Emerging concepts in liquid biopsies

Characterizing and monitoring tumor genomes with blood samples could achieve significant improvements in precision medicine. As tumors shed parts of themselves into the circulation, analyses of circulating tumor cells, circulating tumor DNA, and tumor-derived exosomes, often referred to as “liquid biopsies”, may enable tumor genome characterization by minimally invasive means. Indeed, multiple studies have described how molecular information about parent tumors can be extracted from these components. Here, we briefly summarize current technologies and then elaborate on emerging novel concepts that may further propel the field. We address normal and detectable mutation levels in the context of our current knowledge regarding the gradual accumulation of mutations during aging and in light of technological limitations. Finally, we discuss whether liquid biopsies are ready to be used in routine clinical practice.

[1]  K. Kinzler,et al.  Detection and quantification of rare mutations with massively parallel sequencing , 2011, Proceedings of the National Academy of Sciences.

[2]  Sridhar Ramaswamy,et al.  Circulating Breast Tumor Cells Exhibit Dynamic Changes in Epithelial and Mesenchymal Composition , 2013, Science.

[3]  James Y. Zou.  Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.

[4]  X. Xie,et al.  Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell , 2012, Science.

[5]  A. Morris,et al.  Cancer etiology. Variation in cancer risk among tissues can be explained by the number of stem cell divisions , 2015, BDJ.

[6]  Arthur P. Grollman,et al.  Genome-wide quantification of rare somatic mutations in normal human tissues using massively parallel sequencing , 2016, Proceedings of the National Academy of Sciences.

[7]  Michael A. Hollingsworth,et al.  Pancreatic cancer exosomes initiate pre-metastatic niche formation in the liver , 2015, Nature Cell Biology.

[8]  Johannes G. Reiter,et al.  The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers , 2012, Nature.

[9]  Peter Ulz,et al.  Changes in Colorectal Carcinoma Genomes under Anti-EGFR Therapy Identified by Whole-Genome Plasma DNA Sequencing , 2014, PLoS genetics.

[10]  Andrew Menzies,et al.  The patterns and dynamics of genomic instability in metastatic pancreatic cancer , 2010, Nature.

[11]  V. Wong,et al.  Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients , 2015, Proceedings of the National Academy of Sciences.

[12]  Mark Lee,et al.  Next-Generation Sequencing of Circulating Tumor DNA for Early Cancer Detection , 2017, Cell.

[13]  Toru Kumagai,et al.  Diagnostic Accuracy of Noninvasive Genotyping of EGFR in Lung Cancer Patients by Deep Sequencing of Plasma Cell-Free DNA. , 2015, Clinical chemistry.

[14]  Delila Gasi Tandefelt,et al.  Plasma AR and abiraterone-resistant prostate cancer , 2015, Science Translational Medicine.

[15]  Noah C Welker,et al.  Fragment Length of Circulating Tumor DNA , 2016, PLoS genetics.

[16]  Peter Ulz,et al.  Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing , 2013, Genome Medicine.

[17]  Peter Ulz,et al.  Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing. , 2013, Cancer research.

[18]  Klaus Pantel,et al.  Circulating Tumor DNA as a Cancer Biomarker: Fact or Fiction? , 2016, Clinical chemistry.

[19]  P. Jiang,et al.  Maternal plasma RNA sequencing for genome-wide transcriptomic profiling and identification of pregnancy-associated transcripts. , 2014, Clinical chemistry.

[20]  Christian Pilarsky,et al.  Glypican-1 identifies cancer exosomes and detects early pancreatic cancer , 2015, Nature.

[21]  Chiang-Ching Huang,et al.  Plasma genetic and genomic abnormalities predict treatment response and clinical outcome in advanced prostate cancer , 2015, Oncotarget.

[22]  Ash A. Alizadeh,et al.  Robust enumeration of cell subsets from tissue expression profiles , 2015, Nature Methods.

