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de Leng WWJ, Gadellaa-van Hooijdonk CG, Barendregt-Smouter FAS, Koudijs MJ, Nijman I, Hinrichs JWJ, Cuppen E, van Lieshout S, Loberg RD, de Jonge M, Voest EE, de Weger RA, Steeghs N, Langenberg MHG, Sleijfer S, Willems SM, Lolkema MP. Targeted Next Generation Sequencing as a Reliable Diagnostic Assay for the Detection of Somatic Mutations in Tumours Using Minimal DNA Amounts from Formalin Fixed Paraffin Embedded Material. PLoS One 2016; 11:e0149405. [PMID: 26919633 PMCID: PMC4769293 DOI: 10.1371/journal.pone.0149405] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 02/01/2016] [Indexed: 12/26/2022] Open
Abstract
Background Targeted Next Generation Sequencing (NGS) offers a way to implement testing of multiple genetic aberrations in diagnostic pathology practice, which is necessary for personalized cancer treatment. However, no standards regarding input material have been defined. This study therefore aimed to determine the effect of the type of input material (e.g. formalin fixed paraffin embedded (FFPE) versus fresh frozen (FF) tissue) on NGS derived results. Moreover, this study aimed to explore a standardized analysis pipeline to support consistent clinical decision-making. Method We used the Ion Torrent PGM sequencing platform in combination with the Ion AmpliSeq Cancer Hotspot Panel v2 to sequence frequently mutated regions in 50 cancer related genes, and validated the NGS detected variants in 250 FFPE samples using standard diagnostic assays. Next, 386 tumour samples were sequenced to explore the effect of input material on variant detection variables. For variant calling, Ion Torrent analysis software was supplemented with additional variant annotation and filtering. Results Both FFPE and FF tissue could be sequenced reliably with a sensitivity of 99.1%. Validation showed a 98.5% concordance between NGS and conventional sequencing techniques, where NGS provided both the advantage of low input DNA concentration and the detection of low-frequency variants. The reliability of mutation analysis could be further improved with manual inspection of sequence data. Conclusion Targeted NGS can be reliably implemented in cancer diagnostics using both FFPE and FF tissue when using appropriate analysis settings, even with low input DNA.
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Affiliation(s)
- Wendy W. J. de Leng
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Christa G. Gadellaa-van Hooijdonk
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Françoise A. S. Barendregt-Smouter
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Marco J. Koudijs
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Ies Nijman
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - John W. J. Hinrichs
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Edwin Cuppen
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Stef van Lieshout
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Robert D. Loberg
- Medical Sciences, Amgen Inc., Thousand Oaks, CA, 91320–1799, United States of America
| | - Maja de Jonge
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, 3075 EA Rotterdam, The Netherlands
| | - Emile E. Voest
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands
| | - Roel A. de Weger
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Neeltje Steeghs
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands
| | - Marlies H. G. Langenberg
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Stefan Sleijfer
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, 3075 EA Rotterdam, The Netherlands
| | - Stefan M. Willems
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
| | - Martijn P. Lolkema
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, 3075 EA Rotterdam, The Netherlands
- * E-mail:
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Han HS, Magliocco AM. Molecular Testing and the Pathologist's Role in Clinical Trials of Breast Cancer. Clin Breast Cancer 2016; 16:166-79. [PMID: 27103546 DOI: 10.1016/j.clbc.2016.02.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 01/11/2016] [Accepted: 02/03/2016] [Indexed: 01/26/2023]
Abstract
Molecular characterization of breast cancer is pivotal for identifying new molecular targets and determining the appropriate treatment choices. Advances in molecular profiling technology have given greater insight into this heterogeneous disease, over and above hormone receptor and human epidermal growth factor receptor 2 status. Agents targeting recently characterized molecular biomarkers are under clinical development; the success of these targeted agents is likely to depend on identifying the patient population most likely to benefit. Therefore, clinical trials of breast cancer often require prescreening for, or stratification by, relevant molecular markers or exploratory analyses of biomarkers that can predict or monitor the response to treatment. Consequently, the role of the pathologist has become increasingly important. The key considerations for pathologists include tissue availability, ownership of archival tissue, type of diagnostic/biomarker test required, method of sample processing, concordance between different tests and testing centers, and tumor heterogeneity. In the present review, we explore how pathology is used in current clinical trials of breast cancer and describe the various technologies available for molecular testing. Furthermore, the factors required for the successful application of pathology in clinical trials of breast cancer and the issues that can arise and how these can be circumvented are discussed.
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Affiliation(s)
- Hyo Sook Han
- Department of Women's Oncology, Moffitt Cancer Center, Tampa, FL
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153
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WITHDRAWN: Preanalytical and analytical considerations of circulating plasma tumor DNA for breast oncology. Comput Struct Biotechnol J 2016. [DOI: 10.1016/j.csbj.2016.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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155
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Jovelet C, Ileana E, Le Deley MC, Motté N, Rosellini S, Romero A, Lefebvre C, Pedrero M, Pata-Merci N, Droin N, Deloger M, Massard C, Hollebecque A, Ferté C, Boichard A, Postel-Vinay S, Ngo-Camus M, De Baere T, Vielh P, Scoazec JY, Vassal G, Eggermont A, André F, Soria JC, Lacroix L. Circulating Cell-Free Tumor DNA Analysis of 50 Genes by Next-Generation Sequencing in the Prospective MOSCATO Trial. Clin Cancer Res 2016; 22:2960-8. [DOI: 10.1158/1078-0432.ccr-15-2470] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/07/2015] [Indexed: 11/16/2022]
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156
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Tjensvoll K, Lapin M, Buhl T, Oltedal S, Steen-Ottosen Berry K, Gilje B, Søreide JA, Javle M, Nordgård O, Smaaland R. Clinical relevance of circulating KRAS mutated DNA in plasma from patients with advanced pancreatic cancer. Mol Oncol 2015; 10:635-43. [PMID: 26725968 DOI: 10.1016/j.molonc.2015.11.012] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/10/2015] [Accepted: 11/24/2015] [Indexed: 12/12/2022] Open
Abstract
We used KRAS mutations to investigate the clinical relevance of circulating tumor DNA (ctDNA) measurements in patients with advanced pancreatic cancer. Fifty-three blood samples were collected from 14 prospectively recruited patients prior to chemotherapy (gemcitabine or FOLFIRINOX) and subsequently every month during treatment. Samples were processed by density centrifugation and plasma DNA isolation. A Peptide-nucleic acid-clamp PCR was then used to detect KRAS mutations (present in >90% of pancreatic cancers) as a surrogate marker for ctDNA. Plasma samples from 29 healthy individuals were analyzed as a reference group. Results were compared to conventional monitoring measures and survival data. Median follow-up time was 3.7 months (range 0.6-12.9 months). Ten (71%) patients had a positive KRAS status in the plasma samples obtained prior to chemotherapy, indicating the presence of ctDNA. Among the patients who were ctDNA-positive before chemotherapy, nine (90%) experienced disease progression during follow-up, compared to one (25%) of four ctDNA-negative patients (P = 0.01). The pre-therapy ctDNA level was a statistically significant predictor of both progression-free and overall survival (P = 0.014 and 0.010, respectively). Of the 14 patients, ten had ≥2 follow-up samples; in several of these patients, the ctDNA level changed substantially during the course of chemotherapy. Changes in ctDNA levels corresponded both with radiological follow-up data and CA19-9 levels for several patients. This pilot study supports the hypothesis that ctDNA may be used as a marker for monitoring treatment efficacy and disease progression in pancreatic cancer patients. Recruitment of more patients is ongoing to corroborate these findings.
