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Available Resources

The Childhood Solid Tumor Network (CSTN) at St. Jude offers a comprehensive collection of scientific resources for academic researchers studying pediatric solid tumors and related biology. An overview of available samples and data is provided below; visit our request form for more detailed information. To receive updates on new resources emerging from the CSTN, subscribe to our e-newsletter.

Available resources include:


Preclinical models of childhood solid tumors (GEMMs)

GEMM-derived tissue samples developed at St. Jude are available for a variety of pediatric solid tumors, including neuroblastoma, retinoblastoma and osteosarcoma. Available strains are detailed on the request form.

Protocols (ChIPSeq)

Protocols with various antibodies, targets and tissue types have been developed and validated at St. Jude. Access resources

Orthotopic patient-derived xenografts

Orthotopic patient-derived xenografts (O-PDXs) have been created from a wide variety of pediatric solid tumors collected under the Molecular Analysis of Solid Tumors (MAST) protocol at St. Jude Children’s Research Hospital (ClinicalTrials.gov: NCT01050296). Most O-PDX models are available with a luciferase reporter gene integrated into the genome to enable monitoring of tumor engraftment and growth in vivo. Cryopreserved cells, fresh frozen tissue/cells, and formalin-fixed paraffin-embedded tissue blocks are available.

Access CSTN Data Portal for the full list of tumor types and samples. Extensive molecular and drug sensitivity data are available for the O-PDX models. For each of the O-PDX models, a characterization sheet will be provided when the samples are shipped (see example for SJNBL046_X or visual descriptions of the clonal evolution groups.) Characterization sheets can also be downloaded for each sample in the CSTN Data Portal  to help investigators select the appropriate O-PDX models for their studies. For the samples that have been added most recently, characterization is pending and the completed characterization sheets will be sent to requestors as soon as they are available.

The list of available tumors is updated every year after the new samples have engrafted and sufficient vials have been cryopreserved for distribution.

Bar graph showing list of available tumors

Patient-derived iPSCs

Induced pluripotent stem cells (iPSCs) have been created from 15 patients with retinoblastoma that have germline RB1 mutations collected under the RETCELL (A Study of Children with Heritable Retinoblastoma) protocol at St Jude Children’s Research Hospital (ClinicalTrials.gov NCT02193724). The clinical spectrum of disease varies from early diagnosis (Group A and/or B) to advanced bilateral disease (Group D and/or E). In addition, some participants were found to be unaffected or spontaneously regressed carriers of the heritable mutation or chromosomal abnormality. The RB1 mutations have been validated in each line and they have undergone complete characterization including trilineage differentiation, whole genome sequencing, karyotyping and 3D retinal organoid differentiation. Vials of cryopreserved cells are available upon request. Additional iPSC lines are being developed for other pediatric solid tumor types and the list of available lines will be updated every six months after they have been validated and characterized.

iPSC number laterality (1) sample gene mutation;
protein mutation
SJRB-iPSC-1 OU fibroblasts nonsense
SJRB-iPSC-2 OU, asynchronous fibroblasts frameshift
SJRB-iPSC-3 OU fibroblasts nonsense
SJRB-iPSC-4 OU blood frameshift
SJRB-iPSC-5 OS blood deletion
SJRB-iPSC-6 OU blood frameshift
SJRB-iPSC-7 OU blood frameshift
SJRB-iPSC-8 trilateral blood nonsense
SJRB-iPSC-9 OU blood nonsense
SJRB-iPSC-10 N/A blood nonsense
SJRB-iPSC-11 OU blood splice
SJRB-iPSC-12 OD blood splice
SJRB-iPSC-13 OU blood large deletion
SJRB-iPSC-14 OU blood nonsense
SJRB-iPSC-15 OU blood nonsense

1: OU, oculus uterque (both eyes); OS, oculus sinister (left eye); OD, oculus destrus (right eye), trilateral, OU disease with tumor in the pineal gland at diagnosis 
2: Reese-Ellsworth staging (1-5) and International Classification of Intraocular Retinoblastoma (A-E)

Genomic, drug sensitivity and pharmacokinetic data

We offer molecular and drug sensitivity data of diverse pediatric solid tumors, patient-derived orthotopic xenografts and solid tumor cell lines. (Some cell lines are available. See the request form for details.) High-throughput drug screening (HTS) data are available for many pediatric solid tumor cell lines and orthotopic xenografts, including Ewing sarcoma, neuroblastoma, osteosarcoma, retinoblastoma and rhabdomyosarcoma.

While comprehensive raw datasets are not made available prior to publication, we are happy to accommodate many types of data requests to answer specific research questions.

Raw datasets are available through St. Jude Cloud, following an application and approval process for access. 

