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Ability to Generate Patient-Derived Breast Cancer Xenografts Is Enhanced in Chemoresistant Disease and Predicts Poor Patient Outcomes.

McAuliffe PF, Evans KW, Akcakanat A, Chen K, Zheng X, Zhao H, Eterovic AK, Sangai T, Holder AM, Sharma C, Chen H, Do KA, Tarco E, Gagea M, Naff KA, Sahin A, Multani AS, Black DM, Mittendorf EA, Bedrosian I, Mills GB, Gonzalez-Angulo AM, Meric-Bernstam F - PLoS ONE (2015)

Bottom Line: One BCX model was cultured in vitro and re-implanted, maintaining its genomic profile.BCXs can be established from clinically aggressive breast cancers, especially in TNBC patients with poor response to NeoCT.Future studies will determine the potential of in vivo models for identification of genotype-phenotype correlations and individualization of treatment.

View Article: PubMed Central - PubMed

Affiliation: Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America.

ABSTRACT

Background: Breast cancer patients who are resistant to neoadjuvant chemotherapy (NeoCT) have a poor prognosis. There is a pressing need to develop in vivo models of chemo resistant tumors to test novel therapeutics. We hypothesized that patient-derived breast cancer xenografts (BCXs) from chemo- naïve and chemotherapy-exposed tumors can provide high fidelity in vivo models for chemoresistant breast cancers.

Methods: Patient tumors and BCXs were characterized with short tandem repeat DNA fingerprinting, reverse phase protein arrays, molecular inversion probe arrays, and next generation sequencing.

Results: Forty-eight breast cancers (24 post-chemotherapy, 24 chemo-naïve) were implanted and 13 BCXs were established (27%). BCX engraftment was higher in TNBC compared to hormone-receptor positive cancer (53.8% vs. 15.6%, p = 0.02), in tumors from patients who received NeoCT (41.7% vs. 8.3%, p = 0.02), and in patients who had progressive disease on NeoCT (85.7% vs. 29.4%, p = 0.02). Twelve patients developed metastases after surgery; in five, BCXs developed before distant relapse. Patients whose tumors developed BCXs had a lower recurrence-free survival (p = 0.015) and overall survival (p<0.001). Genomic losses and gains could be detected in the BCX, and three models demonstrated a transformation to induce mouse tumors. However, overall, somatic mutation profiles including potential drivers were maintained upon implantation and serial passaging. One BCX model was cultured in vitro and re-implanted, maintaining its genomic profile.

Conclusions: BCXs can be established from clinically aggressive breast cancers, especially in TNBC patients with poor response to NeoCT. Future studies will determine the potential of in vivo models for identification of genotype-phenotype correlations and individualization of treatment.

No MeSH data available.


Related in: MedlinePlus

Analysis of mutation data.(A) Clustering of whole exome sequencing mutation data based on the mutation status of the genes in P0 and P1 samples of four models. (B) Clustering of targeted exome sequencing data based on the mutation status of 201 genes in P0 and P1 samples of six models. (C) Venn diagram of mutations in P0 and P1 samples of six models on the targeted exome sequencing platform. (D) Venn diagram of high allelic frequency mutations (10% or higher) on targeted exome sequencing in P0 and P1 samples of six models. Allele frequency cutoff was 10%. (E) Genomic stability of PIK3CA mutation in BCX-006 model. Fine needle aspiration biopsy samples of before and after 12 weeks of neoadjuvant chemotherapy (including a rapalog) were sequenced by ion torrent. Patient’s P0 tumor and BCX-006 P1 tumor and subsequent passages were analyzed by targeted exome sequencing. PIK3CA H1047R allele frequencies are presented. (F) Conditionally reprogrammed cells (CRC) derived from BCX-010 were passaged four times in vitro and then injected into mice flanks. The cultured cells and CRC-derived xenografts maintained a mutation profile similar to the originating PDX.
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pone.0136851.g004: Analysis of mutation data.(A) Clustering of whole exome sequencing mutation data based on the mutation status of the genes in P0 and P1 samples of four models. (B) Clustering of targeted exome sequencing data based on the mutation status of 201 genes in P0 and P1 samples of six models. (C) Venn diagram of mutations in P0 and P1 samples of six models on the targeted exome sequencing platform. (D) Venn diagram of high allelic frequency mutations (10% or higher) on targeted exome sequencing in P0 and P1 samples of six models. Allele frequency cutoff was 10%. (E) Genomic stability of PIK3CA mutation in BCX-006 model. Fine needle aspiration biopsy samples of before and after 12 weeks of neoadjuvant chemotherapy (including a rapalog) were sequenced by ion torrent. Patient’s P0 tumor and BCX-006 P1 tumor and subsequent passages were analyzed by targeted exome sequencing. PIK3CA H1047R allele frequencies are presented. (F) Conditionally reprogrammed cells (CRC) derived from BCX-010 were passaged four times in vitro and then injected into mice flanks. The cultured cells and CRC-derived xenografts maintained a mutation profile similar to the originating PDX.

Mentions: Whole exome sequencing was performed in the mouse host DNA as well as the matched P0-P1—normal host DNA in 4 models: BCX-010, -017, -022, and -024 (S4 and S5 Tables). Unsupervised clustering clustered each BCX P1 with the P0 parental tumor (Fig 4A).


