The challenge of intratumour heterogeneity in precision medicine

Cells within tumours have diverse genomes and epigenomes and interact differentially with their surrounding microenvironment generating intratumour heterogeneity, which has critical implications for treating cancer patients. Understanding the cellular and microenvironment composition and characteristics in individual tumours is critical to stratify the patient population that is likely to benefit from specific treatment regimens. Here, we will review the current understanding of intratumour heterogeneity at the genomic, epigenomic and microenvironmental levels. We will also discuss the clinical implications and the challenges posed by intratumour heterogeneity and evaluate noninvasive methods such as circulating biomarkers to characterize the cellular diversity of tumours. Comprehensive assessment of the molecular features of patients based on tumour specimen characterization (including intratumour spatial and temporal variations), ancillary noninvasive methods (such as circulating biomarkers and molecular imaging approaches) and the correct design of clinical trials are required to guide administration of targeted therapy and to control therapeutic resistance. Finding the means to accurately determine and effectively control tumour heterogeneity and translate these achievements into patient benefit are major goals in modern oncology.

[1]  Wei Yin,et al.  The Identification and Characterization of Breast Cancer CTCs Competent for Brain Metastasis , 2013, Science Translational Medicine.

[2]  C. Sautès-Fridman,et al.  The immune contexture in human tumours: impact on clinical outcome , 2012, Nature Reviews Cancer.

[3]  Jorge S Reis-Filho,et al.  Genetic heterogeneity and cancer drug resistance. , 2012, The Lancet. Oncology.

[4]  Fabrice Andre,et al.  Implications of personalized medicine—perspective from a cancer center , 2011, Nature Reviews Clinical Oncology.

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

[6]  Myles A Brown,et al.  PET imaging of oestrogen receptors in patients with breast cancer. , 2013, The Lancet. Oncology.

[7]  Carissa A. Sanchez,et al.  Genetic clonal diversity predicts progression to esophageal adenocarcinoma , 2006, Nature Genetics.

[8]  J. Baselga,et al.  TGF-β Receptor Inhibitors Target the CD44(high)/Id1(high) Glioma-Initiating Cell Population in Human Glioblastoma. , 2010, Cancer cell.

[9]  A. Børresen-Dale,et al.  The Life History of 21 Breast Cancers , 2012, Cell.

[10]  Razelle Kurzrock,et al.  Personalized Medicine in a Phase I Clinical Trials Program: The MD Anderson Cancer Center Initiative , 2012, Clinical Cancer Research.

[11]  F. Markowetz,et al.  The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups , 2012, Nature.

[12]  Napoleone Ferrara,et al.  Angiogenesis as a therapeutic target , 2005, Nature.

[13]  M. Shen,et al.  The roots of cancer: stem cells and the basis for tumor heterogeneity. , 2013, Bioessays.

[14]  Sean J Morrison,et al.  Cancer stem cells: impact, heterogeneity, and uncertainty. , 2012, Cancer cell.

[15]  P. Fortina,et al.  Circulating tumor DNA to monitor metastatic breast cancer. , 2013, The New England journal of medicine.

[16]  John Mendelsohn,et al.  WIN Consortium—challenges and advances , 2011, Nature Reviews Clinical Oncology.

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

[18]  Kikuya Kato,et al.  Intratumor heterogeneity of epidermal growth factor receptor mutations in lung cancer and its correlation to the response to gefitinib , 2008, Cancer science.

[19]  M. Nowak,et al.  Distant Metastasis Occurs Late during the Genetic Evolution of Pancreatic Cancer , 2010, Nature.

[20]  David García-Dorado,et al.  TGF-beta increases glioma-initiating cell self-renewal through the induction of LIF in human glioblastoma. , 2009, Cancer cell.

[21]  Dennis C. Sgroi,et al.  Stromal Fibroblasts Present in Invasive Human Breast Carcinomas Promote Tumor Growth and Angiogenesis through Elevated SDF-1/CXCL12 Secretion , 2005, Cell.

[22]  I. Fidler,et al.  Tumor heterogeneity and the biology of cancer invasion and metastasis. , 1978, Cancer research.

[23]  M. Junttila,et al.  Influence of tumour micro-environment heterogeneity on therapeutic response , 2013, Nature.

[24]  A. Iafrate,et al.  Identification of genotype-correlated sensitivity to selective kinase inhibitors by using high-throughput tumor cell line profiling , 2007, Proceedings of the National Academy of Sciences.

[25]  F. Nicolantonio,et al.  Liquid biopsy: monitoring cancer-genetics in the blood , 2013, Nature Reviews Clinical Oncology.

