A circulating tumor cell-RNA assay for assessment of androgen receptor signaling inhibitor sensitivity in metastatic castration-resistant prostate cancer

Yu Jen Jan, Junhee Yoon, Jie Fu Chen, Pai Chi Teng, Nu Yao, Shirley Cheng, Amber Lozano, Gina C.Y. Chu, Howard Chung, Yi Tsung Lu, Pin Jung Chen, Jasmine J. Wang, Yi Te Lee, Minhyung Kim, Yazhen Zhu, Beatrice S. Knudsen, Felix Y. Feng, Isla P. Garraway, Allen C Gao, Leland W.K. ChungMichael R. Freeman, Sungyong You, Hsian Rong Tseng, Edwin M. Posadas

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Rationale: Our objective was to develop a circulating tumor cell (CTC)-RNA assay for characterizing clinically relevant RNA signatures for the assessment of androgen receptor signaling inhibitor (ARSI) sensitivity in metastatic castration-resistant prostate cancer (mCRPC) patients. Methods: We developed the NanoVelcro CTC-RNA assay by combining the Thermoresponsive (TR)-NanoVelcro CTC purification system with the NanoString nCounter platform for cellular purification and RNA analysis. Based on the well-validated, tissue-based Prostate Cancer Classification System (PCS), we focus on the most aggressive and ARSI-resistant PCS subtype, i.e., PCS1, for CTC analysis. We applied a rigorous bioinformatic process to develop the CTC-PCS1 panel that consists of prostate cancer (PCa) CTC-specific RNA signature with minimal expression in background white blood cells (WBCs). We validated the NanoVelcro CTC-RNA assay and the CTC-PCS1 panel with well-characterized PCa cell lines to demonstrate the sensitivity and dynamic range of the assay, as well as the specificity of the PCS1 Z score (the likelihood estimate of the PCS1 subtype) for identifying PCS1 subtype and ARSI resistance. We then selected 31 blood samples from 23 PCa patients receiving ARSIs to test in our assay. The PCS1 Z scores of each sample were computed and compared with ARSI treatment sensitivity. Results: The validation studies using PCa cell line samples showed that the NanoVelcro CTC-RNA assay can detect the RNA transcripts in the CTC-PCS1 panel with high sensitivity and linearity in the dynamic range of 5-100 cells. We also showed that the genes in CTC-PCS1 panel are highly expressed in PCa cell lines and lowly expressed in background WBCs. Using the artificial CTC samples simulating the blood sample conditions, we further demonstrated that the CTC-PCS1 panel is highly specific in identifying PCS1-like samples, and the high PCS1 Z score is associated with ARSI resistance samples. In patient bloods, ARSI-resistant samples (ARSI-R, n=14) had significantly higher PCS1 Z scores as compared with ARSI-sensitive samples (ARSI-S, n=17) (Rank-sum test, P=0.003). In the analysis of 8 patients who were initially sensitive to ARSI (ARSI-S) and later developed resistance (ARSI-R), we found that the PCS1 Z score increased from the time of ARSI-S to the time of ARSI-R (Pairwise T-test, P=0.016). Conclusions: Using our new methodology, we developed a first-in-class CTC-RNA assay and demonstrated the feasibility of transforming clinically-relevant tissue-based RNA profiling such as PCS into CTC tests. This approach allows for detecting RNA expression relevant to clinical drug resistance in a non-invasive fashion, which can facilitate patient-specific treatment selection and early detection of drug resistance, a goal in precision oncology.

Original languageEnglish (US)
Pages (from-to)2812-2826
Number of pages15
JournalTheranostics
Volume9
Issue number10
DOIs
StatePublished - Jan 1 2019

Fingerprint

Circulating Neoplastic Cells
Castration
Androgen Receptors
Prostatic Neoplasms
RNA
Drug Resistance
Cell Line
Leukocytes
Validation Studies
Nonparametric Statistics
Computational Biology

Keywords

  • Androgen receptor signaling inhibitors
  • Cancer RNA profiling
  • Circulating tumor cell
  • Metastatic castration-resistant prostate cancer

ASJC Scopus subject areas

  • Medicine (miscellaneous)
  • Pharmacology, Toxicology and Pharmaceutics (miscellaneous)

