AR gene aberrations are rare in prostate cancer prior to primary hormone treatment but emerge with castration resistance. To determine AR gene status using a minimally-invasive assay that could have broad clinical utility, we developed a targeted next-generation sequencing approach amenable to plasma DNA that covers all the AR coding bases and regions of the genome highly informative in prostate cancer. We here sequenced 274 plasma samples from 97 castration-resistant prostate cancer patients treated with abiraterone at two institutions. After controlling for the fraction of normal DNA in patients’ circulation, we quantified AR copy number state and point mutations. AR aberrations by the two mechanisms were inversely correlated, supported further by the enrichment of non-synonymous versus synonymous mutations in AR copy number normal as opposed to AR gain samples. While AR copy number was unchanged from pre-treatment to progression and no mutant AR alleles showed signal for acquired gain, we observed emergence of T878A or L702H AR amino acid changes in 13% at progression on abiraterone. Patients with AR gain or T878A or L702H pre-abiraterone (45%) were 4.9 times and 7.8 times less likely to have a decline in PSA by ≥50% or ≥90% respectively and had a significantly worse overall (HR 7.33, 95% CI 3.51-15.34) and progression-free (HR 3.73, 95% CI 2.17-6.41) survival. Evaluation of plasma AR using next-generation sequencing could identify cancers with primary resistance to abiraterone.
Virtually all patients with multiple myeloma become unresponsive to treatment over time. Relapsed/refractory multiple myeloma (RRMM) is accompanied by the clonal evolution of myeloma cells with heterogeneous genomic aberrations and profound changes of the bone marrow microenvironment (BME). However, the molecular mechanisms that drive drug resistance remain elusive. Here, we analyze the heterogeneous tumor cell population and its complex interaction network with the BME of 20 RRMM patients by single cell RNA-sequencing before/after treatment. Subclones with chromosome 1q-gain express a specific transcriptomic signature and frequently expand during treatment. Furthermore, RRMM cells shape an immune suppressive BME by upregulation of inflammatory cytokines and close interaction with the myeloid compartment. It is characterized by the accumulation of PD1+ γδ T-cells and tumor-associated macrophages as well as the depletion of hematopoietic progenitors. Thus, our study resolves transcriptional features of subclones in RRMM and mechanisms of microenvironmental reprogramming with implications for clinical decision-making.
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