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Affiliation(s)
- Kjersti Tjensvoll
- Department of Haematology and Oncology, Stavanger University Hospital, N-4068 Stavanger, Norway; Laboratory for Molecular Biology, Stavanger University Hospital, N-4068 Stavanger, Norway.
| | - Morten Lapin
- Laboratory for Molecular Biology, Stavanger University Hospital, N-4068 Stavanger, Norway
| | - Tove Buhl
- Department of Haematology and Oncology, Stavanger University Hospital, N-4068 Stavanger, Norway
| | - Satu Oltedal
- Department of Haematology and Oncology, Stavanger University Hospital, N-4068 Stavanger, Norway; Laboratory for Molecular Biology, Stavanger University Hospital, N-4068 Stavanger, Norway
| | | | - Bjørnar Gilje
- Department of Haematology and Oncology, Stavanger University Hospital, N-4068 Stavanger, Norway
| | - Jon Arne Søreide
- Department of Gastrointestinal Surgery, Stavanger University Hospital, N-4068 Stavanger, Norway; Department of Clinical Medicine, University of Bergen, N-5021 Bergen, Norway
| | - Millind Javle
- Department of Gastrointestinal (GI) Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Oddmund Nordgård
- Department of Haematology and Oncology, Stavanger University Hospital, N-4068 Stavanger, Norway; Laboratory for Molecular Biology, Stavanger University Hospital, N-4068 Stavanger, Norway
| | - Rune Smaaland
- Department of Haematology and Oncology, Stavanger University Hospital, N-4068 Stavanger, Norway
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Liang DH, Ensor JE, Liu ZB, Patel A, Patel TA, Chang JC, Rodriguez AA. Cell-free DNA as a molecular tool for monitoring disease progression and response to therapy in breast cancer patients. Breast Cancer Res Treat 2015; 155:139-49. [PMID: 26667234 DOI: 10.1007/s10549-015-3635-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 02/07/2023]
Abstract
Due to the spatial and temporal genomic heterogeneity of breast cancer, genomic sequencing obtained from a single biopsy may not capture the complete genomic profile of tumors. Thus, we propose that cell-free DNA (cfDNA) in plasma may be an alternate source of genomic information to provide comprehensive data throughout a patient's clinical course. We performed a retrospective chart review of 100 patients with stage 4 or high-risk stage 3 breast cancer. The degree of agreement between genomic alterations found in tumor DNA (tDNA) and cfDNA was determined by Cohen's Kappa. Clinical disease progression was compared to mutant allele frequency using a two-sided Fisher's exact test. The presence of mutations and mutant allele frequency was correlated with progression-free survival (PFS) using a Cox proportional hazards model and a log-rank test. The most commonly found genomic alterations were mutations in TP53 and PIK3CA, and amplification of EGFR and ERBB2. PIK3CA mutation and ERBB2 amplification demonstrated robust agreement between tDNA and cfDNA (Cohen's kappa = 0.64 and 0.77, respectively). TP53 mutation and EGFR amplification demonstrated poor agreement between tDNA and cfDNA (Cohen's kappa = 0.18 and 0.33, respectively). The directional changes of TP53 and PIK3CA mutant allele frequency were closely associated with response to therapy (p = 0.002). The presence of TP53 mutation (p = 0.0004) and PIK3CA mutant allele frequency [p = 0.01, HR 1.074 (95 % CI 1.018-1.134)] was excellent predictors of PFS. Identification of selected cancer-specific genomic alterations from cfDNA may be a noninvasive way to monitor disease progression, predict PFS, and offer targeted therapy.
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Affiliation(s)
- Diana H Liang
- Department of Surgery, Houston Methodist Hospital, 6550 Fannin St, Smith Tower 1661, Houston, TX, 77030, USA
- Houston Methodist Research Institute, Houston Methodist Hospital, 6670 Bertner Ave., Houston, TX, 77030, USA
| | - Joe E Ensor
- Houston Methodist Research Institute, Houston Methodist Hospital, 6670 Bertner Ave., Houston, TX, 77030, USA
- Houston Methodist Cancer Center, 6445 Main Street OPC 24, Houston, TX, 77030, USA
| | - Zhe-Bin Liu
- Houston Methodist Research Institute, Houston Methodist Hospital, 6670 Bertner Ave., Houston, TX, 77030, USA
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 20032, China
| | - Asmita Patel
- Houston Methodist Cancer Center, 6445 Main Street OPC 24, Houston, TX, 77030, USA
| | - Tejal A Patel
- Houston Methodist Cancer Center, 6445 Main Street OPC 24, Houston, TX, 77030, USA
| | - Jenny C Chang
- Houston Methodist Cancer Center, 6445 Main Street OPC 24, Houston, TX, 77030, USA
| | - Angel A Rodriguez
- Houston Methodist Cancer Center, 6445 Main Street OPC 24, Houston, TX, 77030, USA.
