Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cross-Platform Biomarker Program for Establishment and Validation of Liquid Biopsy for Clinical Decision Making in resectable gastrointestinal stromal tumour (GIST)

ABSTRACT: Interventions: Group 1: Day -30 to -1 prior to start of therapy: Screening examination for all participants. A mutational analysis of a histologic sample is performed to detect cKIT- and PDGFR-mutations (inclusion criteria). Additionally imaging methods according to local standards are performed, blood samples will be taken and participants registered. Participants with cKIT- and/or PDGFR-mutated tumours are further included: During neoadjuvant therapy and during surgical therapy: Day -1 to 0: Blood taking for ctDNA and proteins Day +6 (±2): Blood taking for ctDNA and proteins Day +14 (±2): Blood taking for ctDNA and proteins After surgical therapy: Month +3 to +60, every three months (± 28 d): imaging, blood taking for ctDNA and proteins The current medication and disease stage is ascertained at every visit. The taken blood volume is 63 mL each. Primary outcome(s): 1. detection of tumor-specific mutations in ctDNA isolated from plasma after surgical therapy Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: Prognosis

DISEASE(S): Malignant Neoplasm Of Oesophagus,Malignant Neoplasm Of Small Intestine,Malignant Neoplasm Of Retroperitoneum And Peritoneum,Malignant Neoplasm Of Stomach,Malignant Neoplasm Of Colon

PROVIDER: 2437894 | ecrin-mdr-crc |

REPOSITORIES: ECRIN MDR

ACCESS DATA

Json Xml

Similar Datasets

Transcriptional responses in whole blood of healthy adult volunteers experimentally challenged with S. Paratyphi

Project description:This studies describes the transcriptional response in whole blood derived from healthy adult volunteers experimentally infected with S. Paratyphi A. Samples were collected at pre-challenge baseline (Group: CTRL), at day 7 after challenge in those participants who stayed well over 14 days following challenge (Group: suspected Enteric Fever - sEF). Participants who developed signs of enteric fever were sampled at the time of inititiation of antibiotics (Group: EF).In this group diagnosis was confirmed by blood culture positive for S. Paratyphi (SPT). Antibiotic therapy commenced at time of diagnosis or at day 14 after challenge in those who did not develop symptoms. The clinical results of this study have been published in: Dobinson et al. Evaluation of the Clinical and Microbiological Response to Salmonella Paratyphi A Infection in the First Paratyphoid Human Challenge Model. Clin Infect Dis. 2017 Apr 15;64(8):1066-1073.

2019-09-02 | GSE114033 | GEO

Longitudinal proteomic investigation of COVID-19 vaccination

Project description:163 participants with paired peripheral blood mononuclear cells and serum samples，at D0, D28, day 57 (D57) by TMT-based proteomics

2023-09-06 | PXD039826 |

Gene expression before HAART initiation predicts HIV-infected individuals at risk of poor CD4+ T cell recovery.

Project description:Analysis of peripheral blood mononuclear cells (PBMCs) taken from 24 HIV-infected male participants before the start of highly active antiretroviral therapy (HAART). Results identify biomarkers for the identification of HIV-infected participants that progress to good versus poor CD4+ T cell recovery after 48 weeks of HAART.

2009-12-03 | GSE19087 | GEO

Proteins involved in taking up cyclic peptides

Project description:Proteins involved in taking up cyclic peptides

| PRJNA837234 | ENA

Gene expression data in CD4+ and CD8+ cells in sarcoidosis patients following antimycobacterial therapy

Project description:Many chronic cutaneous diseases associated with microbial antigens demonstrate clinical progression due to T cell hyporesponsiveness. Appropriate antimicrobial therapy restores T cell function, leading to clinical resolution. Due to the association of sarcoidosis with mycobacterial antigens, we compared the efficacy of antimycobacterial therapy with placebo in chronic cutaneous sarcoidosis. We conducted a randomized, placebo-controlled, single-blind trial on chronic cutaneous sarcoidosis subjects. Participants received the oral CLEAR regimen: Levofloxacin 750 mg on day 1, then 500 mg daily, Ethambutol 1200 mg daily, Azithromycin 500 mg on day 1, then 250 mg daily, and Rifampin 300 mg daily, or a comparative placebo regimen, for a total of 8 weeks, with a 180 day follow-up. Participants were monitored for absolute change in lesion diameter and decrease in granulomas burden upon completion of therapy.

2013-07-23 | E-GEOD-39606 | biostudies-arrayexpress

Response and recurrence correlates in patients treated with neoadjuvant anti-PD-1 therapy for resectable oral-cavity squamous cell carcinoma

Project description:Neoadjuvant PD-1 blockade may be efficacious in patients with high-risk, resectable oral-cavity, head-and-neck cancer. To explore correlates of response patterns to neoadjuvant nivolumab treatment and post-surgical recurrences, we analyzed longitudinal tumor and blood samples in a cohort of 12 patients displaying 33% responsiveness. Pretreatment tumor-based detection of FLT4 mutations and PTEN signature enrichment favors response, and high tumor mutational burden improves recurrence-free survival. In contrast, preexisting and/or acquired mutations (in CDKN2A, YAP1, JAK2) correlate with innate resistance and/or tumor recurrence. Immunologically, tumor response after therapy entails T-cell receptor repertoire diversification in peripheral blood and intratumoral expansion of preexisting T-cell clones. A high ratio of regulatory to Th17 T cells in pretreatment blood predicts innate resistance, low cytolytic T-cell signature in pretreatment tumor, and low T-cell receptor repertoire diversity in pretreatment blood. Our study provides a molecular framework to advance neoadjuvant anti-PD-1 therapy for patients with resectable head-and-neck cancer.

