Plasma cell-free DNA-based predictors of response to abiraterone acetate/prednisone and prognostic factors in metastatic castration-resistant prostate cancer
PROSTATE CANCER AND PROSTATIC DISEASES
Authors: Du, Meijun; Tian, Yijun; Tan, Winston; Wang, Liewei; Wang, Liguo; Kilari, Deepak; Huang, Chiang-Ching; Wang, Liang; Kohli, Manish
Abstract
Background The combination of abiraterone acetate and prednisone (AA/P) is used to treat metastatic prostate cancer, but molecular predictors of treatment response are not well elucidated. We evaluated plasma circulating tumor DNA- (ctDNA-) based copy number alterations (CNAs) to determine treatment-related predictive and prognostic biomarkers for metastatic castration-resistant prostate cancer (mCRPC). Methods Serial plasma specimens were prospectively collected from 88 chemotherapy-naive mCRPC patients before and after 12 weeks of AA/P treatment. Sequencing-based CNA analyses were performed on 174 specimens. We evaluated CNA-associated 12-week responses for primary resistance, time to treatment change (TTTC) for secondary resistance, and overall survival for prognosis (P < 0.05). Associations with primary resistance were analyzed using the Fisher exact test. Kaplan-Meier survival curves and Cox regression analyses were used to determine the associations of CNAs with acquired resistance and overall survival. Results ctDNA reduced by 3.89% in responders and increased by 0.94% in nonresponders (P = 0.0043). Thirty-one prostate cancer-related genes from whole genome CNAs were tested. AR and AR enhancer amplification were associated with primary resistance (P = 0.0039) and shorter TTTC (P = 0.0003). ZFHX3 deletion and PIK3CA amplification were associated with primary resistance (P = 0.026 and P = 0.017, respectively), shorter TTTC (P = 0.0008 and P = 0.0016, respectively), and poor survival (P = 0.0025 and P = 0.0022, respectively). CNA-based risk scores combining selected significant associations (AR, NKX3.1, and PIK3CA) at the univariate level with TTTC were predictive of secondary resistance (P = 0.0002). and established prognoses for survival based on CNAs in ZFHX3, RB1, PIK3CA, and OPHN1 (P = 0.002). Multigene risk scores were more predictive than individual genes or clinical risk factors (P < 0.05). Conclusion Plasma ctDNA CNAs and risk scores can predict mCRPC-state treatment and survival outcomes.
Biallelic and monoallelic deletion of the RB1 promoter in six isogenic clonal H9 hESC lines
STEM CELL RESEARCH
Authors: Doepper, Hannah; Horstmann, Marius; Menges, Julia; Bozet, Morgane; Kanber, Deniz; Steenpass, Laura
Abstract
Retinoblastoma is a childhood tumor of the retina that is caused mostly by biallelic inactivation of the tumor suppressor gene RB1 . To generate a research resource, we abrogated expression of RB1 in H9 hESCs by CRISPR/Cas9 induced deletion of the RB1 promoter, either on one or on both alleles. This enables studies on the role of RB1 loss during di fferentiation, for example in di fferentiation towards neural retina. The generation of three isogenic lines per deletion state enables validation of phenotypic results in independent clonal lines.