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Lambrechts S, Smeets D, Moisse M, Braicu EI, Vanderstichele A, Zhao H, Van Nieuwenhuysen E, Berns E, Sehouli J, Zeillinger R, Darb-Esfahani S, Cacsire Castillo-Tong D, Lambrechts D, Vergote I. Genetic heterogeneity after first-line chemotherapy in high-grade serous ovarian cancer. Eur J Cancer 2015; 53:51-64. [PMID: 26693899 DOI: 10.1016/j.ejca.2015.11.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/02/2015] [Indexed: 12/23/2022]
Abstract
BACKGROUND Most high-grade serous ovarian carcinoma (HGSOC) patients benefit from first-line platinum-based chemotherapy, but progressively develop resistance during subsequent lines. Re-activating BRCA1 or MDR1 mutations can underlie platinum resistance in end-stage patients. However, little is known about resistance mechanisms occurring after a single line of platinum, when patients still qualify for other treatments. METHODS In 31 patients with primary platinum-sensitive HGSOC, we profiled tumours collected during debulking surgery before and after first-line chemotherapy using whole-exome sequencing and single nucleotide polymorphism profiling. RESULTS Besides germline BRCA1/2 mutations, we observed frequent loss-of-heterozygosity in homologous recombination (HR) genes and mutation spectra characteristic of HR-deficiency in all tumours. At relapse, tumours differed considerably from their primary counterparts. There was, however, no evidence of events reactivating the HR pathway, also not in tumours resistant to second-line platinum. Instead, a platinum score of 13 copy number regions, among other genes including MECOM, CCNE1 and ERBB2, correlated with platinum-free interval (PFI) after first-line therapy, whereas an increase of this score in recurrent tumours predicted the change in PFI during subsequent therapy. CONCLUSIONS Already after a single line of platinum, there is huge variability between primary and recurrent tumours, advocating that in HGSOC biopsies need to be collected at relapse to tailor treatment options to the underlying genetic profile. Nevertheless, all primary platinum-sensitive HGSOCs remained HR-deficient, irrespective of whether they became resistant to second-line platinum, further suggesting these tumours qualify for second-line Poly APD ribose polymerase (PARP) inhibitor treatment. Finally, chromosomal instability contributes to acquired resistance after a single line of platinum therapy.
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Affiliation(s)
- Sandrina Lambrechts
- Division of Gynecological Oncology, Leuven Cancer Institute, Department of Gynaecology and Obstetrics, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Dominiek Smeets
- Laboratory for Translational Genetics, Vesalius Research Center, VIB, Leuven, Herestraat 49, 3000 Leuven, Belgium; Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Matthieu Moisse
- Laboratory for Translational Genetics, Vesalius Research Center, VIB, Leuven, Herestraat 49, 3000 Leuven, Belgium; Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Elena Ioana Braicu
- Department of Gynecology and Obstetrics, European Competence Center for Ovarian Cancer, Charité-University Medicine of Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Adriaan Vanderstichele
- Division of Gynecological Oncology, Leuven Cancer Institute, Department of Gynaecology and Obstetrics, KU Leuven, Herestraat 49, 3000 Leuven, Belgium; Laboratory for Translational Genetics, Vesalius Research Center, VIB, Leuven, Herestraat 49, 3000 Leuven, Belgium; Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Hui Zhao
- Laboratory for Translational Genetics, Vesalius Research Center, VIB, Leuven, Herestraat 49, 3000 Leuven, Belgium; Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Els Van Nieuwenhuysen
- Division of Gynecological Oncology, Leuven Cancer Institute, Department of Gynaecology and Obstetrics, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Els Berns
- Erasmus MC, Cancer Institute, Department Medical Oncology, s-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - Jalid Sehouli
- Department of Gynecology and Obstetrics, European Competence Center for Ovarian Cancer, Charité-University Medicine of Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Robert Zeillinger
- Department of Obstetrics and Gynecology, Molecular Oncology Group, Comprehensive Cancer Center, Gynecologic Cancer Unit, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
| | - Silvia Darb-Esfahani
- Department of Gynecology and Obstetrics, European Competence Center for Ovarian Cancer, Charité-University Medicine of Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Dan Cacsire Castillo-Tong
- Erasmus MC, Cancer Institute, Department Medical Oncology, s-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Vesalius Research Center, VIB, Leuven, Herestraat 49, 3000 Leuven, Belgium; Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven, Herestraat 49, 3000 Leuven, Belgium.
| | - Ignace Vergote
- Division of Gynecological Oncology, Leuven Cancer Institute, Department of Gynaecology and Obstetrics, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
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Saliou A, Bidard FC, Lantz O, Stern MH, Vincent-Salomon A, Proudhon C, Pierga JY. Circulating tumor DNA for triple-negative breast cancer diagnosis and treatment decisions. Expert Rev Mol Diagn 2015; 16:39-50. [DOI: 10.1586/14737159.2016.1121100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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160
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Clinical utility of circulating tumor DNA in human cancers. MEMO - MAGAZINE OF EUROPEAN MEDICAL ONCOLOGY 2015. [DOI: 10.1007/s12254-015-0217-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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161
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Aarthy R, Mani S, Velusami S, Sundarsingh S, Rajkumar T. Role of Circulating Cell-Free DNA in Cancers. Mol Diagn Ther 2015; 19:339-50. [PMID: 26400814 DOI: 10.1007/s40291-015-0167-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Liquid biopsy is a term used to describe non-invasive tests, which provide information about disease conditions through analysis of circulating cell-free DNA and circulating tumor cells from peripheral blood samples. In patients with cancer, the concentration of cell-free DNA increases, and structural, sequence, and epigenetic changes to DNA can be observed through the disease process and during therapy. Furthermore, cell-free DNA released by the tumor contains the same variants as those in the tumor cells. Therefore, cell-free DNA allows non-invasive assessment of cancer in real time. This review summarizes the origin of cell-free DNA, recent advancements in the detection of cell-free DNA, a possible role in metastasis, and its importance as a non-invasive diagnostic assay for cancer.