Ability to Generate Patient-Derived Breast Cancer Xenografts Is Enhanced in Chemoresistant Disease and Predicts Poor Patient Outcomes.

McAuliffe PF, Evans KW, Akcakanat A, Chen K, Zheng X, Zhao H, Eterovic AK, Sangai T, Holder AM, Sharma C, Chen H, Do KA, Tarco E, Gagea M, Naff KA, Sahin A, Multani AS, Black DM, Mittendorf EA, Bedrosian I, Mills GB, Gonzalez-Angulo AM, Meric-Bernstam F - PLoS ONE (2015)

Analysis of mutation data.(A) Clustering of whole exome sequencing mutation data based on the mutation status of the genes in P0 and P1 samples of four models. (B) Clustering of targeted exome sequencing data based on the mutation status of 201 genes in P0 and P1 samples of six models. (C) Venn diagram of mutations in P0 and P1 samples of six models on the targeted exome sequencing platform. (D) Venn diagram of high allelic frequency mutations (10% or higher) on targeted exome sequencing in P0 and P1 samples of six models. Allele frequency cutoff was 10%. (E) Genomic stability of PIK3CA mutation in BCX-006 model. Fine needle aspiration biopsy samples of before and after 12 weeks of neoadjuvant chemotherapy (including a rapalog) were sequenced by ion torrent. Patient’s P0 tumor and BCX-006 P1 tumor and subsequent passages were analyzed by targeted exome sequencing. PIK3CA H1047R allele frequencies are presented. (F) Conditionally reprogrammed cells (CRC) derived from BCX-010 were passaged four times in vitro and then injected into mice flanks. The cultured cells and CRC-derived xenografts maintained a mutation profile similar to the originating PDX.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4556673&req=5

pone.0136851.g004: Analysis of mutation data.(A) Clustering of whole exome sequencing mutation data based on the mutation status of the genes in P0 and P1 samples of four models. (B) Clustering of targeted exome sequencing data based on the mutation status of 201 genes in P0 and P1 samples of six models. (C) Venn diagram of mutations in P0 and P1 samples of six models on the targeted exome sequencing platform. (D) Venn diagram of high allelic frequency mutations (10% or higher) on targeted exome sequencing in P0 and P1 samples of six models. Allele frequency cutoff was 10%. (E) Genomic stability of PIK3CA mutation in BCX-006 model. Fine needle aspiration biopsy samples of before and after 12 weeks of neoadjuvant chemotherapy (including a rapalog) were sequenced by ion torrent. Patient’s P0 tumor and BCX-006 P1 tumor and subsequent passages were analyzed by targeted exome sequencing. PIK3CA H1047R allele frequencies are presented. (F) Conditionally reprogrammed cells (CRC) derived from BCX-010 were passaged four times in vitro and then injected into mice flanks. The cultured cells and CRC-derived xenografts maintained a mutation profile similar to the originating PDX.
Mentions: Whole exome sequencing was performed in the mouse host DNA as well as the matched P0-P1—normal host DNA in 4 models: BCX-010, -017, -022, and -024 (S4 and S5 Tables). Unsupervised clustering clustered each BCX P1 with the P0 parental tumor (Fig 4A).

Bottom Line: One BCX model was cultured in vitro and re-implanted, maintaining its genomic profile.BCXs can be established from clinically aggressive breast cancers, especially in TNBC patients with poor response to NeoCT.Future studies will determine the potential of in vivo models for identification of genotype-phenotype correlations and individualization of treatment.

View Article: PubMed Central - PubMed

Affiliation: Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America.

ABSTRACT

Background: Breast cancer patients who are resistant to neoadjuvant chemotherapy (NeoCT) have a poor prognosis. There is a pressing need to develop in vivo models of chemo resistant tumors to test novel therapeutics. We hypothesized that patient-derived breast cancer xenografts (BCXs) from chemo- naïve and chemotherapy-exposed tumors can provide high fidelity in vivo models for chemoresistant breast cancers.

Methods: Patient tumors and BCXs were characterized with short tandem repeat DNA fingerprinting, reverse phase protein arrays, molecular inversion probe arrays, and next generation sequencing.

Results: Forty-eight breast cancers (24 post-chemotherapy, 24 chemo-naïve) were implanted and 13 BCXs were established (27%). BCX engraftment was higher in TNBC compared to hormone-receptor positive cancer (53.8% vs. 15.6%, p = 0.02), in tumors from patients who received NeoCT (41.7% vs. 8.3%, p = 0.02), and in patients who had progressive disease on NeoCT (85.7% vs. 29.4%, p = 0.02). Twelve patients developed metastases after surgery; in five, BCXs developed before distant relapse. Patients whose tumors developed BCXs had a lower recurrence-free survival (p = 0.015) and overall survival (p<0.001). Genomic losses and gains could be detected in the BCX, and three models demonstrated a transformation to induce mouse tumors. However, overall, somatic mutation profiles including potential drivers were maintained upon implantation and serial passaging. One BCX model was cultured in vitro and re-implanted, maintaining its genomic profile.

Conclusions: BCXs can be established from clinically aggressive breast cancers, especially in TNBC patients with poor response to NeoCT. Future studies will determine the potential of in vivo models for identification of genotype-phenotype correlations and individualization of treatment.

No MeSH data available.


Related in: MedlinePlus