Categories
Prostate cancer

Deep whole-genome ctDNA chronology of treatment-resistant prostate cancer

  • Ignatiadis, M., Sledge, G. W. & Jeffrey, S. S. Liquid biopsy enters the clinic—implementation issues and future challenges. Nat. Rev. Clin. Oncol. 18, 297–312 (2021).

    PubMed 
    Article 

    Google Scholar
     

  • Weber, Z. T. et al. Modeling clonal structure over narrow time frames via circulating tumor DNA in metastatic breast cancer. Genome Med. 13, 89 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Abbosh, C. et al. Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature 545, 446–451 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Parikh, A. R. et al. Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers. Nat. Med. 25, 1415–1421 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Cresswell, G. D. et al. Mapping the breast cancer metastatic cascade onto ctDNA using genetic and epigenetic clonal tracking. Nat. Commun. 11, 1446 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Annala, M. et al. Evolution of castration-resistant prostate cancer in ctDNA during sequential androgen receptor pathway inhibition. Clin. Cancer Res. 27, 4610–4623 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Wyatt, A. W. et al. Concordance of circulating tumor DNA and matched metastatic tissue biopsy in prostate cancer. J. Natl Cancer Inst. 109, djx118 (2017).

    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Razavi, P. et al. Alterations in PTEN and ESR1 promote clinical resistance to alpelisib plus aromatase inhibitors. Nat. Cancer 1, 382–393 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Siravegna, G. et al. Radiologic and genomic evolution of individual metastases during HER2 blockade in colorectal cancer. Cancer Cell 34, 148–162 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • O’Leary, B. et al. The genetic landscape and clonal evolution of breast cancer resistance to palbociclib plus fulvestrant in the PALOMA-3 trial. Cancer Discov. 8, 1390–1403 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Noorani, A. et al. Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma. Nat. Genet. 52, 74–83 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Woodcock, D. J. et al. Prostate cancer evolution from multilineage primary to single lineage metastases with implications for liquid biopsy. Nat. Commun. 11, 5070 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Snyder, M. W., Kircher, M., Hill, A. J., Daza, R. M. & Shendure, J. Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell 164, 57–68 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Ulz, P. et al. Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection. Nat. Commun. 10, 4666 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Zhu, G. et al. Tissue-specific cell-free DNA degradation quantifies circulating tumor DNA burden. Nat. Commun. 12, 1–11 (2021).

    CAS 
    Article 
    ADS 

    Google Scholar
     

  • Ulz, P. et al. Inferring expressed genes by whole-genome sequencing of plasma DNA. Nat. Genet. 48, 1273–1278 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Peneder, P. et al. Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden. Nat. Commun. 12, 3230 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Sun, K. et al. Orientation-aware plasma cell-free DNA fragmentation analysis in open chromatin regions informs tissue of origin. Genome Res. 29, 418–427 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Khalaf, D. J. et al. Optimal sequencing of enzalutamide and abiraterone acetate plus prednisone in metastatic castration-resistant prostate cancer: a multicentre, randomised, open-label, phase 2, crossover trial. Lancet Oncol. 20, 1730–1739 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Quigley, D. A. et al. Genomic hallmarks and structural variation in metastatic prostate cancer. Cell 174, 758–769 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Abida, W. et al. Genomic correlates of clinical outcome in advanced prostate cancer. Proc. Natl Acad. Sci. USA. 116, 11428–11436 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • van Dessel, L. F. et al. The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact. Nat. Commun. 10, 5251 (2019).

    PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Alexandrov, L. B. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Wu, Y.-M. et al. Inactivation of CDK12 delineates a distinct immunogenic class of advanced prostate cancer. Cell 173, 1770–1782 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Black, J. R. M. & McGranahan, N. Genetic and non-genetic clonal diversity in cancer evolution. Nat. Rev. Cancer 21, 379–392 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Dentro, S. C. et al. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell 184, 2239–2254 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Tarabichi, M. et al. A practical guide to cancer subclonal reconstruction from DNA sequencing. Nat. Methods 18, 144–155 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Bielski, C. M. et al. Genome doubling shapes the evolution and prognosis of advanced cancers. Nat. Genet. 50, 1189–1195 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Quinton, R. J. et al. Whole-genome doubling confers unique genetic vulnerabilities on tumour cells. Nature 590, 492–497 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Cohen-Sharir, Y. et al. Aneuploidy renders cancer cells vulnerable to mitotic checkpoint inhibition. Nature 590, 486–491 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Zaccaria, S. & Raphael, B. J. Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data. Nat. Commun. 11, 4301 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Chen, C. D. et al. Molecular determinants of resistance to antiandrogen therapy. Nat. Med. 10, 33–39 (2004).

