46d2d485-fea1-41b0-843a-5213094cdf9b - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001005423 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Lymph node status is a crucial predictor for the overall survival of invasive breast cancer. However, lymph node involvement is only detected in about half of HER2 positive patients. Currently, there are no biomarkers available for distinguishing small size HER2-positive breast cancers with different lymph node statuses. Thus, in the present study, we applied label-free quantitative proteomic strategy to construct plasma proteomic profiles of ten patients with small size HER2-positive breast cancers (5 patients with lymph node metastasis versus 5 patients with lymph node metastasis).
2018-02-08 | PXD007217 | Pride
Project description:Lung cancer is the leading cause of cancer death both in men and women. Tumor heterogeneity is an impediment to targeted treatment of all cancers, including lung cancer. Here, we sought to characterize changes in tumor proteome and phosphoproteome by longitudinal, prospective collection of tumor tissue of an exceptional responder lung adenocarcinoma patient who survived with metastatic lung adenocarcinoma for more than seven years with HER2-directed therapy in combination with chemotherapy. We employed “Super-SILAC” and TMT labeling strategies to quantify the proteome and phosphoproteome of a lung metastatic site and ten different metastatic progressive lymph nodes collected across a span of seven years, including five lymph nodes procured at autopsy. We identified specific signaling networks enriched in lung compared to the lymph node metastatic sites. We correlated the changes in protein abundance with changes in copy number alteration (CNA) and transcript expression. To further interrogate the mass spectrometry data, patient-specific database was built incorporating all the somatic variants identified by whole genome sequencing (WGS) of genomic DNA from the lung, one lymph node metastatic site and blood. An extensive validation pipeline was built for confirmation of variant peptides. We validated 360 spectra corresponding to 55 germline and 6 somatic variant peptides. Targeted MRM assays demonstrated expression of two novel variant somatic peptides, CDK12 G879V and FASN-R1439Q, with expression in lung and lymph node metastatic sites, respectively. CDK12 G879V mutation likely results in a nonfunctional kinase and knockdown of CDK12 in lung adenocarcinoma cells increased chemotherapy sensitivity, explaining the complete resolution of the lung metastatic sites in this patient.
2019-01-07 | PXD010779 | Pride
Project description:Pancreatic adenocarcinoma (PDAC) is an aggressive disease with an overall 5 year-survival rate of just 5%. A better understanding of both the carcinogenesis processes and the mechanisms of progression of PDAC disease is mandatory. For this, proteomics data from FFPE samples of 173 primary tumor, normal tissue, preneoplastic lesions (PanIN), or lymph node metastases were analyzed from a Systems Biology perspective. Protein expression data was analyzed using probabilistic graphical models, allowing functional characterization. Functional node activities were calculated as the mean of expression of those proteins related to the main function of each node. Comparisons between groups were done using linear mixed models.
2022-06-21 | PXD032076 | Pride
Project description:A total of 14 lymph node samples were collected from 7 mice, with 8 samples obtained from the MI group and 6 from the sham-operated group. Each mouse contributed two lymph node samples: the mediastinal lymph node, MedLN and the sub-iliac lymph node, siLN. Supplementary Table 1 provides a detailed breakdown of sample distribution across the experimental groups.
2025-06-18 | MSV000098260 | MassIVE
Project description:A total of 14 lymph node samples were collected from 7 mice, with 8 samples obtained from the MI group and 6 from the sham-operated group. Each mouse contributed two lymph node samples: the mediastinal lymph node, MedLN and the sub-iliac lymph node, siLN. Supplementary Table 1 provides a detailed breakdown of sample distribution across the experimental groups.
2025-06-16 | MSV000098224 | MassIVE
Project description:A tissue survey of gene expression was conducted using microarray-based transcriptional profiling to compare equine articular cartilage to 10 other normal adult horse tissues. The ten comparative tissues were bladder, cerebellum, kidney, liver, lung, lymph node, muscle, placental villous, spleen, and testis.
2011-01-27 | GSE23862 | GEO
Project description:Regional lymph node metastasis is a major determinant of local recurrence and overall survival rates in patients with colorectal cancer. Because of the poor prognosis associated with the presence of lymph node metastasis, stage III colorectal cancer patients should receive adjuvant treatment with chemo and / or radiation therapy according to the site of tumor. Several authors have investigated the use of revealing solutions for lymph node clearance in colorectal cancer. Most studies comparing conventional histopathological specimen examination to any lymph node clearing technique showed that the use of revealing solutions increases the mean number of lymph nodes harvested, usually in a statistically significant manner. It is still controversial the impact of the use of revealing solutions for upstaging of lymph node status and consequently for the indication for adjuvant therapy. Therefore will be conducted a randomized clinical trial to compares the performance of GEWF and Carnoy solutions for the histopathological examination of patients with colorectal cancer. The aim of this study is to determine the lymph node revealing solution with the best performance (increase in the mean number of lymph node harvested and lymph node upstaging) in patients with colorectal cancer.
| 2193956 | ecrin-mdr-crc
Project description:Regional lymph node metastasis is a major determinant of local recurrence and overall survival rates in patients with colorectal cancer. Because of the poor prognosis associated with the presence of lymph node metastasis, stage III colorectal cancer patients should receive adjuvant treatment with chemo and / or radiation therapy according to the site of tumor. Several authors have investigated the use of revealing solutions for lymph node clearance in colorectal cancer. Most studies comparing conventional histopathological specimen examination to any lymph node clearing technique showed that the use of revealing solutions increases the mean number of lymph nodes harvested, usually in a statistically significant manner. It is still controversial the impact of the use of revealing solutions for upstaging of lymph node status and consequently for the indication for adjuvant therapy. Therefore will be conducted a randomized clinical trial to compares the performance of GEWF and Carnoy solutions for the histopathological examination of patients with colorectal cancer. The aim of this study is to determine the lymph node revealing solution with the best performance (increase in the mean number of lymph node harvested and lymph node upstaging) in patients with colorectal cancer.
| 2209990 | ecrin-mdr-crc
Project description:Expression profiles of porcine liver and tracheobronchial lung lymph node tissues were studied to identify genes being significantly affected by bacterial infection of the lungs. Samples were taken from liver and tracheobronchial lung lymph node tissues in pigs experimentally infected with A. pleuropneumoniae, serotype 5b, and from healthy non-inoculated control pigs from the same herd. Samples were investigated for changes in gene expression by means of global cDNA microarrays. Expression profiling of samples of liver and lung lymph node tissues from ten pigs challenged with Actinobacillus pleuropneumoniae and from five healthy control pigs was conducted by hybridising all 2x15 samples against a tissue specific common reference consisting of a pool of equal amount of total-RNA from all samples of each tissue type and were balanced with respect to control and challenged animals.
2013-01-01 | E-GEOD-16038 | biostudies-arrayexpress
Project description:Wild type or Cd27-/- mice of 8-12 weeks old were immunized intranasally with 500 ug ovalbumin (OVA) protein and 1 ug cholera toxin in 50 ul HBSS. Spleen, draining lymph node (DLN) or lung were isolated at day 3, day 4 or day 8 after immunization. Single cell suspensions of indicated organs were prepared and OT-I T cells were isolated from this using flow cytometric cell sorting.
2013-08-18 | E-MTAB-1772 | biostudies-arrayexpress