Clonal evolution during metastatic spread in high-risk neuroblastoma

  • Maris, J. M. Recent advances in neuroblastoma. N. Engl. J. Med. 362, 2202–2211 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • London, W. B. et al. Historical time to disease progression and progression-free survival in patients with recurrent/refractory neuroblastoma treated in the modern era on Children’s Oncology Group early-phase trials.Cancer 123, 4914–4923 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Abbasi, M. R. et al. Impact of disseminated neuroblastoma cells on the identification of the relapse-seeding clone. Clin. Cancer Res. 23, 4224–4232 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Eleveld, T. F. et al. Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations. Nat. Genet. 47, 864–871 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schramm, A. et al. Mutational dynamics between primary and relapse neuroblastomas. Nat. Genet. 47, 872–877 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chicard, M. et al. Genomic copy number profiling using circulating free tumor DNA highlights heterogeneity in neuroblastoma. Clin. Cancer Res. 22, 5564–5573 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Van Roy, N. et al. Shallow whole genome sequencing on circulating cell-free DNA allows reliable noninvasive copy-number profiling in neuroblastoma patients. Clin. Cancer Res. 23, 6305–6314 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Chicard, M. et al. Whole-exome sequencing of cell-free DNA reveals temporo-spatial heterogeneity and identifies treatment-resistant clones in neuroblastoma. Clin. Cancer Res. 24, 939–949 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Fransson, S. et al. Whole-genome sequencing of recurrent neuroblastoma reveals somatic mutations that affect key players in cancer progression and telomere maintenance. Sci. Rep. 10, 22432 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Karlsson, J. et al. Four evolutionary trajectories underlie genetic intratumoral variation in childhood cancer. Nat. Genet. 50, 944–950 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Andersson, N. et al. Extensive clonal branching shapes the evolutionary history of high-risk pediatric cancers. Cancer Res. 80, 1512–1523 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Schmelz, K. et al. Spatial and temporal intratumour heterogeneity has potential consequences for single biopsy-based neuroblastoma treatment decisions. Nat. Commun. 12, 6804 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Peifer, M. et al. Telomerase activation by genomic rearrangements in high-risk neuroblastoma. Nature 526, 700–704 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Brady, S. W. et al. Pan-neuroblastoma analysis reveals age- and signature-associated driver alterations. Nat. Commun. 11, 5183 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Monclair, T. et al. The International Neuroblastoma Risk Group (INRG) staging system: an INRG Task Force report. J. Clin. Oncol. 27, 298–303 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pugh, T. J. et al. The genetic landscape of high-risk neuroblastoma. Nat. Genet. 45, 279–284 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Valentijn, L. J. et al. TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors. Nat. Genet. 47, 1411–1414 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Amoroso, L. et al. Genomic coamplification of CDK4/MDM2/FRS2 is associated with very poor prognosis and atypical clinical features in neuroblastoma patients. Genes Chromosomes Cancer 59, 277–285 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

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

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415–421 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kucab, J. E. et al. A compendium of mutational signatures of environmental agents. Cell 177, 821–836.e16 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, T. et al. MYCN drives glutaminolysis in neuroblastoma and confers sensitivity to an ROS augmenting agent. Cell Death Dis. 9, 220 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gröbner, S. N. et al. The landscape of genomic alterations across childhood cancers. Nature 555, 321–327 (2018).

    Article 
    PubMed 

    Google Scholar
     

  • Ma, X. et al. Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours. Nature 555, 371–376 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wei, J. S. et al. Clinically relevant cytotoxic immune cell signatures and clonal expansion of T-cell receptors in high-risk MYCN-not-amplified human neuroblastoma. Clin. Cancer Res. 24, 5673–5684 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Layer, J. P. et al. Amplification of N-Myc is associated with a T-cell-poor microenvironment in metastatic neuroblastoma restraining interferon pathway activity and chemokine expression. Oncoimmunology 6, e1320626 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Geoerger, B. et al. Pembrolizumab in paediatric patients with advanced melanoma or a PD-L1-positive, advanced, relapsed, or refractory solid tumour or lymphoma (KEYNOTE-051): interim analysis of an open-label, single-arm, phase 1–2 trial.Lancet 399, 1718–1729 (2022).


