Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of total lymph node cells from inducible ll7 gene deletion mice

ABSTRACT: Il7fx/KO Rosa26CreERT2 mice (samples 4, 5 and 6) and CreERT –ve littermate controls (samples 1, 2 and 3) were treated with tamoxifen for five days. Three weeks later, RNA was isolated from total lymph nodes of individual mice and gene expression determined by RNAseq.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Benedict Seddon

PROVIDER: E-MTAB-6451 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

IL-7-dependent maintenance of ILC3s is required for normal entry of lymphocytes into lymph nodes.

Yang Jie J Cornelissen Ferry F Papazian Natalie N Reijmers Rogier M RM Llorian Miriam M Cupedo Tom T Coles Mark M Seddon Benedict B

The Journal of experimental medicine 20180222 4

IL-7 is essential for the development and homeostasis of T and B lymphocytes and is critical for neonatal lymph node organogenesis because Il7-/- mice lack normal lymph nodes. Whether IL-7 is a continued requirement for normal lymph node structure and function is unknown. To address this, we ablated IL-7 function in normal adult hosts. Either inducible Il7 gene deletion or IL-7R blockade in adults resulted in a rapid loss of lymph node cellularity and a corresponding def ...[more]

PMID: 29472496

Similar Datasets

Targeting Lymph Node Sinus Macrophages to Inhibit Lymph Node Metastasis.

Project description:Lymph nodes are important peripheral immune organs in which numerous important immune responses occur. During the process of lymphatic metastasis, lymph nodes are also sites through which tumor cells must pass. Therefore, it is essential to develop a drug delivery system that can specifically transfer immunostimulatory medicine into lymph nodes to block lymphatic metastasis. Here, we developed a nucleic acid drug delivery system containing cationic agarose (C-agarose) and CpG oligodeoxynucleotides. C-agarose has a high affinity for Siglec-1 on the surface of lymph node sinus macrophages, which have a high specificity for targeting lymph nodes. Subcutaneous implantation of C-agarose+CpG gel caused the accumulation of CpG in the lymph node sinus macrophages and generated antitumor immune responses in the lymph node. C-agarose+CpG gel treatment decreased the metastasis size in the tumor-draining lymph node (TDLN) and lung metastatic nodules and suppressed tumor growth in both a mouse 4T1 breast cancer model and a B16F10 melanoma model. On this basis, this study proposes a nonsurgical invasive lymph node targeting immunotherapy concept that may provide a new approach for antitumor metastasis.

| S-EPMC6529739 | biostudies-literature

Murine chronic lymph node window for longitudinal intravital lymph node imaging.

Project description:Chronic imaging windows in mice have been developed to allow intravital microscopy of many different organs and have proven to be of paramount importance in advancing our knowledge of normal and disease processes. A model system that allows long-term intravital imaging of lymph nodes would facilitate the study of cell behavior in lymph nodes during the generation of immune responses in a variety of disease settings and during the formation of metastatic lesions in cancer-bearing mice. We describe a chronic lymph node window (CLNW) surgical preparation that allows intravital imaging of the inguinal lymph node in mice. The CLNW is custom-made from titanium and incorporates a standard coverslip. It allows stable longitudinal imaging without the need for serial surgeries while preserving lymph node blood and lymph flow. We also describe how to build and use an imaging stage specifically designed for the CLNW to prevent (large) rotational changes as well as respiratory movement during imaging. The entire procedure takes approximately half an hour per mouse, and subsequently allows for longitudinal intravital imaging of the murine lymph node and surrounding structures for up to 14 d. Small-animal surgery experience is required to successfully carry out the protocol.

| S-EPMC5592697 | biostudies-literature

Should the left gastric artery lymph node be considered as the predictive lymph node for extra-gastric lymph node metastases?

Project description:BackgroundTo validate the prognostic impacts of the left gastric artery lymph node (No. 7 LN) metastasis and investigate whether the No. 7 LN metastasis should be considered as the predictive LN for extra-gastric LN metastases.MethodsBetween January 2003 and December 2011, a total of 1,586 patients who underwent R0 gastrectomy were retrospected. Patients with LN metastases were divided into three groups: (I) patients with only peri-gastric LN metastases (peri-gastric group); (II) patients with peri-gastric and only No. 7 LN metastases (No. 7 group); and (III) patients with other extra-gastric LN metastases (extra-gastric group). Propensity score matching (PSM) was adopted to accurately evaluate prognoses of all patients after surgery.ResultsOf 1,586 patients, 235 (14.82%) were pathologically identified to present with the No. 7 LN metastases. Patients with the No. 7 LN metastases presented the significantly lower survival rate both before and after adjustment by pTNM stage, compared to those without the No. 7 LN metastases. Patients in the No. 7 group were identified to present the significant lower survival rate than those in the peri-gastric group, and to present the similar median overall survival (OS) to those in the extra-gastric group. In addition, patients with extra-gastric LN except No. 7 LN metastases failed to show any superiority of survival outcomes, compared with those with extra-gastric LN metastases including the No. 7 LN metastasis.ConclusionsThe No. 7 LN metastases had the crucial survival implications. Nevertheless, the No. 7 LN failed to be considered as the predictive LN for the extra-gastric LN metastases in gastric cancer (GC).