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Affiliation(s)
- Raghu Aarthy
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India
| | - Samson Mani
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India
| | - Sridevi Velusami
- Department of Surgical Oncology, Cancer Institute (WIA), Chennai, India
| | | | - Thangarajan Rajkumar
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India.
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Polivka J, Pesta M, Janku F. Testing for oncogenic molecular aberrations in cell-free DNA-based liquid biopsies in the clinic: are we there yet? Expert Rev Mol Diagn 2015; 15:1631-44. [PMID: 26559503 DOI: 10.1586/14737159.2015.1110021] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The optimal choice of cancer therapy depends upon analysis of the tumor genome for druggable molecular alterations. The spatial and temporal intratumor heterogeneity of cancers creates substantial challenges, as molecular profile depends on time and site of tumor tissue collection. To capture the entire molecular profile, multiple biopsies from primary and metastatic sites at different time points would be required, which is not feasible for ethical or economic reasons. Molecular analysis of circulating cell-free DNA offers a novel, minimally invasive method that can be performed at multiple time-points and plausibly better represents the prevailing molecular profile of the cancer. Molecular analysis of this cell-free DNA offers multiple clinically useful applications, such as identification of molecular targets for cancer therapy, monitoring of tumor molecular profile in real time, detection of emerging molecular aberrations associated with resistance to particular therapy, determination of cancer prognosis and diagnosis of cancer recurrence or progression.
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Affiliation(s)
- Jiri Polivka
- a Department of Histology and Embryology and Biomedical Centre, Faculty of Medicine in Plzen , Charles University in Prague , Plzen , Czech Republic.,b Department of Neurology , Faculty Hospital Plzen , Plzen , Czech Republic
| | - Martin Pesta
- c Department of Biology, Faculty of Medicine in Plzen , Charles University in Prague , Plzen , Czech Republic
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Wang P, Bahreini A, Gyanchandani R, Lucas PC, Hartmaier RJ, Watters RJ, Jonnalagadda AR, Trejo Bittar HE, Berg A, Hamilton RL, Kurland BF, Weiss KR, Mathew A, Leone JP, Davidson NE, Nikiforova MN, Brufsky AM, Ambros TF, Stern AM, Puhalla SL, Lee AV, Oesterreich S. Sensitive Detection of Mono- and Polyclonal ESR1 Mutations in Primary Tumors, Metastatic Lesions, and Cell-Free DNA of Breast Cancer Patients. Clin Cancer Res 2015; 22:1130-7. [PMID: 26500237 DOI: 10.1158/1078-0432.ccr-15-1534] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 10/07/2015] [Indexed: 12/21/2022]
Abstract
PURPOSE Given the clinical relevance of ESR1 mutations as potential drivers of resistance to endocrine therapy, this study used sensitive detection methods to determine the frequency of ESR1 mutations in primary and metastatic breast cancer, and in cell-free DNA (cfDNA). EXPERIMENTAL DESIGN Six ESR1 mutations (K303R, S463P, Y537C, Y537N, Y537S, D538G) were assessed by digital droplet PCR (ddPCR), with lower limits of detection of 0.05% to 0.16%, in primary tumors (n = 43), bone (n = 12) and brain metastases (n = 38), and cfDNA (n = 29). Correlations between ESR1 mutations in metastatic lesions and single (1 patient) or serial blood draws (4 patients) were assessed. RESULTS ESR1 mutations were detected for D538G (n = 13), Y537S (n = 3), and Y537C (n = 1), and not for K303R, S463P, or Y537N. Mutation rates were 7.0% (3/43 primary tumors), 9.1% (1/11 bone metastases), 12.5% (3/24 brain metastases), and 24.1% (7/29 cfDNA). Two patients showed polyclonal disease with more than one ESR1 mutation. Mutation allele frequencies were 0.07% to 0.2% in primary tumors, 1.4% in bone metastases, 34.3% to 44.9% in brain metastases, and 0.2% to 13.7% in cfDNA. In cases with both cfDNA and metastatic samples (n = 5), mutations were detected in both (n = 3) or in cfDNA only (n = 2). Treatment was associated with changes in ESR1 mutation detection and allele frequency. CONCLUSIONS ESR1 mutations were detected at very low allele frequencies in some primary breast cancers, and at high allele frequency in metastases, suggesting that in some tumors rare ESR1-mutant clones are enriched by endocrine therapy. Further studies should address whether sensitive detection of ESR1 mutations in primary breast cancer and in serial blood draws may be predictive for development of resistant disease. See related commentary by Gu and Fuqua, p. 1034.
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Affiliation(s)
- Peilu Wang
- School of Medicine, Tsinghua University, Beijing, People's Republic of China. Womens Cancer Research Center, Magee-Women Research Institute, Pittsburgh, Pennsylvania
| | - Amir Bahreini
- Womens Cancer Research Center, Magee-Women Research Institute, Pittsburgh, Pennsylvania. Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rekha Gyanchandani
- Womens Cancer Research Center, Magee-Women Research Institute, Pittsburgh, Pennsylvania. Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Peter C Lucas
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ryan J Hartmaier
- Womens Cancer Research Center, Magee-Women Research Institute, Pittsburgh, Pennsylvania. Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rebecca J Watters
- Womens Cancer Research Center, Magee-Women Research Institute, Pittsburgh, Pennsylvania. Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Amruth R Jonnalagadda
- Womens Cancer Research Center, Magee-Women Research Institute, Pittsburgh, Pennsylvania
| | | | - Aaron Berg
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ronald L Hamilton
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Brenda F Kurland
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kurt R Weiss
- Department of Orthopedic Surgery, University of Pittsburgh Medical Center (UPMC) Pittsburgh, Pittsburgh, Pennsylvania
| | - Aju Mathew
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh Cancer Institute and UPMC Cancer Center, Pittsburgh, Pennsylvania
| | - Jose Pablo Leone
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh Cancer Institute and UPMC Cancer Center, Pittsburgh, Pennsylvania
| | - Nancy E Davidson
- Womens Cancer Research Center, Magee-Women Research Institute, Pittsburgh, Pennsylvania. Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh Cancer Institute and UPMC Cancer Center, Pittsburgh, Pennsylvania
| | | | - Adam M Brufsky
- Womens Cancer Research Center, Magee-Women Research Institute, Pittsburgh, Pennsylvania. Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh Cancer Institute and UPMC Cancer Center, Pittsburgh, Pennsylvania
| | - Tadeu F Ambros
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh Cancer Institute and UPMC Cancer Center, Pittsburgh, Pennsylvania
| | - Andrew M Stern
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Shannon L Puhalla
- Womens Cancer Research Center, Magee-Women Research Institute, Pittsburgh, Pennsylvania. Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh Cancer Institute and UPMC Cancer Center, Pittsburgh, Pennsylvania
| | - Adrian V Lee
- Womens Cancer Research Center, Magee-Women Research Institute, Pittsburgh, Pennsylvania. Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania. Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.
