PDX Breast Cancer Model WHIM3

Technical Information
Published in Cell Reports, WHIM3 is a highly characterized, triple negative (HER2-, ER-, PR-) PDX model of breast cancer, derived from the primary tumor.

Technical Data

Whole Genome Sequenced
No
RNA Sequence
No

Tumor Information

Availability
Available
Tumor Site
Primary: Breast
Patient Number
3

Patient Demographics

Age at Diagnosis
62
Patient Race
Caucasian
Family History
None

PAM50 Subtype

PAM50 Originating Tumor
N/A
PAM50 Early Passage
HER2-E
PAM50 Late Passage
HER2-E

Genotype/Mutations

ER Status
Negative
PR Status
Negative
HER2 Status
Negative
p53 Genotype
WT
PIK3CA Genotype
WT
ESR1 Genotype
WT
Phosphoprotein Highest Rank
Src_pY527

Pathology

Specimen Type
Ultrasound guided needle biopsy. Primary
Clinical Stage, Diagnosis
4
Pathological Stage
4
Sample Stage
4
Pathology
Ductal
Tumor Grade
2
Metastatic Site List
Bone; Nodes; Lung; Adrenal glands
Systemic Treatments
Grafted sample for WHIM3; Gemcitabine x1
Overall Survival (months)
3

PAM50 Subtype Expression

PAM50 Microarray Validation
PDX Breast Cancer Model WHIM3 - PAM50 Microarray Validation
Validation of PAM50 microarray. Coclustering of 250 human breast samples representing all the PAM50 intrinsic subtypes and 22 HIM models using the 50 PAM50 genes. Gene expression data of all samples has been obtained using 244K Agilent microarrays.
Claudin Low Signature
PDX Breast Cancer Model WHIM3 - Claudin Low Signature
Microarray of 807 genes that make up the Claudin-low signature. On the right, the expression of each gene (up- or downregulated) of the Claudin-low signature is shown. The two Claudin-low samples (WHIM12 and WHIM17) are identified below the array tree.

Circos Plots & Phosphoprotein Expression

Phosphoprotein Expression
PDX Breast Cancer Model WHIM3 - Phosphoprotein Expression
Phosphoprotein expression by RPPA. The RPPA data for WHIM samples and 386 TCGA samples were combined after standardizing the data for each marker (i.e., subtracting the mean and then divided by the standard deviation) in the separate data sets. The combined samples were hierarchically clustered using a Pearson correlation based distance matrix ((1-rho)/2, where rho is the Pearson correlation matrix) and the “ward” linkage based on Ward’s minimum variance. In every case the samples from each WHIM line clustered adjacently, including the two double PDX model isolations (WHIM2 and WHIM5, WHIM20 and WHIM23). This demonstrates that intra-PDX heterogeneity was considerably less than the inter-tumoral heterogeneity in a large RPPA data set and was relatively stable over time and passage.
Protocols & Documents
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