Cite this

A circulating tumor cell-RNA assay for assessment of androgen receptor signaling inhibitor sensitivity in metastatic castration-resistant prostate cancer. / Jan, Yu Jen; Yoon, Junhee; Chen, Jie Fu; Teng, Pai Chi; Yao, Nu; Cheng, Shirley; Lozano, Amber; Chu, Gina C.Y.; Chung, Howard; Lu, Yi Tsung; Chen, Pin Jung; Wang, Jasmine J.; Lee, Yi Te; Kim, Minhyung; Zhu, Yazhen; Knudsen, Beatrice S.; Feng, Felix Y.; Garraway, Isla P.; Gao, Allen C; Chung, Leland W.K.; Freeman, Michael R.; You, Sungyong; Tseng, Hsian Rong; Posadas, Edwin M.

In: Theranostics, Vol. 9, No. 10, 01.01.2019, p. 2812-2826.

Research output: Contribution to journalArticle

Jan, YJ, Yoon, J, Chen, JF, Teng, PC, Yao, N, Cheng, S, Lozano, A, Chu, GCY, Chung, H, Lu, YT, Chen, PJ, Wang, JJ, Lee, YT, Kim, M, Zhu, Y, Knudsen, BS, Feng, FY, Garraway, IP, Gao, AC, Chung, LWK, Freeman, MR, You, S, Tseng, HR & Posadas, EM 2019, 'A circulating tumor cell-RNA assay for assessment of androgen receptor signaling inhibitor sensitivity in metastatic castration-resistant prostate cancer', Theranostics, vol. 9, no. 10, pp. 2812-2826. https://doi.org/10.7150/thno.34485
Jan, Yu Jen ; Yoon, Junhee ; Chen, Jie Fu ; Teng, Pai Chi ; Yao, Nu ; Cheng, Shirley ; Lozano, Amber ; Chu, Gina C.Y. ; Chung, Howard ; Lu, Yi Tsung ; Chen, Pin Jung ; Wang, Jasmine J. ; Lee, Yi Te ; Kim, Minhyung ; Zhu, Yazhen ; Knudsen, Beatrice S. ; Feng, Felix Y. ; Garraway, Isla P. ; Gao, Allen C ; Chung, Leland W.K. ; Freeman, Michael R. ; You, Sungyong ; Tseng, Hsian Rong ; Posadas, Edwin M. / A circulating tumor cell-RNA assay for assessment of androgen receptor signaling inhibitor sensitivity in metastatic castration-resistant prostate cancer. In: Theranostics. 2019 ; Vol. 9, No. 10. pp. 2812-2826.
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title = "A circulating tumor cell-RNA assay for assessment of androgen receptor signaling inhibitor sensitivity in metastatic castration-resistant prostate cancer",
abstract = "Rationale: Our objective was to develop a circulating tumor cell (CTC)-RNA assay for characterizing clinically relevant RNA signatures for the assessment of androgen receptor signaling inhibitor (ARSI) sensitivity in metastatic castration-resistant prostate cancer (mCRPC) patients. Methods: We developed the NanoVelcro CTC-RNA assay by combining the Thermoresponsive (TR)-NanoVelcro CTC purification system with the NanoString nCounter platform for cellular purification and RNA analysis. Based on the well-validated, tissue-based Prostate Cancer Classification System (PCS), we focus on the most aggressive and ARSI-resistant PCS subtype, i.e., PCS1, for CTC analysis. We applied a rigorous bioinformatic process to develop the CTC-PCS1 panel that consists of prostate cancer (PCa) CTC-specific RNA signature with minimal expression in background white blood cells (WBCs). We validated the NanoVelcro CTC-RNA assay and the CTC-PCS1 panel with well-characterized PCa cell lines to demonstrate the sensitivity and dynamic range of the assay, as well as the specificity of the PCS1 Z score (the likelihood estimate of the PCS1 subtype) for identifying PCS1 subtype and ARSI resistance. We then selected 31 blood samples from 23 PCa patients receiving ARSIs to test in our assay. The PCS1 Z scores of each sample were computed and compared with ARSI treatment sensitivity. Results: The validation studies using PCa cell line samples showed that the NanoVelcro CTC-RNA assay can detect the RNA transcripts in the CTC-PCS1 panel with high sensitivity and linearity in the dynamic range of 5-100 cells. We also showed that the genes in CTC-PCS1 panel are highly expressed in PCa cell lines and lowly expressed in background WBCs. Using the artificial CTC samples simulating the blood sample conditions, we further demonstrated that the CTC-PCS1 panel is highly specific in identifying PCS1-like samples, and the high PCS1 Z score is associated with ARSI resistance samples. In patient bloods, ARSI-resistant samples (ARSI-R, n=14) had significantly higher PCS1 Z scores as compared with ARSI-sensitive samples (ARSI-S, n=17) (Rank-sum test, P=0.003). In the analysis of 8 patients who were initially sensitive to ARSI (ARSI-S) and later developed resistance (ARSI-R), we found that the PCS1 Z score increased from the time of ARSI-S to the time of ARSI-R (Pairwise T-test, P=0.016). Conclusions: Using our new methodology, we developed a first-in-class CTC-RNA assay and demonstrated the feasibility of transforming clinically-relevant tissue-based RNA profiling such as PCS into CTC tests. This approach allows for detecting RNA expression relevant to clinical drug resistance in a non-invasive fashion, which can facilitate patient-specific treatment selection and early detection of drug resistance, a goal in precision oncology.",
keywords = "Androgen receptor signaling inhibitors, Cancer RNA profiling, Circulating tumor cell, Metastatic castration-resistant prostate cancer",
author = "Jan, {Yu Jen} and Junhee Yoon and Chen, {Jie Fu} and Teng, {Pai Chi} and Nu Yao and Shirley Cheng and Amber Lozano and Chu, {Gina C.Y.} and Howard Chung and Lu, {Yi Tsung} and Chen, {Pin Jung} and Wang, {Jasmine J.} and Lee, {Yi Te} and Minhyung Kim and Yazhen Zhu and Knudsen, {Beatrice S.} and Feng, {Felix Y.} and Garraway, {Isla P.} and Gao, {Allen C} and Chung, {Leland W.K.} and Freeman, {Michael R.} and Sungyong You and Tseng, {Hsian Rong} and Posadas, {Edwin M.}",
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TY - JOUR

