RNA-Seq of Circulating Tumor Cells in Stage II-III Breast Cancer.
- Lang JE Section of Surgical Oncology, Department of Surgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA, USA. julie.lang@med.usc.edu.
- Ring A Department of Oncology, University Hospital Zurich, Zurich, Switzerland.
- Porras T Section of Surgical Oncology, Department of Surgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA, USA.
- Kaur P Section of Surgical Oncology, Department of Surgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA, USA.
- Forte VA Division of Medical Oncology, Department of Medicine, Maimonides Medical Center, New York, NY, USA.
- Mineyev N Section of Surgical Oncology, Department of Surgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA, USA.
- Tripathy D Department of Breast Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA.
- Press MF Department of Pathology and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA, USA.
- Campo D Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
- 2018-06-06
Published in:
- Annals of surgical oncology. - 2018
Biomarkers, Tumor
Breast Neoplasms
Feasibility Studies
Female
Follow-Up Studies
High-Throughput Nucleotide Sequencing
Humans
Immunomagnetic Separation
Neoplasm Staging
Neoplastic Cells, Circulating
Pilot Projects
Prognosis
Prospective Studies
RNA, Neoplasm
Survival Rate
English
BACKGROUND
We characterized the whole transcriptome of circulating tumor cells (CTCs) in stage II-III breast cancer to evaluate correlations with primary tumor biology.
METHODS
CTCs were isolated from peripheral blood (PB) via immunomagnetic enrichment followed by fluorescence-activated cell sorting (IE/FACS). CTCs, PB, and fresh tumors were profiled using RNA-seq. Formalin-fixed, paraffin-embedded (FFPE) tumors were subjected to RNA-seq and NanoString PAM50 assays with risk of recurrence (ROR) scores.
RESULTS
CTCs were detected in 29/33 (88%) patients. We selected 21 cases to attempt RNA-seq (median number of CTCs = 9). Sixteen CTC samples yielded results that passed quality-control metrics, and these samples had a median of 4,311,255 uniquely mapped reads (less than PB or tumors). Intrinsic subtype predicted by comparing estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) versus PAM50 for FFPE tumors was 85% concordant. However, CTC RNA-seq subtype assessed by the PAM50 classification genes was highly discordant, both with the subtype predicted by ER/PR/HER2 and by PAM50 tumors. Two patients died of metastatic disease, both of whom had high ROR scores and high CTC counts. We identified significant genes, canonical pathways, upstream regulators, and molecular interaction networks comparing CTCs by various clinical factors. We also identified a 75-gene signature with highest expression in CTCs and tumors taken together that was prognostic in The Cancer Genome Atlas and Molecular Taxonomy of Breast Cancer International Consortium datasets.
CONCLUSION
It is feasible to use RNA-seq of CTCs in non-metastatic patients to discover novel tumor biology characteristics.
We characterized the whole transcriptome of circulating tumor cells (CTCs) in stage II-III breast cancer to evaluate correlations with primary tumor biology.
METHODS
CTCs were isolated from peripheral blood (PB) via immunomagnetic enrichment followed by fluorescence-activated cell sorting (IE/FACS). CTCs, PB, and fresh tumors were profiled using RNA-seq. Formalin-fixed, paraffin-embedded (FFPE) tumors were subjected to RNA-seq and NanoString PAM50 assays with risk of recurrence (ROR) scores.
RESULTS
CTCs were detected in 29/33 (88%) patients. We selected 21 cases to attempt RNA-seq (median number of CTCs = 9). Sixteen CTC samples yielded results that passed quality-control metrics, and these samples had a median of 4,311,255 uniquely mapped reads (less than PB or tumors). Intrinsic subtype predicted by comparing estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) versus PAM50 for FFPE tumors was 85% concordant. However, CTC RNA-seq subtype assessed by the PAM50 classification genes was highly discordant, both with the subtype predicted by ER/PR/HER2 and by PAM50 tumors. Two patients died of metastatic disease, both of whom had high ROR scores and high CTC counts. We identified significant genes, canonical pathways, upstream regulators, and molecular interaction networks comparing CTCs by various clinical factors. We also identified a 75-gene signature with highest expression in CTCs and tumors taken together that was prognostic in The Cancer Genome Atlas and Molecular Taxonomy of Breast Cancer International Consortium datasets.
CONCLUSION
It is feasible to use RNA-seq of CTCs in non-metastatic patients to discover novel tumor biology characteristics.
- Language
-
- English
- Open access status
- green
- Identifiers
-
- DOI 10.1245/s10434-018-6540-4
- PMID 29868978
- Persistent URL
- https://folia.unifr.ch/global/documents/258734
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