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MRNA-seq with Agnostic Splice Site Discovery for CNS Transcriptomics Tested in Chronic Pain

ABSTRACT: The study pursued dual goals: To advance mRNA-seq bioinformatics towards unbiased transcriptome capture and to demonstrate its potential for discovery in neuroscience by applying the approach to an in vivo model of neurological disease. We found that 12.4% of known genes were induced and 7% were suppressed in the dysfunctional (but anatomically intact) L4 dorsal root ganglion (DRG) 2 weeks after L5 spinal Nerve Ligation (SNL). A new algorithm for agnostic mapping of pre-mRNA splice junctions (SJ) achieved a precision of 97%.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE20895 | GEO | 2010/05/02

SECONDARY ACCESSION(S): PRJNA124389

REPOSITORIES: GEO

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RNA-seq of rat dorsal root ganglia after ligation to investigate central nervous system transcriptomics in chronic pain using agnostic splice site discovery methods

Project description:The study pursued dual goals: To advance mRNA-seq bioinformatics towards unbiased transcriptome capture and to demonstrate its potential for discovery in neuroscience by applying the approach to an in vivo model of neurological disease. We found that 12.4% of known genes were induced and 7% were suppressed in the dysfunctional (but anatomically intact) L4 dorsal root ganglion (DRG) 2 weeks after L5 spinal Nerve Ligation (SNL). A new algorithm for agnostic mapping of pre-mRNA splice junctions (SJ) achieved a precision of 97%. mRNA-seq of L4 DRG 2 weeks and 2 months after L5 spinal nerve ligation. CONTROL and SNL were used to identify differential gene expression between chronic pain and standard conditions in Rattus norvegicus. CONTROL and SNL and PILOT were used to perform 'agnostic splice site discovery' in the nervous system transcriptome in Rattus norvegicus

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Gene expression signatures for lumber 5 dorsal horn of spinal cord in spinal nerve ligation (SNL) mice with WTD intervention

Project description:For development of gene expression of L5 spinal tissue in SNL mice, L5 spinal nerve was first tightly ligated to construct the neuropathic pain model, and sham-operated group as a control. After chronic administrations of vehicle (distilled water, 10 mg/kg) or WTD (12.60 g/kg, p.o.), L5 spinal cord of dorsal horn were collected, and then, Agilent Whole Mouse Genome Microarray 4×44K expression profiling were employed as a discovery platform to identify genes with the potential to provide basis for the clinical application of WTD for neuropathic pain. A 579-gene consensus signature was identified that distinguished between sham and SNL samples, and a 456-gene consensus signature was identified that distinguished between WTD and SNL samples. Expression of 12 genes (Crk1, Fgf13, Fgfr1, Crk1, Adrbk1, Erbb3, Gnas, Vegfa, Crk1, Erbb3, Drd2, Gnas) were identified as the efficacy of differentially expressed genes.

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A novel functional role for the serine protease inhibitor SerpinA3N and its substrate leukocyte elastase in neuropathic pain

Project description:Two out-bred rat selection lines were separated to produce different hypersensitivity phenotypes following nerve injury. These lines were termed High Pain and Low Pain (HP or LP). Each sub-strain was either subject to a Sham surgery or a Spinal Nerve Ligation (SNL) surgery to the L4 and L5 spinal nerves. Three days following surgery L4/L5 Dorsal Root Ganglia (DRG) were dissected from these animals. For the rat line separation protocol see: Devor M, Raber P (1990) Heritability of symptoms in an experimental model of neuropathic pain. Pain 42:51-67. 12 Hybridizations, 3 per condition; Sham HP DRG; 3 day SNL HP DRG; Sham LP DRG; 3 day SNL LP DRG.

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A novel functional role for the serine protease inhibitor SerpinA3N and its substrate leukocyte elastase in neuropathic pain

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Application of annotation-agnostic RNA sequencing data analysis tools for biomarker discovery in liquid biopsy.

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CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing

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Project description: Not available

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Tripartite target-agnostic combination immunotherapy cures established poorly immunogenic tumors

Project description:Single-agent immunotherapy, such as immune checkpoint inhibition, has shown remarkable efficacy in selected cancer entities and individual patients. However, most patients fail to respond. This is likely due to diverse immunosuppressive mechanisms acting in a concerted way to suppress the host anti-tumor immune response reducing the efficacy of single-agent immunotherapy. Combination immunotherapy approaches that are effective in such poorly immunogenic tumors mostly rely on precise knowledge of immunological targets on tumor cells by vaccinations or antibodies engineered to directly target those. Thus, creating a target-agnostic combination immunotherapy that is effective in poorly immunogenic tumors for which an immunological target is not known is a major challenge. We show that combined adoptive cellular therapy (ACT) with lymphokine-activated killer cells (LAKs), cytokine-induced killer cells (CIKs), Vγ9Vδ2-T-cells (γδ-T-cells) and adaptive, tumor-specific T-cells (CTLs) display synergistic anti-tumor treatment effects, which is further enhanced by co-treatment with anti-PD1 antibodies. Most strikingly, combination of this ACT with anti-PD1 antibodies, local immunotherapy of agonists against Toll-like receptor 3, 7 and 9 and pre-ACT lymphodepletion, a protocol we named TRI-IT, eradicates established, poorly immunogenic tumors and induces durable anti-tumor immunity in a variety of poorly immunogenic syngeneic, autochthonous, as well as autologous humanized patient-derived models. Mechanistically, we show that TRI-IT co-activates adaptive cellular and humoral, as well as innate anti-tumor immune responses to mediate its anti-tumor effect without inducing off-target toxicity. Our data demonstrate the efficacy of a target-agnostic combination immunotherapy that eradicates and potentially cures established poorly immunogenic tumors.

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Ivy Glioblastoma Atlas Project (SNP)

Project description:The Ivy Glioblastoma Atlas Project (Ivy GAP) is a detailed anatomically based transcriptomic atlas of human glioblastoma tumors. As collaborators, the Ivy Foundation funded the Allen Institute and the Swedish Neuroscience Institute to design and create the atlas. The Paul G. Allen Family Foundation also supported the project. This resource consists of a viewer interface that resolves the manually- and machine-annotated histologic images (H&E and RNA in situ hybridization) at 0.5 µm/pixel, a transcriptome browser to view and mine the anatomically-based RNA-Seq samples, an application programming interface, help documentation that describes the methods and how to use the resource, as well as SNP array data and the supporting longitudinal clinical information and MRI time course data. The resource is made available to the public without charge as part of the Ivy GAP (http://glioblastoma.alleninstitute.org/) via the Allen Institute data portal (http://www.brain-map.org), the Ivy GAP Clinical and Genomic Database (http://ivygap.org/) via the Swedish Neuroscience Institute (http://www.swedish.org/services/neuroscience-institute), and The Cancer Imaging Archive (https://wiki.cancerimagingarchive.net/display/Public/Ivy+GAP). The Ivy GAP processed data at GEO includes normalized RNA-Seq FPKM files used for analysis in "An anatomic transcriptional atlas of glioblastoma,” which is under review. Other processed data files as well as sample and donor meta-data and QC metrics are available at http://glioblastoma.alleninstitute.org/static/download.html. The raw RNA-Seq and SNP array data will be submitted to dbGaP.

2017-12-01 | GSE107558 | GEO

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