2021-09-30 | GSE179730 | GEO

NanoString profiling of host response in healthy volunteers vaccinated with ARCT-021 self-amplifying mRNA vaccine or placebo

Project description:Transcriptomic profiling was conducted on whole blood collected from study participants (NCT04480957). A total of 106 healthy participants were randomized into single and two-injection cohorts. Gene transcript levels were determined at baseline (pre-dose 1), day 2, 3, and 8 for all vaccinees. In addition, gene expression was profiled at day 29 (pre-dose 2), 30 and 36 among vaccinees in the two-injection cohort. Whole blood was collected in Tempus Blood RNA tubes, and RNA was extracted from whole blood using the Tempus Spin RNA Isolation Kit.

2022-11-30 | E-MTAB-11315 | biostudies-arrayexpress

Reliable tumor detection using cerebrospinal fluid cell-free DNA methylomes in pediatric medulloblastoma

Project description:Medulloblastoma (MB) is an embryonal tumor of the cerebellum and a highly malignant childhood brain tumor. Cell-free circulating tumor DNA (ctDNA) from the cerebrospinal fluid (CSF) of patients with brain tumors faithfully represent genomic alterations of brain tumors. Distinct epigenetic signatures among subgroups of MB allow us to detect epigenetic alterations in CSF to aid classify and guide therapy of MB tumors. Here, we evaluate DNA methylation and hydroxymethylation of ctDNA derived from small amount of CSF (200 µL) and matched tumor DNA from 3 MB patients. We find highly concordance of DNA methylation and hydroxymethylation between CSF ctDNA and tumor DNA, especially in CpG islands. Importantly, CSF ctDNA can mostly recapitulate the dynamic changes of DNA methylation and hydroxymehtylation in tumor species compared to healthy cerebellums. Those MB tumor signature CpGs’ DNA methylation status are recovered in CSF ctDNA can clearly distinguish MB subgroups by utilizing public large cohort data. We further identified potential diagnostic and prognostic DNA methylation markers in CSF ctDNA. Our results show that CSF ctNDA methylation and hydroxymethylation can be a minimal invasive method to assess epigenetic alterations of MB, which is complementary to current diagnoses of MB tumors.

2020-10-28 | GSE142241 | GEO

Dose-dependent dual roles of PDGF-BB–PDGFR-? in vascular remodeling and opposing effects of anti-PDGF drug-induced metastasis

Project description:Anti-PDGF agents are routinely used as a key component in front-line therapy for the treatment of various cancers. However, molecular mechanisms underlying their impact on vascular remodeling in relation to the dose issue remain poorly understood. Here we show that in high PDGF-BB-producing tumors, anti-PDGF drugs significantly inhibited tumor growth and metastasis by preventing pericyte (PC) loss and vascular permeability. Surprisingly, the same anti-PDGF-BB drugs promoted tumor cell dissemination and metastasis in PDGF-BB-low-producing or negative tumors by ablating PCs from tumor vessels. At the molecular level, we show that the PDGFR-? signaling pathway in PCs mediated the opposing effects and persistent exposure of PCs to PDGF-BB led to marked downregulation of PDGFR-?. Inactivation of the PDGFR-? signaling system led to decreased levels of integrin ?1?1, resulted in impaired adhesion of PCs to collagen I, IV and laminin, two principal extracellular matrix components in blood vessels for interaction with these integrins. Our data suggest that tumor PDGF-BB levels may serve as an important biomarker for selection of tumor-bearing hosts for beneficial therapy and unsupervised practice of this group of drugs could potentially promote tumor invasion and metastasis. Pericytes were isolated and treated with PDGF-BB or control for 5 days.

2013-07-22 | E-GEOD-46564 | biostudies-arrayexpress

ESR1 Y537S and D538G mutations drive resistance to CDK4/6 inhibitors in estrogen receptor-positive breast cancer

Project description:Purpose: Breast cancers with ESR1 mutations are resistant to antiestrogen therapy. We aimed to investigate the association of ESR1 mutations with resistance to CDK4/6 inhibitors (CDK4/6i) using real-world data analysis and experimental validation. Patients and Methods: A total of 3,958 patients with estrogen receptor-positive (ER+) metastatic breast cancer with DNA sequencing data were analyzed. Breast tumor DNA and circulating tumor (ct) DNA were sequenced using the Tempus xT tumor assay and Tempus xF liquid biopsy, respectively. Patients were stratified into either treated with CDK4/6i (breast tumors: 1,070; ctDNA: 1,885) or CDK4/6i naïve (breast tumors: 750; ctDNA: 253). Engineered MCF7 cells carrying ESR1 Y537S or D538G knock-in mutations were used to study antitumor efficacy of the CDK4/6i, palbociclib in vitro and in vivo. Results: In both xF and xT assays, ESR1 mutations were the only somatic alterations significantly more frequent in those who received CDK4/6i than those who did not. Knock-in of ESR1 Y537S or ESR1 D538G in MCF7 cells resulted in upregulation of cell cycle-related gene signatures upon treatment with CDK4/6i ± antiestrogen compared to cells with non-mutant ESR1. MCF7 xenografts harboring ESR1 Y537S and D538G mutations established in nude mice were resistant to palbociclib. Conclusions: We report herein real-world and preclinical evidence that ESR1 mutations, particularly Y537S and D538G, can drive resistance to CDK4/6 inhibitors.

2024-11-12 | GSE281302 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data