title: Integrated Analysis of Multiple Biomarkers from Circulating Tumor Cells Enabled by Exclusion-Based Analyte Isolation.
abstract: There is a critical clinical need for new predictive and pharmacodynamic biomarkers that evaluate pathway activity in patients treated with targeted therapies. A microscale platform known as VERSA (versatile exclusion-based rare sample analysis) was developed to integrate readouts across protein, mRNA, and DNA in circulating tumor cells (CTC) for a comprehensive analysis of the androgen receptor (AR) signaling pathway.
  
  
  
  Utilizing exclusion-based sample preparation principles, a handheld chip was developed to perform CTC capture, enumeration, quantification, and subcellular localization of proteins and extraction of mRNA and DNA. This technology was validated across integrated endpoints in cell lines and a cohort of patients with castrate-resistant prostate cancer (CRPC) treated with AR-targeted therapies and chemotherapies.
  
  
  
  The VERSA was validated in cell lines to analyze AR protein expression, nuclear localization, and gene expression targets. When applied to a cohort of patients, radiographic progression was predicted by the presence of multiple AR splice variants and activity in the canonical AR signaling pathway. AR protein expression and nuclear localization identified phenotypic heterogeneity. Next-generation sequencing with the FoundationOne panel detected copy number changes and point mutations. Longitudinal analysis of CTCs identified acquisition of multiple AR variants during targeted treatments and chemotherapy.
  
  
  
  Complex mechanisms of resistance to AR-targeted therapies, across RNA, DNA, and protein endpoints, exist in patients with CRPC and can be quantified in CTCs. Interrogation of the AR signaling pathway revealed distinct patterns relevant to tumor progression and can serve as pharmacodynamic biomarkers for targeted therapies. Clin Cancer Res; 1-11. ©2016 AACR.
authors.affiliation: Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin.
authors.forename: Jamie M
authors.initials: JM
authors.lastname: Sperger
authors.affiliation: Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin.
authors.forename: Lindsay N
authors.initials: LN
authors.lastname: Strotman
authors.affiliation: Foundation Medicine, Cambridge, Massachusetts.
authors.forename: Allison
authors.initials: A
authors.lastname: Welsh
authors.affiliation: Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin.
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Casavant
authors.affiliation: Foundation Medicine, Cambridge, Massachusetts.
authors.forename: Zachery
authors.initials: Z
authors.lastname: Chalmers
authors.affiliation: Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin.
authors.forename: Sacha
authors.initials: S
authors.lastname: Horn
authors.affiliation: Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin.
authors.forename: Erika
authors.initials: E
authors.lastname: Heninger
authors.affiliation: Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin.
authors.forename: Stephanie M
authors.initials: SM
authors.lastname: Thiede
authors.affiliation: Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin.
authors.forename: Jacob
authors.initials: J
authors.lastname: Tokar
authors.affiliation: Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin.
authors.forename: Benjamin K
authors.initials: BK
authors.lastname: Gibbs
authors.affiliation: Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin.
authors.forename: David J
authors.initials: DJ
authors.lastname: Guckenberger
authors.affiliation: Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin.
authors.forename: Lakeesha
authors.initials: L
authors.lastname: Carmichael
authors.affiliation: Masonic Cancer Center and Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota.
authors.forename: Scott M
authors.initials: SM
authors.lastname: Dehm
authors.affiliation: Foundation Medicine, Cambridge, Massachusetts.
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Stephens
authors.affiliation: Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin.|Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin.
authors.forename: David J
authors.initials: DJ
authors.lastname: Beebe
authors.affiliation: Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin.
authors.forename: Scott M
authors.initials: SM
authors.lastname: Berry
authors.affiliation: Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin. jmlang@medicine.wisc.edu.|Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin.
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Lang