T1 - A circulating tumor cell-RNA assay for assessment of androgen receptor signaling inhibitor sensitivity in metastatic castration-resistant prostate cancer

AU - Jan, Yu Jen

AU - Yoon, Junhee

AU - Chen, Jie Fu

AU - Teng, Pai Chi

AU - Yao, Nu

AU - Cheng, Shirley

AU - Lozano, Amber

AU - Chu, Gina C.Y.

AU - Chung, Howard

AU - Lu, Yi Tsung

AU - Chen, Pin Jung

AU - Wang, Jasmine J.

AU - Lee, Yi Te

AU - Kim, Minhyung

AU - Zhu, Yazhen

AU - Knudsen, Beatrice S.

AU - Feng, Felix Y.

AU - Garraway, Isla P.

AU - Gao, Allen C

AU - Chung, Leland W.K.

AU - Freeman, Michael R.

AU - You, Sungyong

AU - Tseng, Hsian Rong

AU - Posadas, Edwin M.

PY - 2019/1/1

Y1 - 2019/1/1

N2 - Rationale: Our objective was to develop a circulating tumor cell (CTC)-RNA assay for characterizing clinically relevant RNA signatures for the assessment of androgen receptor signaling inhibitor (ARSI) sensitivity in metastatic castration-resistant prostate cancer (mCRPC) patients. Methods: We developed the NanoVelcro CTC-RNA assay by combining the Thermoresponsive (TR)-NanoVelcro CTC purification system with the NanoString nCounter platform for cellular purification and RNA analysis. Based on the well-validated, tissue-based Prostate Cancer Classification System (PCS), we focus on the most aggressive and ARSI-resistant PCS subtype, i.e., PCS1, for CTC analysis. We applied a rigorous bioinformatic process to develop the CTC-PCS1 panel that consists of prostate cancer (PCa) CTC-specific RNA signature with minimal expression in background white blood cells (WBCs). We validated the NanoVelcro CTC-RNA assay and the CTC-PCS1 panel with well-characterized PCa cell lines to demonstrate the sensitivity and dynamic range of the assay, as well as the specificity of the PCS1 Z score (the likelihood estimate of the PCS1 subtype) for identifying PCS1 subtype and ARSI resistance. We then selected 31 blood samples from 23 PCa patients receiving ARSIs to test in our assay. The PCS1 Z scores of each sample were computed and compared with ARSI treatment sensitivity. Results: The validation studies using PCa cell line samples showed that the NanoVelcro CTC-RNA assay can detect the RNA transcripts in the CTC-PCS1 panel with high sensitivity and linearity in the dynamic range of 5-100 cells. We also showed that the genes in CTC-PCS1 panel are highly expressed in PCa cell lines and lowly expressed in background WBCs. Using the artificial CTC samples simulating the blood sample conditions, we further demonstrated that the CTC-PCS1 panel is highly specific in identifying PCS1-like samples, and the high PCS1 Z score is associated with ARSI resistance samples. In patient bloods, ARSI-resistant samples (ARSI-R, n=14) had significantly higher PCS1 Z scores as compared with ARSI-sensitive samples (ARSI-S, n=17) (Rank-sum test, P=0.003). In the analysis of 8 patients who were initially sensitive to ARSI (ARSI-S) and later developed resistance (ARSI-R), we found that the PCS1 Z score increased from the time of ARSI-S to the time of ARSI-R (Pairwise T-test, P=0.016). Conclusions: Using our new methodology, we developed a first-in-class CTC-RNA assay and demonstrated the feasibility of transforming clinically-relevant tissue-based RNA profiling such as PCS into CTC tests. This approach allows for detecting RNA expression relevant to clinical drug resistance in a non-invasive fashion, which can facilitate patient-specific treatment selection and early detection of drug resistance, a goal in precision oncology.