| | - Steffi Oesterreich
- Womens Cancer Research Center, Magee-Women Research Institute, Pittsburgh, Pennsylvania. Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.
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164
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Abstract
As the release of tumor-associated DNA into blood circulation is a common event in patients with cancer, screening of plasma or serum DNA may provide information on genetic and epigenetic profiles associated with breast cancer development, progression, and response to therapy. Quantitative testing of circulating DNA can reflect tumor burden, and molecular characterization of circulating DNA can reveal important tumor characteristics relevant to the choice of targeted therapies in individual patients. Contrary to circulating DNA from blood that presents molecular changes in tumor DNA in real time, tissue biopsies can deliver only a spatially and temporally limited snapshot of the heterogeneous tumor. Analyses of circulating DNA might provide prognostic and predictive information and therefore advance personalized medicine. However, standardization of different technical platforms as well as the control of pre-analytical and analytical factors is mandatory before its introduction into clinical practice. In the present review, we discussed technical aspects and clinical relevance of the analyses of circulating plasma/serum DNA in patients with breast cancer.
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Affiliation(s)
- Heidi Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraβe 52, 20246, Hamburg, Germany
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraβe 52, 20246, Hamburg, Germany.
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165
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Kimbung S, Loman N, Hedenfalk I. Clinical and molecular complexity of breast cancer metastases. Semin Cancer Biol 2015; 35:85-95. [PMID: 26319607 DOI: 10.1016/j.semcancer.2015.08.009] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/17/2015] [Accepted: 08/21/2015] [Indexed: 12/24/2022]
Abstract
Clinical oncology is advancing toward a more personalized treatment orientation, making the need to understand the biology of metastasis increasingly acute. Dissecting the complex molecular, genetic and clinical phenotypes underlying the processes involved in the development of metastatic disease, which remains the principal cause of cancer-related deaths, could lead to the identification of more effective prognostication and targeted approaches to prevent and treat metastases. The past decade has witnessed significant progress in the field of cancer metastasis research. Clinical and technological milestones have been reached which have tremendously enriched our understanding of the complex pathways undertaken by primary tumors to progress into lethal metastases and how some of these processes might be amenable to therapy. The aim of this review article is to highlight the recent advances toward unraveling the clinical and molecular complexity of breast cancer metastases. We focus on genes mediating breast cancer metastases and organ-specific tropism, and discuss gene signatures for prediction of metastatic disease. The challenges of translating this information into clinically applicable tools for improving the prognostication of the metastatic potential of a primary breast tumor, as well as for therapeutic interventions against latent and active metastatic disease are addressed.
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Affiliation(s)
- Siker Kimbung
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden; CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Niklas Loman
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden; Department of Oncology, Skåne University Hospital, Lund/Malmö, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden; CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden.
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166
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Characterization of RNA from Exosomes and Other Extracellular Vesicles Isolated by a Novel Spin Column-Based Method. PLoS One 2015; 10:e0136133. [PMID: 26317354 PMCID: PMC4552735 DOI: 10.1371/journal.pone.0136133] [Citation(s) in RCA: 257] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/31/2015] [Indexed: 12/24/2022] Open
Abstract
Exosomes and other extracellular vesicles (commonly referred to as EVs) have generated a lot of attention for their potential applications in both diagnostics and therapeutics. The contents of these vesicles are the subject of intense research, and the relatively recent discovery of RNA inside EVs has raised interest in the biological function of these RNAs as well as their potential as biomarkers for cancer and other diseases. Traditional ultracentrifugation-based protocols to isolate EVs are labor-intensive and subject to significant variability. Various attempts to develop methods with robust, reproducible performance have not yet been completely successful. Here, we report the development and characterization of a spin column-based method for the isolation of total RNA from EVs in serum and plasma. This method isolates highly pure RNA of equal or higher quantity compared to ultracentrifugation, with high specificity for vesicular over non-vesicular RNA. The spin columns have a capacity to handle up to 4 mL sample volume, enabling detection of low-abundance transcripts in serum and plasma. We conclude that the method is an improvement over traditional methods in providing a faster, more standardized way to achieve reliable high quality RNA preparations from EVs in biofluids such as serum and plasma. The first kit utilizing this new method has recently been made available by Qiagen as “exoRNeasy Serum/Plasma Maxi Kit”.
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167
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Evaluation of targeted therapies in advanced breast cancer: the need for large-scale molecular screening and transformative clinical trial designs. Oncogene 2015; 35:1743-9. [PMID: 26119941 DOI: 10.1038/onc.2015.249] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 04/13/2015] [Accepted: 04/13/2015] [Indexed: 12/15/2022]
Abstract
Breast cancer (BC) has been classified into four intrinsic subtypes through seminal studies employing gene expression profiling analysis of primary tumours, namely the luminal A and B subtypes, the human epidermal growth factor receptor 2-like subtype and the basal-like subtype. More recently, the emergence of high-throughput genomic sequencing techniques, such as next-generation or massive parallel sequencing has expanded our understanding of the complex genomic landscapes of BC, with marked intertumour heterogeneity seen among different patients. In addition, increasing evidence indicates intratumour heterogeneity, with molecular differences observed within one patient, both spatially and longitudinally. These phenomena have an impact on the clinical development of molecularly targeted agents, with the classical paradigm of population-based clinical trials being no longer efficient. In the era of genomically driven oncology, three complementary tools can accelerate the clinical development of targeted agents for advanced BC as follows: (i) the implementation of molecular profiling of metastatic tumour lesions, as exemplified by the AURORA (Aiming to Understand the Molecular Aberrations in Metastatic Breast Cancer) programme; (ii) serial assessments of circulating tumour DNA, allowing a more thorough molecular interrogation of metastatic tumour burden; and (iii) new innovative clinical trial designs able to address the challenges of the increasing molecular fragmentation of BC.