Genomic sequencing and integrated epigenetic profiling have been performed on pediatric solid tumors and orthotopic patient-derived xenografts as part of the St. Jude-Washington University Pediatric Cancer Genome Project and is actively ongoing in St. Jude investigator-led labs. Available data may include:

  • Whole-genome sequencing (WGS)
  • Whole-exome sequencing (WES)
  • RNA-seq
  • Whole-genome bisulfite sequencing (WGBS)
  • ChIP-seq

High-throughput drug screening (HTS) data are available for many pediatric solid tumor cell lines and orthotopic xenografts, including Ewing sarcoma, neuroblastoma, osteosarcoma, retinoblastoma and rhabdomyosarcoma. In addition, we offer preclinical pharmacokinetic data for a number of high-priority drugs that are being explored for activity against pediatric solid tumors. Standard of Care regimens used in current preclinical trials are available in the appendix. Data from completed preclinical Phase I (tolerability), Phase II (small pilot efficacy study) and Phase III (randomized, placebo-controlled) trials are available by request. For more details and descriptions of Phase I, II and III, please see Stewart et al, 2014 Cell Reports.

  1. 5-Fluorodeoxycytidine
    5-Fluorouracil (5-FU)
    6-Mercaptopurine
    6-Thioguanine
    7-Hydroxystaurosporine
    Abiraterone Acetate
    Actinomycin D
    Afatinib
    Alisertib
    Arimidex
    Arry-520
    Artesunate
    Aurorafin
    Axinitib
    Azacitidine
    AZD-1775
    AZD-4547
    AZD-5363
    AZD-7762
    Binimetinib
    Blenoxane
    Bmn673 (Talazoparib)
    Bms-777607
    Bordoxolone
    Bortezomib
    Bosisunib
    Brivudine
    Buparlisib
    Cabazitaxel
    Cabozantinib
    Carfilzomib
    Ceritinib
    Chlorambucil
    Ciclopirox
    Cladribine
    Clofarabine
    Cobimetinib
    Crenolanib
    Crizotinib
    Cyclophosphamide
    Cyt11387
    Cytadren
    Cytidine
    Dabrafenib
    Daclctisib
    Dacogen
    Daraprim
    Dasatinib
    Dexamthasone
    Dfmo
    Dihydroartemisinin (DHA)
    Docetaxol
    Doxorubicin

    ENMD-981693
    Enzalutamide
    Erlotinib
    Etoposide
    Everolimus
    Fedratinib
    Floxuridine
    Fludara
    Fluphenazine HCL
    Fluvastatin
    Foretinib
    Ganetespib
    GDC-0068
    GDC-0199
    GDC-0994
    Gedatolisib
    Gefifinib
    Gemcitabine
    GMX-1778
    Golotimod
    Hydroxychloroquine
    Idronoxil
    Ifosfamide
    Itraconazole
    Ixabepilone
    JQ1
    Lapatinib
    LEE011
    Leflunomide
    LGX-818
    LY2157299
    Masitinib
    Mepacrine
    Methotrexate
    Midostaurin
    Mithramycin
    Mitomycin
    Mitotane
    Mitoxantrone
    MK-2206
    MK-8776
    Motatenib Diphosphate
    Mycophenolate Mofetil Hydrochloride
    Namenda
    Navitoclax
    Neratinib
    Niftfuimox
    Nililonib
    Nimtmuine
    Noscapine
    NSC-617593
    NSC-714598 | NSC-286644

    Obatoclax
    Olaparib
    Omipalisib
    Ouabain
    Pacritnib
    Palbociclib
    Panobinostat
    Pazopanib
    PD 325901
    Pemetrexed Disodium
    Pentostatin
    Pimasertib
    Pioglitazone
    Ponatinib
    Rabusertib
    Raltitrexed
    Regorafenib
    Retinoic Acid
    RG7112
    Romidepsin
    Ruxolitinib
    Selinexor
    Selumetinib
    Sirolimus
    SN-38
    Sorafenib
    Streptozotocin
    Sulindac
    Sunitinib
    Tamibarotene
    Tamoxifen
    Targretin Bexarotene
    Taselisib
    Tazarotene
    Temozolomide
    Temsirolimus
    Tivantinib
    Tivozanib
    Topotecan
    Trametinib
    Trimetrexate
    Trisenox
    Vantndanib
    VE821
    Vemurafenib
    Vinblastine
    Vincristine
    Vinorelbine
    Vismodegib
    Volelartib
    Vorinostat
    Vosaroxin

  2. Vincristine + Irinotecan (Low-dose protracted)
    Vincristine + Irinotecan (High-dose 5 day dosing)
    Vincristine + Irinotecan + Panobinostat
    Vinorelbine + Cyclophosphamide
    Panobinostat + Bortezomib
    Vincristine + Dactinomycin + Cyclophosphamide
    Cisplatin + Doxorubicin + Methotrexate + Ifosfamide + Etoposide (MAP/IE)
    Gemcitabine + Docetaxel
    Cyclophosphamide + Doxorubicin + Etoposide
    Cisplatin + Etoposide
    Irinotecan + Temozolomide
    BMN-673 + Irinotecan + Temozolomide
    Olaparib + Irinotecan + Temozolomide
    Veliparib + Irinotecan + Temozolomide