    PubMed 
    Article 
    CAS 

    Google Scholar
     

  • Henzler, C. et al. Truncation and constitutive activation of the androgen receptor by diverse genomic rearrangements in prostate cancer. Nat. Commun. 7, 13668 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Takeda, D. Y. et al. A somatically acquired enhancer of the androgen receptor is a noncoding driver in advanced prostate cancer. Cell 174, 422–432 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Li, Y. et al. Diverse AR gene rearrangements mediate resistance to androgen receptor inhibitors in metastatic prostate cancer. Clin. Cancer Res. 26, 1965–1976 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Annala, M. et al. Circulating tumor dna genomics correlate with resistance to abiraterone and enzalutamide in prostate cancer. Cancer Discov. 8, 444–457 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Baca, S. C. et al. Punctuated evolution of prostate cancer genomes. Cell 153, 666–677 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Viswanathan, S. R. et al. Structural alterations driving castration-resistant prostate cancer revealed by linked-read genome sequencing. Cell 174, 433–447 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Esfahani, M. S. et al. Inferring gene expression from cell-free DNA fragmentation profiles. Nat. Biotechnol. 40, 585–597 (2022).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Davies, A. H., Beltran, H. & Zoubeidi, A. Cellular plasticity and the neuroendocrine phenotype in prostate cancer. Nat. Rev. Urol. 15, 271–286 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Pomerantz, M. M. et al. The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis. Nat. Genet. 47, 1346–1351 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Morova, T. et al. Androgen receptor-binding sites are highly mutated in prostate cancer. Nat. Commun. 11, 832 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Rebello, R. J. et al. Prostate cancer. Nat Rev. Dis. Primers 7, 9 (2021).

    PubMed 
    Article 

    Google Scholar
     

  • Chi, K. N. et al. A prognostic index model for predicting overall survival in patients with metastatic castration-resistant prostate cancer treated with abiraterone acetate after docetaxel. Ann. Oncol. 27, 454–460 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Turajlic, S. et al. Deterministic evolutionary trajectories influence primary tumor growth: TRACERx Renal. Cell 173, 595–610 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Gundem, G. et al. The evolutionary history of lethal metastatic prostate cancer. Nature 520, 353–357 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Kumar, A. et al. Substantial interindividual and limited intraindividual genomic diversity among tumors from men with metastatic prostate cancer. Nat. Med. 22, 369–378 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Quigley, D. et al. Analysis of circulating cell-free DNA identifies multiclonal heterogeneity of reversion mutations associated with resistance to PARP inhibitors. Cancer Discov. 7, 999–1005 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Unterrainer, M. et al. Recent advances of PET imaging in clinical radiation oncology. Radiat. Oncol. 15, 88 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Brandão, M., Caparica, R., Eiger, D. & de Azambuja, E. Biomarkers of response and resistance to PI3K inhibitors in estrogen receptor-positive breast cancer patients and combination therapies involving PI3K inhibitors. Ann. Oncol. 30, x27–x42 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Parikh, A. et al. Systematic liquid biopsy identifies novel and heterogeneous mechanisms of acquired resistance in gastrointestinal (GI) cancer patients. Ann. Oncol. 28, iii137 (2017).

    Article 

    Google Scholar
     

  • Balanis, N. G. et al. Pan-cancer Convergence to a small-cell neuroendocrine phenotype that shares susceptibilities with hematological malignancies. Cancer Cell 36, 17–34 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Herberts, C. & Wyatt, A. W. Technical and biological constraints on ctDNA-based genotyping. Trends Cancer Res. 7, 995–1009 (2021).

    CAS 
    Article 

    Google Scholar
     

  • Turajlic, S., Sottoriva, A., Graham, T. & Swanton, C. Resolving genetic heterogeneity in cancer. Nat. Rev. Genet. 20, 404–416 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Scher, H. I. et al. Trial design and objectives for castration-resistant prostate cancer: updated recommendations from the prostate cancer clinical trials working group 3. J. Clin. Oncol. 34, 1402–1418 (2016).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Warner, E. et al. BRCA2, ATM, and CDK12 defects differentially shape prostate tumor driver genomics and clinical aggression. Clin. Cancer Res. 27, 1650–1662 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10 (2011).

    Article 

    Google Scholar
     

  • Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Faust, G. G. & Hall, I. M. SAMBLASTER: fast duplicate marking and structural variant read extraction. Bioinformatics 30, 2503–2505 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Rosenthal, R., McGranahan, N., Herrero, J., Taylor, B. S. & Swanton, C. DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution. Genome Biol. 17, 31 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Bergstrom, E. N. et al. SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events. BMC Genomics 20, 685 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Landrum, M. J. et al. ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Res. 46, D1062–D1067 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008 (2021).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Eisenberg, E. & Levanon, E. Y. Human housekeeping genes, revisited. Trends Genet. 29, 569–574 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Leave a Reply