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168
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Francis G, Stein S. Circulating Cell-Free Tumour DNA in the Management of Cancer. Int J Mol Sci 2015; 16:14122-42. [PMID: 26101870 PMCID: PMC4490543 DOI: 10.3390/ijms160614122] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 04/23/2015] [Accepted: 05/26/2015] [Indexed: 12/22/2022] Open
Abstract
With the development of new sensitive molecular techniques, circulating cell-free tumour DNA containing mutations can be identified in the plasma of cancer patients. The applications of this technology may result in significant changes to the care and management of cancer patients. Whilst, currently, these "liquid biopsies" are used to supplement the histological diagnosis of cancer and metastatic disease, in the future these assays may replace the need for invasive procedures. Applications include the monitoring of tumour burden, the monitoring of minimal residual disease, monitoring of tumour heterogeneity, monitoring of molecular resistance and early diagnosis of tumours and metastatic disease.
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Affiliation(s)
- Glenn Francis
- Director Pathology, Genomics for Life, Herston 4006, Australia.
- School of Medicine, Griffith University, Gold Coast 4215, Australia.
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia 4067, Australia.
| | - Sandra Stein
- Laboratory Director, Genomics for Life, Herston 4006, Australia.
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169
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Sefrioui D, Perdrix A, Sarafan-Vasseur N, Dolfus C, Dujon A, Picquenot JM, Delacour J, Cornic M, Bohers E, Leheurteur M, Rigal O, Tennevet I, Thery JC, Alexandru C, Guillemet C, Moldovan C, Veyret C, Frebourg T, Di Fiore F, Clatot F. Short report: Monitoring ESR1 mutations by circulating tumor DNA in aromatase inhibitor resistant metastatic breast cancer. Int J Cancer 2015; 137:2513-9. [PMID: 25994408 DOI: 10.1002/ijc.29612] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 05/07/2015] [Indexed: 12/29/2022]
Abstract
Acquired estrogen receptor gene (ESR1) mutations have been recently reported as a marker of resistance to aromatase inhibitors in hormone receptor positive metastatic breast cancer. We retrospectively considered seven patients treated for metastatic breast cancer with available samples from the primary tumor before any treatment, cryopreserved metastasis removed during progression and concomitant plasmas. All these seven patients were in disease progression after previous exposure to aromatase inhibitors for at least 6 months, and were assessed for ESR1 mutations detection in tumor and circulating DNA. For these patients, Sanger sequencing identified four metastases with clear ESR1 mutation and one possible, whereas digital PCR identified six mutated metastases. Then, under blind conditions and using digital PCR, corresponding circulating ESR1 mutations were successfully detected in four of these six metastatic breast cancer patients. Moreover, in two patients with serial blood samples following treatments exposure, the monitoring of circulating ESR1 mutations clearly predicted disease evolution. In the context of high interest for ESR1 mutations, our results highlight that these acquired recurrent mutations may be tracked in circulating tumor DNA and may be of clinical relevance for metastatic breast cancer patient monitoring.
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Affiliation(s)
- David Sefrioui
- INSERM U1079, Rouen, France.,Department of Gastroenterology, Rouen University Hospital, Rouen, France.,Equipe De Recherche En Oncologie (IRON), Rouen University Hospital and Centre Henri Becquerel, Rouen, France
| | - Anne Perdrix
- Equipe De Recherche En Oncologie (IRON), Rouen University Hospital and Centre Henri Becquerel, Rouen, France.,Department of Bio-Pathology, Centre Henri Becquerel, Rouen, France
| | - Nasrin Sarafan-Vasseur
- INSERM U1079, Rouen, France.,Equipe De Recherche En Oncologie (IRON), Rouen University Hospital and Centre Henri Becquerel, Rouen, France
| | - Claire Dolfus
- Equipe De Recherche En Oncologie (IRON), Rouen University Hospital and Centre Henri Becquerel, Rouen, France.,Department of Pathology, Rouen University Hospital, Rouen, France
| | - Antoine Dujon
- Department of Surgery, Clinique Du Cèdre, Bois-Guillaume, France
| | - Jean-Michel Picquenot
- Department of Bio-Pathology, Centre Henri Becquerel, Rouen, France.,INSERM U918, Centre Henri Becquerel, Rouen, France
| | - Julien Delacour
- INSERM U1079, Rouen, France.,Equipe De Recherche En Oncologie (IRON), Rouen University Hospital and Centre Henri Becquerel, Rouen, France
| | - Marie Cornic
- Department of Bio-Pathology, Centre Henri Becquerel, Rouen, France
| | | | | | - Olivier Rigal
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France
| | - Isabelle Tennevet
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France
| | - Jean-Christophe Thery
- Equipe De Recherche En Oncologie (IRON), Rouen University Hospital and Centre Henri Becquerel, Rouen, France.,Department of Medical Oncology, Centre Henri Becquerel, Rouen, France
| | | | - Cécile Guillemet
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France
| | - Cristian Moldovan
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France
| | - Corinne Veyret
- Department of Medical Oncology, Centre Henri Becquerel, Rouen, France
| | | | - Frédéric Di Fiore
- INSERM U1079, Rouen, France.,Department of Gastroenterology, Rouen University Hospital, Rouen, France.,Equipe De Recherche En Oncologie (IRON), Rouen University Hospital and Centre Henri Becquerel, Rouen, France.,Department of Medical Oncology, Centre Henri Becquerel, Rouen, France
| | - Florian Clatot
- Equipe De Recherche En Oncologie (IRON), Rouen University Hospital and Centre Henri Becquerel, Rouen, France.,INSERM U918, Centre Henri Becquerel, Rouen, France.,Department of Medical Oncology, Centre Henri Becquerel, Rouen, France
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170
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Di Paolo A, Polillo M, Lastella M, Bocci G, Del Re M, Danesi R. Methods: for studying pharmacogenetic profiles of combination chemotherapeutic drugs. Expert Opin Drug Metab Toxicol 2015; 11:1253-67. [PMID: 26037261 DOI: 10.1517/17425255.2015.1053460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
INTRODUCTION Molecular and genetic analysis of tumors and individuals has led to patient-centered therapies, through the discovery and identification of genetic markers predictive of drug efficacy and tolerability. Present therapies often include a combination of synergic drugs, each of them directed against different targets. Therefore, the pharmacogenetic profiling of tumor masses and patients is becoming a challenge, and several questions may arise when planning a translational study. AREAS COVERED The review presents the different techniques used to stratify oncology patients and to tailor antineoplastic treatments according to individual pharmacogenetic profiling. The advantages of these methodologies are discussed as well as current limits. EXPERT OPINION Facing the rapid technological evolution for genetic analyses, the most pressing issues are the choice of appropriate strategies (i.e., from gene candidate up to next-generation sequencing) and the possibility to replicate study results for their final validation. It is likely that the latter will be the major obstacle in the future. However, the present landscape is opening up new possibilities, overcoming those hurdles that have limited result translation into clinical settings for years.