| S-EPMC7327347 | biostudies-literature

Groin lymph node detection and sentinel lymph node biopsy in vulvar cancer.

Project description:ObjectiveTo identify suitable diagnostic tools and evaluate the efficacy of sentinel lymph node (SLN) biopsy for inguinal lymph node metastasis in vulvar cancer.MethodsData from 41 patients with vulvar cancer were evaluated retrospectively, including magnetic resonance imaging (MRI) measurements, SLN biopsy status, groin lymph node metastasis, and prognosis.ResultsSLN biopsy was conducted in 12 patients who had stage I to III disease. Groin lymphadenectomy was omitted in five of the nine patients with negative SLNs. All SLN-negative patients who did not undergo groin lymphadenectomy showed no evidence of disease after treatment. On MRI, the long and short diameters of the inguinal node were significantly longer in metastasis-positive cases, compared with negative cases, in 25 patients whose nodes were evaluated pathologically (long diameter, 12.8 mm vs. 8.8 mm, p=0.025; short diameter, 9.2 mm vs. 6.7 mm, p=0.041). The threshold of >10.0 mm for the long axis gave a sensitivity, specificity, positive predictive value, and negative predictive value of 87.5%, 70.6%, 58.3%, and 92.3%, respectively, using a binary classification test. Decision tree analysis revealed a sensitivity, specificity, and accuracy of 87.5%, 70.6%, and 76.0%, respectively, with the threshold of >10.0 mm for the long axis on MRI. The criteria of >10.0 mm for the long axis on MRI predicted an advanced stage and poorer prognosis using a validation set of 15 cases (p=0.028).ConclusionMinimally invasive surgery after preoperative evaluation on MRI and SLN biopsy is a feasible strategy for patients with vulvar cancer.

| S-EPMC5078820 | biostudies-literature

Sentinel lymph node biopsy followed by lymph node dissection for localised primary cutaneous melanoma.

Project description: Not available

| S-EPMC6461196 | biostudies-literature

Efficacy of lymph node dissection for duodenal cancer according to the lymph node station.

Project description:BackgroundLymph node metastasis (LNM) is associated with poor prognosis in patients with duodenal cancer (DC). However, the efficacy and optimal extent of lymph node (LN) dissection have not been thoroughly discussed.MethodsA total of 98 consecutive patients with DC who underwent surgical resection (pancreatoduodenectomy, n = 55; partial resection, n = 32; pancreas-sparing total duodenectomy, n = 9) were retrospectively analyzed. The LN stations located upstream of the lymphatic flow were defined as Np stations according to tumor location, whereas the others were defined as Nd stations. The association between the dissection of each LN station and survival outcome was investigated using the efficacy index (EI; percentage of metastases to lymph nodes in each station multiplied by the 5-year survival rate of metastatic cases).ResultsThe survival of patients with LNM at the Nd stations (n = 6) was significantly worse than that of patients with LNM only at the Np stations (n = 20) (relapse-free survival, median survival time [MST], 6.0 vs. 48.4 months, p < 0.001; overall survival, MST, 15.1 vs. 96.0 months, p < 0.001). Multivariate analysis identified LNM at Nd stations as an independent prognostic factor for overall survival (hazard ratio 9.92; p = 0.015). The Np stations had a high EI (range, 8.34-20.88), whereas the Nd stations had an EI of 0, regardless of the tumor location.ConclusionsLN dissection of the Np stations contributed to acceptable survival, whereas LNM of the Nd stations led to poor survival, possibly reflecting advanced tumor progression to systemic disease in patients with DC.

| S-EPMC10797846 | biostudies-literature

Internal Guidelines for Reducing Lymph Node Contour Variability in Total Marrow and Lymph Node Irradiation.