[23]  Peter Ulz,et al.  Circulating tumor DNA as a liquid biopsy for cancer. , 2015, Clinical chemistry.

[24]  Hans Clevers,et al.  Organoid Cultures Derived from Patients with Advanced Prostate Cancer , 2014, Cell.

[25]  Henrik Zetterberg,et al.  Identification of tissue-specific cell death using methylation patterns of circulating DNA , 2016, Proceedings of the National Academy of Sciences.

[26]  Stephen R. Quake,et al.  Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm , 2012, Cell.

[27]  Lynda Chin,et al.  Identification of Double-stranded Genomic DNA Spanning All Chromosomes with Mutated KRAS and p53 DNA in the Serum Exosomes of Patients with Pancreatic Cancer* , 2014, The Journal of Biological Chemistry.

[28]  M. Stratton,et al.  Use of cancer‐specific genomic rearrangements to quantify disease burden in plasma from patients with solid tumors , 2010, Genes, chromosomes & cancer.

[29]  L. Kwak,et al.  Detection of tumor messenger RNA in the serum of patients with malignant melanoma. , 1999, Clinical cancer research : an official journal of the American Association for Cancer Research.

[30]  Raghu Kalluri,et al.  The biology and function of exosomes in cancer. , 2016, The Journal of clinical investigation.

[31]  Udo Schumacher,et al.  Establishment and characterization of a cell line from human circulating colon cancer cells. , 2015, Cancer research.

[32]  Aviv Regev,et al.  Whole exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer , 2014, Nature Biotechnology.

[33]  J. Troge,et al.  Tumour evolution inferred by single-cell sequencing , 2011, Nature.

[34]  Vinay Prasad,et al.  Precision oncology: origins, optimism, and potential. , 2016, The Lancet. Oncology.

[35]  Klaus Pantel,et al.  Cell-free nucleic acids as biomarkers in cancer patients , 2011, Nature Reviews Cancer.

[36]  Carlos Caldas,et al.  Analysis of circulating tumor DNA to monitor metastatic breast cancer. , 2013, The New England journal of medicine.

[37]  X. Breakefield,et al.  Introduction to Extracellular Vesicles: Biogenesis, RNA Cargo Selection, Content, Release, and Uptake , 2016, Cellular and Molecular Neurobiology.

[38]  P. A. Futreal,et al.  Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. , 2012, The New England journal of medicine.

[39]  Bert Vogelstein,et al.  DETECTION OF CIRCULATING TUMOR DNA IN EARLY AND LATE STAGE HUMAN MALIGNANCIES , 2014 .

[40]  Tao Wang,et al.  Meta-Analysis of the Prognostic Value of Circulating Tumor Cells in Breast Cancer , 2012, Clinical Cancer Research.

[41]  P. Gonzalez-Alegre,et al.  Towards precision medicine , 2017 .

[42]  Matthew W. Snyder,et al.  Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin , 2016, Cell.

[43]  Beatriz Bellosillo,et al.  Clonal evolution and resistance to EGFR blockade in the blood of colorectal cancer patients , 2015, Nature Medicine.

[44]  X. Xie,et al.  Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients , 2013, Proceedings of the National Academy of Sciences.

[45]  Anthony T Papenfuss,et al.  A community-based model of rapid autopsy in end-stage cancer patients , 2016, Nature Biotechnology.

[46]  Klaus Pantel,et al.  Clinical Applications of Circulating Tumor Cells and Circulating Tumor DNA as Liquid Biopsy. , 2016, Cancer discovery.

[47]  V. Velculescu,et al.  Blood-based analyses of cancer: circulating tumor cells and circulating tumor DNA. , 2014, Cancer discovery.

[48]  Mahmood Ayub,et al.  Tumorigenicity and genetic profiling of circulating tumor cells in small-cell lung cancer , 2014, Nature Medicine.

[49]  S. Pomeroy,et al.  Tumour microvesicles contain retrotransposon elements and amplified oncogene sequences. , 2011, Nature communications.

