|
| Status |
Public on Jan 29, 2024 |
| Title |
Tumor-5x-A |
| Sample type |
RNA |
| |
|
| Source name |
Tumor
|
| Organism |
Canis lupus familiaris |
| Characteristics |
melanoma: Oral malignant melanoma
tumor stage: IV
age: 10
weight: 40.4
treatment: 9Gy RT + Intratumoral IL-2 and IL-12
dose level: 5x dose level (87 ug/kg IL-2; 10.4 ug/kg IL-12)
survival: 31
|
| Treatment protocol |
Dogs with malignant melanoma were enrolled into four treatment cohorts to examine the safety and efficacy of different doses of intratumoral collagen-binding cytokines IL-2 and IL-12 after a single 9Gy dose of radiation therapy. Tissue from primary and metastatic tumors was collected from patients upon progression and euthanasia to examine modes of resistance to this combination therapy.
|
| Growth protocol |
n/a - client-owned dogs with malignant melanoma
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from FFPE tissue scrolls (10um) using Qiagen FFPE RNEasy kit following manufacturer's protocol. Samples were QC'd for concentration and fragment analysis on Bioanalyzer (Agilent) prior to hybridization to the nCounter panel probe set.
|
| Label |
n/a
|
| Label protocol |
n/a
|
| |
|
| Hybridization protocol |
Hybridization of RNA to the Canine IO nCounter panel probe set (Nanostring) was performed according to manufacturer's instructions for 23 hours at 65C. Hybridized RNA was loaded into the analysis cartridge using Nanostring PrepStation.
|
| Scan protocol |
Scanning of analysis cartridge was performed on Nanostring Digital Analyzer under maximum resolution.
|
| Description |
Nanostring Canine IO nCounter panel (XT-CIO-12)
|
| Data processing |
Nanostring nSolver software was used to process count data, beginning with batch correction between cartridge scans using a panel standard control. Background thresholding was performed using the mean of 8 negative control probes. Normalization was performed in nSolver prior to analysis of differential gene expression and pathway analysis between cohorts.
|
| |
|
| Submission date |
Jan 15, 2024 |
| Last update date |
Jan 29, 2024 |
| Contact name |
K Dane Wittrup |
| E-mail(s) |
wittrup@mit.edu
|
| Phone |
6172534578
|
| Organization name |
Massachusetts Institute of Technology
|
| Department |
Koch Institute for Integrative Cancer Research
|
| Lab |
Wittrup Lab
|
| Street address |
500 Main St, 76-261
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL32796 |
| Series (1) |
| GSE253243 |
Characterization of resistance to tumor-localized interleukin-2 and interleukin-12 therapy in pet dogs with advanced malignant melanoma |
|
