoma, and myxoid/round cell liposarcoma. Gene expression, immunohistochemistry for programmed cell death protein (PD‐1) and programmed death‐ligand 1 (PD‐L1), and T‐cell receptor Vβ gene sequencing were performed on formalin‐fixed, paraffin‐embedded tumors from 81 patients. Differences in liposarcoma subsets also were evaluated.RESULTSUPS and leiomyosarcoma had high expression levels of genes related to antigen presentation and T‐cell infiltration. UPS were found to have higher levels of PD‐L1 (P≤.001) and PD‐1 (P≤.05) on immunohistochemistry and had the highest T‐cell infiltration based on T‐cell receptor sequencing, significantly more than SS, which had the lowest (P≤.05). T‐cell infiltrates in UPS also were more oligoclonal compared with SS and liposarcoma (P≤.05). A model adjusted for STS histologic subtype found that for all sarcomas, T‐cell infiltration and clonality were highly correlated with PD‐1 and PD‐L1 expression levels (P≤.01).CONCLUSIONSIn the current study, the authors provide the most detailed overview of the immune microenvironment in sarcoma subtypes to date. UPS, which is a more highly mutated STS subtype, provokes a substantial immune response, suggesting that it may be well suited to treatment with immune checkpoint inhibitors. The SS and liposarcoma subsets are less mutated but do express immunogenic self‐antigens, and therefore strategies to improve antigen presentation and T‐cell infiltration may allow for successful immunotherapy in patients with these diagnoses. Cancer 2017;123:3291‐304. © 2017 The Authors. Cancer published by Wiley Periodicals, Inc. on behalf of American Cancer Society. This is an open access article under the terms of the Creative Commons Attribution NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

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“…Collectively, these studies demonstrate the feasibility of subclassifying patients with septic shock, in a clinically relevant manner, based on the expression patterns of a discrete set of genes having relevance to sepsis biology. The availability of clinical microfluidics [58] and digital mRNA measurement technology [59] may allow for clinical feasibility of measuring the 100 class-defining genes in a timely manner that is suitable to direct patient care or for clinical trial stratification.…”

Section: Gene-expression-based Identification Of Septic Shock Subclassesmentioning

confidence: 99%

Clinical review: Sepsis and septic shock - the potential of gene arrays

Wong

2012

Critical Care

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Over the past decade several investigators have applied microarray technology and related bioinformatic approaches to clinical sepsis and septic shock, thus allowing for an assessment of how, or if, this branch of genomic medicine has meaningfully impacted the field of sepsis research. The ability to simultaneously and efficiently measure the steady-state mRNA abundance of thousands of transcripts from a given tissue source (that is, 'transcriptomics') has provided an unprecedented opportunity to gain a broader, genome-level 'picture' of complex and heterogeneous clinical syndromes such as sepsis. A trancriptomic approach to sepsis and septic shock is technically challenging on multiple levels, but nonetheless modest, tangible advances are being realized. These include a genome-level understanding of the complexity of sepsis and septic shock, identification of novel candidate pathways and targets for potential intervention, discovery of novel, candidate diagnostic and stratification biomarkers, and the ability to stratify patients into clinically relevant, expression-based subclasses. The challenges moving forward include robust validation studies, standardization of technical approaches, standardization and further development of analytical algorithms, and large-scale collaborations.

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Direct multiplexed measurement of gene expression with color-coded probe pairs

Cited by 1,827 publications

References 18 publications

Expression profiling of 519 kinase genes in matched malignant peripheral nerve sheath tumor/plexiform neurofibroma samples is discriminatory and identifies mitotic regulators BUB1B, PBK and NEK2 as overexpressed with transformation

Expression profiling of 519 kinase genes in matched malignant peripheral nerve sheath tumor/plexiform neurofibroma samples is discriminatory and identifies mitotic regulators BUB1B, PBK and NEK2 as overexpressed with transformation

T‐cell infiltration and clonality correlate with programmed cell death protein 1 and programmed death‐ligand 1 expression in patients with soft tissue sarcomas

Clinical review: Sepsis and septic shock - the potential of gene arrays

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