[26]  Kenny Q. Ye,et al.  Mapping copy number variation by population scale genome sequencing , 2010, Nature.

[27]  S. Stone-Elander,et al.  Radiolabelled receptor-tyrosine-kinase targeting drugs for patient stratification and monitoring of therapy response: prospects and pitfalls. , 2010, The Lancet. Oncology.

[28]  Joshua M. Korn,et al.  Comprehensive genomic characterization defines human glioblastoma genes and core pathways , 2008, Nature.

[29]  K. Polyak,et al.  Intra-tumour heterogeneity: a looking glass for cancer? , 2012, Nature Reviews Cancer.

[30]  J. Ross,et al.  The HER-2 receptor and breast cancer: ten years of targeted anti-HER-2 therapy and personalized medicine. , 2009, The oncologist.

[31]  M. Mazumdar,et al.  Intra- and Inter-Tumor Heterogeneity of BRAFV600EMutations in Primary and Metastatic Melanoma , 2012, PloS one.

[32]  L. Chung,et al.  Can Stroma Reaction Predict Cancer Lethality? , 2013, Clinical Cancer Research.

[33]  M. Berger,et al.  Establishing the origin of metastatic deposits in the setting of multiple primary malignancies: The role of massively parallel sequencing , 2014, Molecular Oncology.

[34]  Benjamin J. Raphael,et al.  Integrated Genomic Analyses of Ovarian Carcinoma , 2011, Nature.

[35]  I. Tannock,et al.  Drug resistance and the solid tumor microenvironment. , 2007, Journal of the National Cancer Institute.

[36]  Jeffrey W. Clark,et al.  Anaplastic lymphoma kinase inhibition in non-small-cell lung cancer. , 2010, The New England journal of medicine.

[37]  Edward S. Kim,et al.  The BATTLE trial: personalizing therapy for lung cancer. , 2011, Cancer discovery.

[38]  D. Schadendorf,et al.  Improved survival with ipilimumab in patients with metastatic melanoma. , 2010, The New England journal of medicine.

[39]  J. Baselga,et al.  Bringing precision medicine to the clinic: from genomic profiling to the power of clinical observation. , 2013, Annals of oncology : official journal of the European Society for Medical Oncology.

[40]  A Pilot Clinical Study of Treatment Guided by Personalized Tumorgrafts in Patients with Advanced Cancer , 2011, Molecular Cancer Therapeutics.

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

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

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

[44]  Serafim Batzoglou,et al.  Genome evolution during progression to breast cancer , 2013, Genome research.

[45]  S. Morrison,et al.  Heterogeneity in Cancer: Cancer Stem Cells versus Clonal Evolution , 2009, Cell.

[46]  A. Sivachenko,et al.  Sequence analysis of mutations and translocations across breast cancer subtypes , 2012, Nature.

[47]  Max S Wicha,et al.  Implications of the cancer stem-cell hypothesis for breast cancer prevention and therapy. , 2008, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[48]  Ali Bashashati,et al.  Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling , 2013, The Journal of pathology.

[49]  Lee T. Sam,et al.  Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study , 2011, Science Translational Medicine.

[50]  Steven J. M. Jones,et al.  Comprehensive molecular portraits of human breast tumors , 2012, Nature.

[51]  A. Børresen-Dale,et al.  The landscape of cancer genes and mutational processes in breast cancer , 2012, Nature.

[52]  V. P. Collins,et al.  Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics , 2013, Proceedings of the National Academy of Sciences.

[53]  Vincent Ferretti,et al.  Feasibility of real time next generation sequencing of cancer genes linked to drug response: Results from a clinical trial , 2013, International journal of cancer.

[54]  W. Isaacs,et al.  Tracking the clonal origin of lethal prostate cancer. , 2013, The Journal of clinical investigation.

[55]  S. Gabriel,et al.  Advances in understanding cancer genomes through second-generation sequencing , 2010, Nature Reviews Genetics.

[56]  Michael Bittner,et al.  Pilot study using molecular profiling of patients' tumors to find potential targets and select treatments for their refractory cancers. , 2010, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[57]  Jorge S. Reis-Filho,et al.  Circulating tumour cells and cell-free DNA as tools for managing breast cancer , 2013, Nature Reviews Clinical Oncology.

[58]  S A Forbes,et al.  The Catalogue of Somatic Mutations in Cancer (COSMIC) , 2008, Current protocols in human genetics.

[59]  N. McGranahan,et al.  The causes and consequences of genetic heterogeneity in cancer evolution , 2013, Nature.

