title: An improved CTC isolation scheme for pairing with downstream genomics: Demonstrating clinical utility in metastatic prostate, lung and pancreatic cancer.
abstract: Improvements in technologies to yield purer circulating tumor cells (CTCs) will enable a broader range of clinical applications. We have previously demonstrated the use of a commercially available cell-adhesion matrix (CAM) assay to capture invasive CTCs (iCTCs). To improve the purity of the isolated iCTCs, here we used fluorescence-activated cell sorting (FACS) in combination with the CAM assay (CAM + FACS). Our results showed an increase of median purity from the CAM assay to CAM + FACS for the spiked-in cell lines and patient samples analyzed from three different metastatic cancer types: castration resistant prostate cancer (mCRPC), non-small cell lung cancer (mNSCLC) and pancreatic ductal adenocarcinoma cancer (mPDAC). Copy number profiles for spiked-in mCRPC cell line and mCRPC patient iCTCs were similar to expected mCRPC profiles and a matched biopsy. A somatic epidermal growth factor receptor (EGFR) mutation specific to mNSCLC was observed in the iCTCs recovered from EGFR(+) mNSCLC cell lines and patient samples. Next-generation sequencing (NGS) of spiked-in pancreatic cancer cell line and mPDAC patient iCTCs showed mPDAC common mutations. CAM + FACS iCTC enrichment enables multiple downstream genomic characterizations across different tumor types.
authors.affiliation: Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Gayatri
authors.initials: G
authors.lastname: Premasekharan
authors.affiliation: Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Gilbert
authors.affiliation: Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Ross A
authors.initials: RA
authors.lastname: Okimoto
authors.affiliation: Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Ashiya
authors.initials: A
authors.lastname: Hamirani
authors.affiliation: Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Karla J
authors.initials: KJ
authors.lastname: Lindquist
authors.affiliation: Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Vy T
authors.initials: VT
authors.lastname: Ngo
authors.affiliation: Computational Biology Core, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Ritu
authors.initials: R
authors.lastname: Roy
authors.affiliation: Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Hough
authors.affiliation: Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Edwards
authors.affiliation: Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Rosa
authors.initials: R
authors.lastname: Paz
authors.affiliation: Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Foye
authors.affiliation: Genome Analysis Core, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Riddhi
authors.initials: R
authors.lastname: Sood
authors.affiliation: Genome Analysis Core, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Kirsten A
authors.initials: KA
authors.lastname: Copren
authors.affiliation: Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Gubens
authors.affiliation: Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Small
authors.affiliation: Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Trever G
authors.initials: TG
authors.lastname: Bivona
authors.affiliation: Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Eric A
authors.initials: EA
authors.lastname: Collisson
authors.affiliation: Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
authors.forename: Terence W
authors.initials: TW
authors.lastname: Friedlander
authors.affiliation: Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA; Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA. Electronic address: Pamela.Paris@ucsf.edu.
authors.forename: Pamela L
authors.initials: PL
authors.lastname: Paris
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics / Q000378:metabolism / Q000473:pathology*; D021441:Carcinoma, Pancreatic Ductal / Q000235:genetics / Q000378:metabolism / Q000473:pathology*; D002448:Cell Adhesion; D045744:Cell Line, Tumor; D002465:Cell Movement; D002469:Cell Separation / Q000379:methods*; D003094:Collagen / Q000378:metabolism; D004252:DNA Mutational Analysis; D066246:ErbB Receptors / Q000235:genetics; D005434:Flow Cytometry; D020022:Genetic Predisposition to Disease; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics / Q000378:metabolism / Q000473:pathology*; D008297:Male; D009154:Mutation; D009361:Neoplasm Invasiveness; D014411:Neoplastic Stem Cells / Q000378:metabolism / Q000473:pathology*; D010190:Pancreatic Neoplasms / Q000235:genetics / Q000378:metabolism / Q000473:pathology*; D010641:Phenotype; D064129:Prostatic Neoplasms, Castration-Resistant / Q000235:genetics / Q000378:metabolism / Q000473:pathology*
chemical_list: D014408:Biomarkers, Tumor; D003094:Collagen; C512478:EGFR protein, human; D066246:ErbB Receptors
keywords: Cell adhesion matrix; Circulating tumor cells; Copy number; Fluorescence-activated cell sorting; High-purity; Sequencing