  3. Rhabdomyosarcoma

    SHRHB026_X1:  Vincristine + Irinotecan
    SHRHB026_X1:  Panobinostat
    SHRHB026_X1:  Panobinostat + Bortezomib
    SHRHB026_X1:  Vincristine + Dactinomycin + Cyclophosphamide

    SHRHB026_X2:  Vincristine + Dactinomycin + Cyclophosphamide
    SHRHB026_X2:  Vinorelbine + Cyclophosphamide

    SJRHB010927_X1:  Vincristine + Dactinomycin + Cyclophosphamide

    SJRHB012_Y:  Vincristine + Irinotecan
    SJRHB012_Y:  Panobinostat + Bortezomib

    SJRHB013759_X1:  Vincristine + Irinotecan
    SJRHB013759_X1:  Panobinostat + Bortezomib

    Neuroblastoma

    SJNBL046_X:  Cyclophosphamide + Doxorubicin + Etoposide / Cisplatin + Etoposide
    SJNBL046_X:  OSI-906 + BEZ-235
    SJNBL046_X:  OSI-906 + BKM-120

    NB5:  Cyclophosphamide + Doxorubicin + Etoposide / Cisplatin + Etoposide
    NB5:  OSI-906 + BEZ-235
    NB5:  OSI-906 + BKM-120

    Ewing sarcoma

    ES-8: Irinotecan + Temozolomide
    ES-8: BMN-673 + Irinotecan + Temozolomide
    ES-8: Olaparib + Irinotecan + Temozolomide
    ES-8: Veliparib + Irinotecan + Temozolomide
    EW-8: Irinotecan + Temozolomide
    EW-8: BMN-673 + Irinotecan + Temozolomide
    EW-8: Olaparib + Irinotecan + Temozolomide
    EW-8: Veliparib + Irinotecan + Temozolomide
    ES-6: Irinotecan + Temozolomide
    ES-6: BMN-673 + Irinotecan + Temozolomide
    ES-6: Olaparib + Irinotecan + Temozolomide
    ES-2: Irinotecan + Temozolomide
    ES-2: BMN-673 + Irinotecan + Temozolomide
    ES-3: Irinotecan + Temozolomide
    ES-3: BMN-673 + Irinotecan + Temozolomide

  4. Ewing sarcoma

    ES-8:  PARP inhibitor trial (BMN-673, Olaparib, Veliparib, Irinotecan, Temozolamide)

Integrated Rhabdomyosarcoma Database (iRDb) 

Integrated rhabdomyosarcoma database (iRDb)

We have collected and integrated genomic, epigenetic, proteomic and drug-sensitivity data into a central database. The genomic data includes whole genome, exome and RNA-sequence, as well as clonal analysis that allows us to reconstruct the clonal heterogeneity of the tumor and corresponding O-PDX. The epigenetic data includes whole genome bisulfite (WGBS) and ChIP-seq data for eight histone marks and CTCF, Brd4 and RNA PolII for a total of over 750 ChIP-seq libraries. The data have been integrated to define chromatin states using chromatin Hidden Markov Modeling. Quantitative proteomic and phosphoproteomic data were obtained for RMS tumors using mass coded peptides derived from batches of 10 samples. Drug-sensitivity data includes primary cultures of O-PDX tumors in high throughput drug screening of 168 oncology drugs in 10-point dose response in triplicate with biological replicates.

Integrated Rhabdomyosarcoma Database

 
 
 

Integrated Neuroblastoma Database (iNBDb)

.
 

We have collected and integrated genomic, epigenetic, proteomic and drug-sensitivity data into a central database for neuroblastoma. We have focused on age at diagnosis because there is an inverse relationship between age at diagnosis and outcome. Moreover, ATRX mutations are significantly associated with older age at diagnosis so we have included several ATRX mutant NBs. The genomic data includes whole genome, exome and RNA-sequence (transcriptome) as well as clonal analysis that allows us to reconstruct the clonal heterogeneity of the tumor and corresponding O-PDX. The epigenetic data includes whole genome bisulfite (WGBS) and ChIP-seq data for eight histone marks and CTCF, Brd4 and RNA PolII for a total of over 350 ChIP-seq libraries. The data have been integrated to define chromatin states using chromatin Hidden Markov Modeling. Drug-sensitivity data includes primary cultures of O-PDX tumors in high throughput drug screening of 168 oncology drugs in 10-point dose response in triplicate with biological replicates.

Integrated Neuroblastoma Database

 
 

About the Childhood Solid Tumor Network

Childhood solid tumors are often difficult to study and treat because they are rare and originate in the complex biological context of developing organs. CSTN was established to disseminate resources and data that have been developed at St. Jude Children’s Research Hospital, with the aim of stimulating basic research and speeding translation to the clinic.

The effort was launched in 2013 by Howard Hughes Medical Institute investigator Michael Dyer, PhD, of St. Jude Developmental Neurobiology, and Alberto Pappo, MD, of St. Jude Oncology.

For more information, contact us: CSTN@stjude.org