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Affiliation(s)
- Antonello Di Paolo
- University of Pisa, Department of Clinical and Experimental Medicine, Via Roma 55, 56126 Pisa , Italy +39 050 2218755 ; +39 050 2218758 ;
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171
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Patel KM, Tsui DWY. The translational potential of circulating tumour DNA in oncology. Clin Biochem 2015; 48:957-61. [PMID: 25889059 DOI: 10.1016/j.clinbiochem.2015.04.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 04/02/2015] [Accepted: 04/03/2015] [Indexed: 02/05/2023]
Abstract
The recent understanding of tumour heterogeneity and cancer evolution in response to therapy has raised questions about the value of historical or single site biopsies for guiding treatment decisions. The ability of ctDNA analysis to reveal de novo mutations (i.e., without prior knowledge), allows monitoring of clonal heterogeneity without the need for multiple tumour biopsies. Additionally, ctDNA monitoring of such heterogeneity and novel mutation detection will allow clinicians to detect resistant mechanisms early and tailor treatment therapies accordingly. If ctDNA can be used to detect low volume cancerous states, it will have important applications in treatment stratification post-surgery/radical radiotherapy and may have a role in patient screening. Mutant cfDNA can also be detected in other bodily fluids that are easily accessible and may aid detection of rare mutant alleles in certain cancer types. This article outlines recent advances in these areas.
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Affiliation(s)
- K M Patel
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; Department of Academic Urology, University of Cambridge Hospitals, Box 243, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - D W Y Tsui
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
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172
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Abstract
Advances in next-generation sequencing and bioinformatics have led to an unprecedented view of the cancer genome and its evolution. Genomic studies have demonstrated the complex and heterogeneous clonal landscape of tumors of different origins and the potential impact of intratumor heterogeneity on treatment response and resistance, cancer progression, and the risk of disease relapse. However, the significance of subclonal mutations, in particular mutations in driver genes, and their evolution through time and their dynamics in response to cancer therapies, is yet to be determined. The necessary tools are now available to prospectively determine whether clonal heterogeneity can be used as a biomarker of clinical outcome and to what extent subclonal somatic alterations might influence clinical outcome. Studies that use longitudinal tissue sampling, integrating both genomic and clinical data, have the potential to reveal the subclonal composition and track the evolution of tumors to address these questions and to begin to define the breadth of genetic diversity in different tumor types and its relevance to patient outcome. Such studies may provide further evidence for drug-resistance mechanisms informing combinatorial, adaptive, and tumor immune therapies placed within the context of tumor evolution.
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Affiliation(s)
- Mariam Jamal-Hanjani
- UCL Cancer Institute, Paul O'Gorman Building, London, United Kingdom. Cancer Research UK London Research institute, London, United Kingdom
| | - Sergio A Quezada
- UCL Cancer Institute, Paul O'Gorman Building, London, United Kingdom
| | - James Larkin
- Department of Oncology, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Charles Swanton
- UCL Cancer Institute, Paul O'Gorman Building, London, United Kingdom. Cancer Research UK London Research institute, London, United Kingdom.
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173
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Migliaccio I, Malorni L, Hart CD, Guarducci C, Di Leo A. Endocrine therapy considerations in postmenopausal patients with hormone receptor positive, human epidermal growth factor receptor type 2 negative advanced breast cancers. BMC Med 2015; 13:46. [PMID: 25857348 PMCID: PMC4350905 DOI: 10.1186/s12916-015-0280-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/20/2015] [Indexed: 12/22/2022] Open
Abstract
The standard of care for patients with hormone receptor positive, human epidermal growth factor receptor type 2 negative advanced breast cancer is endocrine therapy. Endocrine agents, including aromatase inhibitors, tamoxifen, and fulvestrant, are often administered alone as first line treatment and demonstrate durable responses with limited side effects. Endocrine resistance represents a major clinical problem. In the future, poly-endocrine therapy and combination therapies with biological agents might become valuable options for the first line treatment of hormone receptor-positive advanced breast cancer. However, it will be critical to develop clinical tools that can reliably identify the subgroup of patients most likely to benefit from endocrine therapy alone, and those who might benefit from alternative approaches. Herein, we will review and discuss current issues in the endocrine treatment of postmenopausal patients with hormone receptor positive, human epidermal growth factor receptor type 2 negative advanced breast cancer.