Project description:BackgroundThe total marrow and lymph node irradiation (TMLI) target includes the bones, spleen, and lymph node chains, with the latter being the most challenging structures to contour. We evaluated the impact of introducing internal contour guidelines to reduce the inter- and intraobserver lymph node delineation variability in TMLI treatments.MethodsA total of 10 patients were randomly selected from our database of 104 TMLI patients so as to evaluate the guidelines' efficacy. The lymph node clinical target volume (CTV_LN) was recontoured according to the guidelines (CTV_LN_GL_RO1) and compared to the historical guidelines (CTV_LN_Old). Both topological (i.e., Dice similarity coefficient (DSC)) and dosimetric (i.e., V95 (the volume receiving 95% of the prescription dose) metrics were calculated for all paired contours.ResultsThe mean DSCs were 0.82 ± 0.09, 0.97 ± 0.01, and 0.98 ± 0.02, respectively, for CTV_LN_Old vs. CTV_LN_GL_RO1, and between the inter- and intraobserver contours following the guidelines. Correspondingly, the mean CTV_LN-V95 dose differences were 4.8 ± 4.7%, 0.03 ± 0.5%, and 0.1 ± 0.1%.ConclusionsThe guidelines reduced the CTV_LN contour variability. The high target coverage agreement revealed that historical CTV-to-planning-target-volume margins were safe, even if a relatively low DSC was observed.

| S-EPMC10000500 | biostudies-literature

Intrahepatic cholangiocarcinoma patients without indications of lymph node metastasis not benefit from lymph node dissection.

Project description:BackgroundTo investigate the necessity of routine lymph node dissection (LND) in intrahepatic cholangiocarcinoma (ICC) patients without indications of lymph node metastasis (LNM) preoperatively.Methods422 consecutive ICC patients who undergone curative resection from January 2009 to December 2014 were enrolled and categorized as two groups (hepatectomy only or hepatectomy plus LND). Clinicopathologic data was compared between the groups by χ2 or Fisher's exact test. Overall survival (OS) and recurrence-free survival (RFS) were calculated by the Kaplan-Meier method and differences were analyzed using the log-rank test. Cox regression model was adopted for multivariable analysis.ResultsThe median OS time of all 422 patients was 41.4 months. One-, 3-, and 5-year OS was 67%, 47%, and 35%, respectively. A total of 73 patients had undergone curative resection combined with LND, of whom 20.5% (15/73) were confirmed lymph node positive pathologically. The clinicopathologic characteristics between LND and control groups showed no significant differences. Of the 422 patients, 271 patients had recurrence. The recurrence rates were 65.8% for the LND group and 63.9% for the non-LND group. Survival analysis revealed that, neither the OS (LND vs. non-LND: 32.2 months vs. 46.2 months; p = 0.16) nor the RFS (LND vs. non-LND: 23.1 months vs. 17.0 months; p = 0.09) had significant difference. Multivariate analysis revealed that tumor size, tumor number, carbohydrate antigen19-9, carcinoembryonic antigen, and gamma-glutamyl transpeptidase were independent predictive factors for OS and RFS.ConclusionRoutine LND may not improve survival in resectable ICC patients with negative LNM diagnosis before operation.

| S-EPMC5768365 | biostudies-literature

Harnessing the lymph node microenvironment.

Project description:Purpose of reviewTo evaluate role of the lymph node in immune regulation and tolerance in transplantation and recent advances in the delivery of antigen and immune modulatory signals to the lymph node.Recent findingsLymph nodes are a primary site of immune cell priming, activation, and modulation, and changes within the lymph node microenvironment have the potential to induce specific regulation, suppression, and potentially tolerance. Antigen enters the lymph node either from tissues via lymphatics, from blood via high endothelial venules, or directly via injection. Here we review different techniques and materials to deliver antigen to the lymph node including microparticles or nanoparticles, ex-vivo antigen presenting cell manipulation, and use of receptor conjugation for specific intralymph node targeting locations.SummaryThe promising results point to powerful techniques to harness the lymph node microenvironment and direct systemic immune regulation. The materials, techniques, and approaches suggest that translational and clinical trials in nonhuman primate and patients may soon be possible.

| S-EPMC6309445 | biostudies-literature

RNAseq analysis of colon and ileum tissue from naive wild type, MR1-/- and IL-17A-/- mice

Project description:Determination of differentially expressed genes in the proximal colon and distal ileum tissue in MR1 and IL-17A deficiency at steady-state. Tissue from naïve mice was harvested, total RNA extracted and subjected to RNASeq analysis.

2018-03-31 | E-MTAB-6547 | biostudies-arrayexpress

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