[50]  Gyan Bhanot,et al.  Single Cell Profiling of Circulating Tumor Cells: Transcriptional Heterogeneity and Diversity from Breast Cancer Cell Lines , 2012, PloS one.

[51]  W. Koh,et al.  Noninvasive in vivo monitoring of tissue-specific global gene expression in humans , 2014, Proceedings of the National Academy of Sciences.

[52]  Ash A. Alizadeh,et al.  An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage , 2013, Nature Medicine.

[53]  Nucleosome mapping in plasma DNA predicts cancer gene expression , 2016, Nature Genetics.

[54]  M. Stratton,et al.  The cancer genome , 2009, Nature.

[55]  J. Lötvall,et al.  Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells , 2007, Nature Cell Biology.

[56]  Giovanni Parmigiani,et al.  Half or more of the somatic mutations in cancers of self-renewing tissues originate prior to tumor initiation , 2013, Proceedings of the National Academy of Sciences.

[57]  M R Speicher,et al.  The biology of circulating tumor cells , 2016, Oncogene.

[58]  M. Ahn,et al.  Osimertinib or Platinum–Pemetrexed in EGFR T790M–Positive Lung Cancer , 2017, The New England journal of medicine.

[59]  Ash A. Alizadeh,et al.  Integrated digital error suppression for improved detection of circulating tumor DNA , 2016, Nature Biotechnology.

[60]  Klaus Pantel,et al.  [The circulating tumor cells: liquid biopsy of cancer]. , 2014, Klinicheskaia laboratornaia diagnostika.

[61]  L. Cope,et al.  Digital Karyotyping , 2012, Molecular Diagnosis & Therapy.

[62]  Peiyong Jiang,et al.  Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. , 2013, Clinical chemistry.

[63]  Sridhar Ramaswamy,et al.  Ex vivo culture of circulating breast tumor cells for individualized testing of drug susceptibility , 2014, Science.

[64]  Sridhar Ramaswamy,et al.  Circulating Tumor Cell Clusters Are Oligoclonal Precursors of Breast Cancer Metastasis , 2014, Cell.

[65]  W. Isaacs,et al.  AR-V7 and resistance to enzalutamide and abiraterone in prostate cancer. , 2014, The New England journal of medicine.

[66]  Y. Wang,et al.  Plasma extracellular RNA profiles in healthy and cancer patients , 2016, Scientific Reports.

[67]  Gema Moreno-Bueno,et al.  Melanoma exosomes educate bone marrow progenitor cells toward a pro-metastatic phenotype through MET , 2012, Nature Medicine.

[68]  Francisco M. De La Vega,et al.  Development of Personalized Tumor Biomarkers Using Massively Parallel Sequencing , 2010, Science Translational Medicine.

[69]  Hakho Lee,et al.  Label-free detection and molecular profiling of exosomes with a nano-plasmonic sensor , 2014, Nature Biotechnology.

[70]  A. Guha,et al.  Intercellular transfer of the oncogenic receptor EGFRvIII by microvesicles derived from tumour cells , 2008, Nature Cell Biology.

[71]  N. Rosenfeld,et al.  Noninvasive Identification and Monitoring of Cancer Mutations by Targeted Deep Sequencing of Plasma DNA , 2012, Science Translational Medicine.

[72]  Juergen A. Knoblich,et al.  Organogenesis in a dish: Modeling development and disease using organoid technologies , 2014, Science.

[73]  Peter Ulz,et al.  Whole-genome plasma sequencing reveals focal amplifications as a driving force in metastatic prostate cancer , 2016, Nature Communications.

[74]  Hans Clevers,et al.  Tissue-specific mutation accumulation in human adult stem cells during life , 2016, Nature.

[75]  L. Poon,et al.  Presence of fetal RNA in maternal plasma. , 2000, Clinical chemistry.

[76]  M. Lynch.  Evolution of the mutation rate. , 2010, Trends in genetics : TIG.

