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Profiling the transcriptional heterogeneity of diverse pediatric solid tumors – Other solid tumors

11 Downloadable Samples

Nucleus

10Xv3.1

Abstract

Pediatric solid tumors are rare compared to common adult malignancies and they are also remarkably diverse. For example, rhabdomyosarcomas have features of skeletal muscle, osteosarcomas have features of bone and neuroblastomas have features of cells in the sympathoadrenal lineage. The diversity and rarity of pediatric solid tumors makes it difficult to accelerate biomedical research that can improve patient outcomes. For example, even with the large number of patients treated at St. Jude, it can be difficult to obtain fresh pediatric solid tumor tissue that is suitable for single cell sequencing. To overcome this barrier in the field, we have developed carefully validated methods to process fresh and frozen tissue for single-cell or single-nucleus RNA-sequencing. Our data show that we can capture the transcriptional heterogeneity of the tumors and the complexity of the tumor microenvironment using single-nuclei RNA-sequencing of patient tumors from the St. Jude biorepository. In addition, over the past 9 years, we have generated 166 orthotopic patient derived xenografts (O-PDXs) representing 21 different pediatric solid tumor types. The O-PDXs and corresponding patient tumors have undergone some of the most comprehensive characterization of any pediatric cancer model including detailed analysis of the clonal heterogeneity (Stewart et al. Nature, 2018). We performed single-cell or single-nuclei RNA-sequencing of 3 tissue samples from adrenocortical carcinoma patient tumors and 2 matched O-PDX, 1 tissue sample from a germ cell patient tumor, 1 tissue sample from a hepatoblastoma patient tumor, and 3 tissue samples from melanoma patient tumors and 2 matched O-PDX as part of a larger effort to perform single-cell/single-nuclei RNA-sequencing on a large cohort of patient tumors and O-PDXs. This research proposal will fill a fundamental gap in our knowledge of the transcriptome heterogeneity across pediatric solid tumor clones and of the normal cells found in the tumor microenvironment.

We would greatly appreciate if you cite the listed publications when using this data.

Publications
Not Specified
Also deposited under
Not Specified
DOI
Not Specified
Disease Timing

Initial diagnosis, Recurrence, NA

Sample Count

11

Primary Investigator

Dyer/Chen

Contact Information
Additional Restrictions

Research or academic purposes only

Sample Summary
Diagnosis
Sequencing Unit
Technology
Library Count
Adrenocortical carcinoma
nucleus
10Xv3.1
5
Germ cell tumor
nucleus
10Xv3.1
1
Hepatoblastoma
nucleus
10Xv3.1
1
Melanoma
nucleus
10Xv3.1
4
Alex’s Lemonade Stand Foundation for Childhood Cancer333 E. Lancaster Ave, #414, Wynnewood, PA 19096 USAPhone: 866.333.1213 • Fax: 610.649.3038Email: scpca@ccdatalab.org