AB - Rationale: Our objective was to develop a circulating tumor cell (CTC)-RNA assay for characterizing clinically relevant RNA signatures for the assessment of androgen receptor signaling inhibitor (ARSI) sensitivity in metastatic castration-resistant prostate cancer (mCRPC) patients. Methods: We developed the NanoVelcro CTC-RNA assay by combining the Thermoresponsive (TR)-NanoVelcro CTC purification system with the NanoString nCounter platform for cellular purification and RNA analysis. Based on the well-validated, tissue-based Prostate Cancer Classification System (PCS), we focus on the most aggressive and ARSI-resistant PCS subtype, i.e., PCS1, for CTC analysis. We applied a rigorous bioinformatic process to develop the CTC-PCS1 panel that consists of prostate cancer (PCa) CTC-specific RNA signature with minimal expression in background white blood cells (WBCs). We validated the NanoVelcro CTC-RNA assay and the CTC-PCS1 panel with well-characterized PCa cell lines to demonstrate the sensitivity and dynamic range of the assay, as well as the specificity of the PCS1 Z score (the likelihood estimate of the PCS1 subtype) for identifying PCS1 subtype and ARSI resistance. We then selected 31 blood samples from 23 PCa patients receiving ARSIs to test in our assay. The PCS1 Z scores of each sample were computed and compared with ARSI treatment sensitivity. Results: The validation studies using PCa cell line samples showed that the NanoVelcro CTC-RNA assay can detect the RNA transcripts in the CTC-PCS1 panel with high sensitivity and linearity in the dynamic range of 5-100 cells. We also showed that the genes in CTC-PCS1 panel are highly expressed in PCa cell lines and lowly expressed in background WBCs. Using the artificial CTC samples simulating the blood sample conditions, we further demonstrated that the CTC-PCS1 panel is highly specific in identifying PCS1-like samples, and the high PCS1 Z score is associated with ARSI resistance samples. In patient bloods, ARSI-resistant samples (ARSI-R, n=14) had significantly higher PCS1 Z scores as compared with ARSI-sensitive samples (ARSI-S, n=17) (Rank-sum test, P=0.003). In the analysis of 8 patients who were initially sensitive to ARSI (ARSI-S) and later developed resistance (ARSI-R), we found that the PCS1 Z score increased from the time of ARSI-S to the time of ARSI-R (Pairwise T-test, P=0.016). Conclusions: Using our new methodology, we developed a first-in-class CTC-RNA assay and demonstrated the feasibility of transforming clinically-relevant tissue-based RNA profiling such as PCS into CTC tests. This approach allows for detecting RNA expression relevant to clinical drug resistance in a non-invasive fashion, which can facilitate patient-specific treatment selection and early detection of drug resistance, a goal in precision oncology.

KW - Androgen receptor signaling inhibitors

KW - Cancer RNA profiling

KW - Circulating tumor cell

KW - Metastatic castration-resistant prostate cancer

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