[77]  M. Olivier,et al.  Identification of Circulating Tumor DNA for the Early Detection of Small-cell Lung Cancer , 2016, EBioMedicine.

[78]  Jesse J. Salk,et al.  Detection of ultra-rare mutations by next-generation sequencing , 2012, Proceedings of the National Academy of Sciences.

[79]  Frank Diehl,et al.  Detection and quantification of mutations in the plasma of patients with colorectal tumors. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[80]  L. Diaz,et al.  Liquid biopsies: genotyping circulating tumor DNA. , 2014, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[81]  M. Stroun,et al.  Neoplastic characteristics of the DNA found in the plasma of cancer patients. , 1989, Oncology.

[82]  Hamid Cheshmi.  Glioblastoma microvesicles transport RNA and proteins that promote tumour growth and provide diagnostic biomarkers , 2011 .

[83]  K. Pantel,et al.  Challenges in circulating tumour cell research , 2014, Nature Reviews Cancer.

[84]  Karl Kashofer,et al.  Inferring expressed genes by whole-genome sequencing of plasma DNA , 2016, Nature Genetics.

[85]  E. Ma,et al.  Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments , 2015, Proceedings of the National Academy of Sciences.

[86]  Peter Ulz,et al.  Non‐invasive detection of genome‐wide somatic copy number alterations by liquid biopsies , 2016, Molecular oncology.

[87]  F. Demichelis,et al.  Tumor clone dynamics in lethal prostate cancer , 2014, Science Translational Medicine.

[88]  N. Navin.  Cancer genomics: one cell at a time , 2014, Genome Biology.

[89]  K. Kinzler,et al.  Cancer Genome Landscapes , 2013, Science.

[90]  G. Parmigiani,et al.  Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing , 2012, Science Translational Medicine.

[91]  Min Seong Kim,et al.  Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma , 2015, Scientific Reports.

[92]  F. O. Fackelmayer,et al.  DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells. , 2001, Cancer research.

[93]  N. McGranahan,et al.  Biological and therapeutic impact of intratumor heterogeneity in cancer evolution. , 2015, Cancer cell.

[94]  K. Kinzler,et al.  Evaluating the evaluation of cancer driver genes , 2016, Proceedings of the National Academy of Sciences.

[95]  Peter Ulz,et al.  Circulating tumor cells and DNA as liquid biopsies , 2013, Genome Medicine.

[96]  Bert Vogelstein,et al.  The Path to Cancer --Three Strikes and You're Out. , 2015, The New England journal of medicine.

[97]  S. Jeffrey,et al.  Enumeration and targeted analysis of KRAS, BRAF and PIK3CA mutations in CTCs captured by a label-free platform: Comparison to ctDNA and tissue in metastatic colorectal cancer , 2016, Oncotarget.

[98]  Enzo Medico,et al.  Emergence of KRAS mutations and acquired resistance to anti-EGFR therapy in colorectal cancer , 2012, Nature.

[99]  N. Rosenfeld,et al.  Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA , 2013, Nature.

[100]  Y. Hannun,et al.  Substantial contribution of extrinsic risk factors to cancer development , 2015, Nature.

[101]  H. Ribbert,et al.  Zur Frage der Entstehung maligner Tumoren , 1914, Naturwissenschaften.

[102]  Harry Hemingway,et al.  Health and population effects of rare gene knockouts in adult humans with related parents , 2015, Science.

[103]  Peter Ulz,et al.  The dynamic range of circulating tumor DNA in metastatic breast cancer , 2014, Breast Cancer Research.

[104]  Carlos Caldas,et al.  Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer , 2015, Nature Communications.

[105]  Sridhar Ramaswamy,et al.  RNA-Seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance , 2015, Science.

[106]  B. Vogelstein,et al.  Variation in cancer risk among tissues can be explained by the number of stem cell divisions , 2015, Science.

[107]  John W. Cassidy,et al.  A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds , 2016, Cell.