PDX Breast Cancer Model WHIM16

Technical Information
Published in Cell Reports, WHIM16 is a highly characterized, HER2-, ER+, PR+ PDX model of breast cancer. Derived from a skin metastasis, this line possesses an amplification in ESR1, an R248W mutation in p53, and a H1047R mutation in PIK3CA. This line is responsive to estradiol. Whole genome sequencing data is available for this line.

Technical Data

Estradiol Response
Whole Genome Sequenced
RNA Sequence

Tumor Information

Tumor Site
Metastasis: Skin
Patient Number

Patient Demographics

Age at Diagnosis
Patient Race
Family History
Mother, maternal aunt x2

PAM50 Subtype

PAM50 Originating Tumor
Luminal B
PAM50 Early Passage
Luminal A
PAM50 Late Passage
Luminal B


ER Status
PR Status
HER2 Status
p53 Genotype
PIK3CA Genotype
ESR1 Genotype
Phosphoprotein Highest Rank


Specimen Type
Punch -- skin recurrence
Clinical Stage, Diagnosis
Pathological Stage
Sample Stage
Tumor Grade
Metastatic Site List
Bone; Nodes; Liver; Skin
Systemic Treatments
8 cycles of adjuvant DD doxorubicin, cylcophosphomide followed by gemcitabine, completed; radiation to right breast, axilla, completed; exemestane; recurrence to bone; fulvestrant; palliative radiation to thoracic spine; capecitabine; estradiol; Grafted sample for WHIM16; paclitaxel, bevacizumab
Overall Survival (months)

PAM50 Subtype Expression

PAM50 Subtype Microarray
PDX Breast Cancer Model WHIM16 - PAM50 Subtype Microarray
Microarray showing PAM50 subtype. Unsupervised hierarchical clustering of samples using all genes of the microarrays except the stromal-related genes. The colors of the array tree and the squares below the tree denote the subtype call of each sample. Red, basal-like; pink, HER2-enriched; dark blue, lumenal A; light blue, lumenal B; yellow, Claudin-low. Below the array tree and the subtype identification row, the heatmap of the 50 PAM50 genes as well as selected tight-junction-related genes (E-cadherin [CDH1], claudin 3 [CLDN3], CLDN4, and CLDN7) are shown. The stromal-related genes were identified after a two-class paired SAM was performed with an FDR of 0% between 18 paired progenitor human tumors and xenografts.
PAM50 Microarray Validation
PDX Breast Cancer Model WHIM16 - 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 WHIM16 - 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.

ER, HER2 and PR Expression

ER and HER2 Western Blots
PDX Breast Cancer Model WHIM16 - ER and HER2 Western Blots
ER and HER2 protein expression. Tumor lysates from ER-positive (A) and ER-negative (B) WHIM lines were analyzed by western blot to confirm ER and HER2 status. Lysates from ER-negative WHIM lines were also probed with antibodies against the cytokeratin 5/6 (CK 5/6) and CD44 markers. The MCF7 (ER-positive), SKBR3 (ER-negative, HER2-positive) and MDA-MB-231 (ER-negative, CD44-positive) breast cancer cell lines were included as blotting controls.
PR Western Blot
PDX Breast Cancer Model WHIM16 - PR Western Blot
PR protein expression. Six ER+ WHIM tumors were analyzed for PR and TFF1 expression levels by western blot. Three breast cancer cell lines were probed in parallel as positive (MCF7 and MCF7-LTED) and negative (MDA-MB-231) controls. Actin was used as the loading control.

Circos Plots & Phosphoprotein Expression

Circos Plots
PDX Breast Cancer Model WHIM16 - Circos Plots
Circos Plots and Variant Allele Frequency Plots. Overall the Circos plots show closely matched SV and CNV in the tumor of origin and the paired WHIM line. To compare differences in mutant allele frequency between the originating tumor and the PDX counterpart, the read counts for each mutant and wild-type allele were expressed as a percentage of all reads at that position and analyzed by scatter plot and simple correlation coefficient. These show considerably more variation in the human to PDX comparisons but variant allele frequencies are, nonetheless, often preserved.
Phosphoprotein Expression
PDX Breast Cancer Model WHIM16 - 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.

Estradiol Response & ESR1 Expression

Estradiol Response
PDX Breast Cancer Model WHIM16 - Estradiol Response
Estradiol Dependency and Tumor Doubling Times. Figure 1: Tumor cells were subcutaneously injected into ovariectomized NOD/SCID mice and then immediately treated with 17ß-estradiol pellets or observed.

Figure 2: WHIM16 cells were allowed to establish tumor nodules in ovariectomized nonobese diabetic (NOD)/severe combined immunodeficiency (SCID) mice and then treated with or without 17ß-estradiol pellets.
ESR1 Western Blot
PDX Breast Cancer Model WHIM16 - ESR1 Western Blot
Western blot for the expression of endogenous and exogenous ESR1. Western blot for the expression of endogenous and exogenous ESR1 using an N-terminal antibody and two direct ESR1 downstream targets (progesterone receptor [PR-A and PR-B] and TFF1) with an actin loading control. Due to the substantially lower basal TFF1 expression in T47D cells compared with MCF7 cells, the T47D TFF1 blot was intentionally exposed for a longer time for visualization.
Protocols & Documents

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