[60]  J. Minna,et al.  Precision medicine for cancer patients: lessons learned and the path forward. , 2013, Journal of the National Cancer Institute.

[61]  Max S Wicha,et al.  Cancer stem cells: an old idea--a paradigm shift. , 2006, Cancer research.

[62]  Gary D Bader,et al.  International network of cancer genome projects , 2010, Nature.

[63]  Levi A Garraway,et al.  Precision oncology: an overview. , 2013, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[64]  A. Spradling,et al.  The stem cell niche: theme and variations. , 2004, Current opinion in cell biology.

[65]  N. Rosenfeld,et al.  Circulating tumor DNA to monitor metastatic breast cancer. , 2013, The New England journal of medicine.

[66]  J. Dick,et al.  Stem cell concepts renew cancer research. , 2008, Blood.

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

[68]  E. Fuchs,et al.  The harmonies played by TGF-β in stem cell biology. , 2012, Cell stem cell.

[69]  Mark J. Ratain,et al.  Tumour heterogeneity in the clinic , 2013, Nature.

[70]  C. Swanton Intratumor heterogeneity: evolution through space and time. , 2012, Cancer research.

[71]  Charles Swanton,et al.  Intratumor Heterogeneity: Seeing the Wood for the Trees , 2012, Science Translational Medicine.

[72]  A. Hauschild,et al.  Improved survival with vemurafenib in melanoma with BRAF V600E mutation. , 2011, The New England journal of medicine.

[73]  James L Tatum,et al.  Hypoxia: Importance in tumor biology, noninvasive measurement by imaging, and value of its measurement in the management of cancer therapy , 2006, International journal of radiation biology.

[74]  Chen-Hsiang Yeang,et al.  Impact of genetic dynamics and single-cell heterogeneity on development of nonstandard personalized medicine strategies for cancer , 2012, Proceedings of the National Academy of Sciences.

[75]  Davide Corà,et al.  A molecularly annotated platform of patient-derived xenografts ("xenopatients") identifies HER2 as an effective therapeutic target in cetuximab-resistant colorectal cancer. , 2011, Cancer discovery.

[76]  S. Scherer,et al.  Clonal Selection Drives Genetic Divergence of Metastatic Medulloblastoma , 2012, Nature.

[77]  D. Hayes,et al.  Circulating tumour cells: insights into tumour heterogeneity , 2013, Journal of internal medicine.

[78]  D. Berry,et al.  I‐SPY 2: An Adaptive Breast Cancer Trial Design in the Setting of Neoadjuvant Chemotherapy , 2009, Clinical pharmacology and therapeutics.

[79]  L. Liotta,et al.  Signal transduction for chemotaxis and haptotaxis by matrix molecules in tumor cells , 1990, The Journal of cell biology.

[80]  L. De Mattos-Arruda,et al.  Pilot studies for personalized cancer medicine: focusing on the patient for treatment selection. , 2013, The oncologist.

[81]  David T. W. Jones,et al.  Signatures of mutational processes in human cancer , 2013, Nature.

[82]  L. Coussens,et al.  Tumor stroma and regulation of cancer development. , 2006, Annual review of pathology.

[83]  C. de Lange Davies,et al.  Interstitial fluid pressure in human osteosarcoma xenografts: significance of implantation site and the response to intratumoral injection of hyaluronidase. , 2000, Anticancer research.

[84]  Steven J. M. Jones,et al.  Comprehensive molecular portraits of human breast tumours , 2013 .

[85]  Joe W. Gray,et al.  What are we learning from the cancer genome? , 2012, Nature Reviews Clinical Oncology.

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

[87]  D. Hanahan,et al.  Hallmarks of Cancer: The Next Generation , 2011, Cell.

[88]  R. Jain,et al.  Role of extracellular matrix assembly in interstitial transport in solid tumors. , 2000, Cancer research.

[89]  Aleix Prat Aparicio Comprehensive molecular portraits of human breast tumours , 2012 .

[90]  A. Ashworth,et al.  Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers. , 2009, The New England journal of medicine.

[91]  Irmtraud M. Meyer,et al.  The clonal and mutational evolution spectrum of primary triple-negative breast cancers , 2012, Nature.

[92]  N. Takakura Formation and regulation of the cancer stem cell niche , 2012, Cancer science.

[93]  J. Izbicki,et al.  Heterogeneity of epidermal growth factor receptor status and mutations of KRAS/PIK3CA in circulating tumor cells of patients with colorectal cancer. , 2013, Clinical chemistry.

[94]  Joshua F. McMichael,et al.  Genome Remodeling in a Basal-like Breast Cancer Metastasis and Xenograft , 2010, Nature.