    Google Scholar
     

  • Geoerger, B. et al. Atezolizumab for children and young adults with previously treated solid tumours, non-Hodgkin lymphoma, and Hodgkin lymphoma (iMATRIX): a multicentre phase 1–2 study.Lancet Oncol. 21, 134–144 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Davis, K. L. et al. Nivolumab in children and young adults with relapsed or refractory solid tumours or lymphoma (ADVL1412): a multicentre, open-label, single-arm, phase 1-2 trial. Lancet Oncol. 21, 541–550 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Havel, J. J., Chowell, D. & Chan, T. A. The evolving landscape of biomarkers for checkpoint inhibitor immunotherapy. Nat. Rev. Cancer 19, 133–150 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pich, O. et al. The mutational footprints of cancer therapies. Nat. Genet. 51, 1732–1740 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Angus, L. et al. The genomic landscape of metastatic breast cancer highlights changes in mutation and signature frequencies. Nat. Genet. 51, 1450–1458 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kocakavuk, E. et al. Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer. Nat. Genet. 53, 1088–1096 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Behjati, S. et al. Mutational signatures of ionizing radiation in second malignancies. Nat. Commun. 7, 12605 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gerstung, M. et al. The evolutionary history of 2,658 cancers. Nature 578, 122–128 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mitchell, T. J. et al. Timing the landmark events in the evolution of clear cell renal cell cancer: TRACERx renal. Cell 173, 611–623.e17 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rustad, E. H. et al. Timing the initiation of multiple myeloma. Nat. Commun. 11, 1917 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Coorens, T. H. H. et al. Inherent mosaicism and extensive mutation of human placentas. Nature 592, 80–85 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schleiermacher, G. et al. Emergence of new ALK mutations at relapse of neuroblastoma. J. Clin. Oncol. 32, 2727–2734 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Althoff, K. et al. A Cre-conditional MYCN-driven neuroblastoma mouse model as an improved tool for preclinical studies. Oncogene 34, 3357–3368 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Schwab, M. et al. Amplified DNA with limited homology to myc cellular oncogene is shared by human neuroblastoma cell lines and a neuroblastoma tumour.Nature 305, 245–248 (1983).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kohl, N. E. et al. Transposition and amplification of oncogene-related sequences in human neuroblastomas. Cell 35, 359–367 (1983).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Cobrinik, D. et al. Recurrent pre-existing and acquired DNA copy number alterations, including focal TERT gains, in neuroblastoma central nervous system metastases. Genes Chromosomes Cancer 52, 1150–1166 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Cheung, N.-K. V. et al. Association of age at diagnosis and genetic mutations in patients with neuroblastoma. JAMA 307, 1062–1071 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Franks, L. M., Bollen, A., Seeger, R. C., Stram, D. O. & Matthay, K. K. Neuroblastoma in adults and adolescents: an indolent course with poor survival. Cancer 79, 2028–2035 (1997).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ackermann, S. et al. A mechanistic classification of clinical phenotypes in neuroblastoma. Science 362, 1165–1170 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Carr-Wilkinson, J. et al. High frequency of p53/MDM2/p14ARF pathway abnormalities in relapsed neuroblastoma. Clin. Cancer Res. 16, 1108–1118 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • DuBois, S. G. et al. Metastatic sites in stage IV and IVS neuroblastoma correlate with age, tumor biology, and survival. J. Pediatr. Hematol. Oncol. 21, 181–189 (1999).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Landau, H. J. et al. Accelerated single cell seeding in relapsed multiple myeloma. Nat. Commun. 11, 3617 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Berlanga, P. et al. Central nervous system relapse in high-risk stage 4 neuroblastoma: The HR-NBL1/SIOPEN trial experience. Eur. J. Cancer 144, 1–8 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ishida, M. et al. Sprouty2 regulates growth and differentiation of human neuroblastoma cells through RET tyrosine kinase. Cancer Sci. 98, 815–821 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

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

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Keshelava, N. et al. Loss of p53 function confers high-level multidrug resistance in neuroblastoma cell lines. Cancer Res. 61, 6185–6193 (2001).

    CAS 
    PubMed 

    Google Scholar
     

  • Koche, R. P. et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nat. Genet. 52, 29–34 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kim, H. et al. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nat. Genet. 52, 891–897 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kushner, B. H. et al. Efficacy of naxitamab in patients with refractory/relapse (R/R) high-risk neuroblastoma (HR-NB) by bone/bone marrow (BM) evaluation, potential sites of residual disease. J. Clin. Oncol. 39, 10022–10022. Preprint at doi.org/10.1200/jco.2021.39.15_suppl.10022 (2021).

  • Yarmarkovich, M. et al. Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs. Nature doi.org/10.1038/s41586-021-04061-6 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Diolaiti, D. et al. A recurrent novel MGA–NUTM1 fusion identifies a new subtype of high-grade spindle cell sarcoma.Cold Spring Harb. Mol. Case Stud. 4, a003194 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zehir, A. et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat. Med. 23, 703–713 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chakravarty, D. et al. OncoKB: Annotation of the oncogenic effect and treatment implications of somatic mutations in cancer.JCO Precis. Oncol. 2017, PO.17.00011 (2017).

    PubMed 

    Google Scholar
     

  • Medina-Martínez, J. S. et al. Isabl Platform, a digital biobank for processing multimodal patient data.BMC Bioinformatics 21, 549 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Landrum, M. J. et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 44, D862–D868 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Forbes, S. A. et al. COSMIC: somatic cancer genetics at high-resolution. Nucleic Acids Res. 45, D777–D783 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Karczewski, K. J. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McLaren, W. et al. The Ensembl Variant Effect Predictor. Genome Biol. 17, 122 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Srivastava, A. et al. Alignment and mapping methodology influence transcript abundance estimation. Genome Biol. 21, 239 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Aran, D., Hu, Z. & Butte, A. J. xCell: digitally portraying the tissue cellular heterogeneity landscape. Genome Biol. 18, 220 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Alexandrov, L. B., Nik-Zainal, S., Wedge, D. C., Campbell, P. J. & Stratton, M. R. Deciphering signatures of mutational processes operative in human cancer. Cell Rep. 3, 246–259 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Blokzijl, F., Janssen, R., van Boxtel, R. & Cuppen, E. MutationalPatterns: comprehensive genome-wide analysis of mutational processes. Genome Med. 10, 33 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, Y. et al. Patterns of somatic structural variation in human cancer genomes. Nature 578, 112–121 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cortés-Ciriano, I. et al. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat. Genet. 52, 331–341 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nik-Zainal, S. et al. The life history of 21 breast cancers. Cell 149, 994–1007 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dang, H. X. et al. ClonEvol: clonal ordering and visualization in cancer sequencing. Ann. Oncol. 28, 3076–3082 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kaufmann, T. L. et al. MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution. Genome Biol. 23, 241 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shen, R. & Seshan, V. E. FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. Nucleic Acids Res. 44, e131 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Read more here: Source link