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174
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Treatment strategy for metastatic breast cancer with estrogen receptor-positive tumor. Int J Clin Oncol 2015; 20:249-52. [PMID: 25666484 DOI: 10.1007/s10147-015-0795-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 01/26/2015] [Indexed: 02/06/2023]
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175
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Fasching PA, Brucker SY, Fehm TN, Overkamp F, Janni W, Wallwiener M, Hadji P, Belleville E, Häberle L, Taran FA, Lüftner D, Lux MP, Ettl J, Müller V, Tesch H, Wallwiener D, Schneeweiss A. Biomarkers in Patients with Metastatic Breast Cancer and the PRAEGNANT Study Network. Geburtshilfe Frauenheilkd 2015; 75:41-50. [PMID: 25684786 DOI: 10.1055/s-0034-1396215] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 01/05/2015] [Accepted: 01/06/2015] [Indexed: 12/17/2022] Open
Abstract
Progress has been made in the treatment of metastatic breast cancer in recent decades, but very few therapies use patient or tumor-specific characteristics to tailor individualized treatment. More than ten years after the publication of the reference human genome sequence, analysis methods have improved enormously, fostering the hope that biomarkers can be used to individualize therapies and offer precise treatment based on tumor and patient characteristics. Biomarkers at every level of the system (genetics, epigenetics, gene expression, micro-RNA, proteomics and others) can be used for this. This has led to changes in clinical study designs, with drug developments often only focusing on small or very small subgroups of patients and tumors. The screening and registration of patients and their molecular tumor data has therefore become very important for the successful completion of clinical studies. This new form of medicine presents particular challenges for patients and physicians. Even in this new age of genome-wide analysis, the focus should still be on the patients' quality of life. This review summarizes recent developments and describes how the PRAEGNANT study network manages the aforementioned medical challenges and changes to create a professional infrastructure for patients and physicians.
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Affiliation(s)
- P A Fasching
- Frauenklinik des Universitätsklinikums Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen ; Wissenschaftliche Leitung PRAEGNANT-Studiennetzwerk
| | - S Y Brucker
- Forschungsinstitut für Frauengesundheit, Department für Frauengesundheit, Universitätsklinikum Tübingen, Eberhard Karls Universität Tübingen, Tübingen ; Wissenschaftliche Leitung PRAEGNANT-Studiennetzwerk
| | - T N Fehm
- Universitäts-Frauenklinik Düsseldorf, Heinrich-Heine Universität Düsseldorf, Düsseldorf
| | - F Overkamp
- Oncologianova GmbH Recklinghausen, Recklinghausen
| | - W Janni
- Universitätsfrauenklinik Ulm, Ulm
| | - M Wallwiener
- Universitätsfrauenklinik Heidelberg, Ruprecht-Karls-Universität Heidelberg, Heidelberg
| | - P Hadji
- Krankenhaus Nordwest, Klinik für Gynäkologie und Geburtshilfe, Frankfurt am Main
| | | | - L Häberle
- Frauenklinik des Universitätsklinikums Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen ; Unit of Biostatistics, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen
| | - F-A Taran
- Universitäts-Frauenklinik, Department für Frauengesundheit, Universitätsklinikum Tübingen, Eberhard Karls Universität Tübingen, Tübingen
| | - D Lüftner
- Medizinische Klinik mit Schwerpunkt Hämatologie und Onkologie; Charité Campus Benjamin Franklin Berlin, Berlin
| | - M P Lux
- Frauenklinik des Universitätsklinikums Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen
| | - J Ettl
- Abteilung Gynäkologie und Geburtshilfe, Klinikum rechts der Isar, Technische Universität München, Munich
| | - V Müller
- Klinik für Gynäkologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg
| | - H Tesch
- Onkologie Bethanien, Frankfurt am Main ; Studienleitung PRAEGNANT-Studie
| | - D Wallwiener
- Universitäts-Frauenklinik, Department für Frauengesundheit, Universitätsklinikum Tübingen, Eberhard Karls Universität Tübingen, Tübingen ; Studienleitung PRAEGNANT-Studie
| | - A Schneeweiss
- Universitätsfrauenklinik Ulm, Ulm ; Nationales Centrum für Tumorerkrankungen, Heidelberg
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176
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Maass N, Schütz F, Fasching PA, Fehm T, Janni W, Kümmel S, Kolberg HC, Lüftner D, Wallwiener M, Lux MP. Breast Cancer Update 2014 - Focus on the Patient and the Tumour. Geburtshilfe Frauenheilkd 2015; 75:170-182. [PMID: 25797960 PMCID: PMC4361168 DOI: 10.1055/s-0035-1545704] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 01/27/2015] [Accepted: 01/27/2015] [Indexed: 02/06/2023] Open
Abstract
The therapy for patients with breast cancer has developed markedly in the past ten years. Our understanding of the molecular biology of tumours and the characteristics of the patients has shaped the recent advances. In this review we present the latest knowledge about the therapy for breast cancer. There are new tests and options not only in the field of anti-HER2 therapy but also in the management of triple negative and hormone receptor-positive patients. Comprehension of prognosis and therapeutic response to chemotherapies is little by little helping to define patient groups who will not respond to chemotherapy or who do not need treatment because their prognosis is extremely good. In the field of anti-HER2 therapy, work is continuing on the development of drugs suitable for and able to overcome trastuzumab resistance. For hormone receptor-positive cancers, we now have a better understanding of which therapy groups will benefit from which anti-endocrine drugs, and which will be able to overcome a possible resistance (treatment of the PI3K pathways, inhibition of the cell cycle). Molecular tests are still being evaluated with regard to the clinical situations in which they may have the greatest relevance for therapeutic decision-making; however, evidence is also increasing as to the fields in which good predictions for the prognosis can be obtained. On the whole, more work is needed to promote our understanding of the new developments in diagnostics and therapy and to involve both physicians and patients equally in the procedures.
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Affiliation(s)
- N. Maass
- Department of Gynecology and Obstetrics, University Hospital Aachen, Aachen
| | - F. Schütz
- Frauenklinik, Universitätsklinikum Heidelberg, Heidelberg
| | - P. A. Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen
| | - T. Fehm
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf
| | - W. Janni
- Frauenklinik, Klinikum der Universität Ulm, Ulm
| | - S. Kümmel
- Brustzentrum, Kliniken Essen Mitte, Evang. Huyssens-Stiftung/Knappschaft GmbH, Essen
| | - H.-C. Kolberg
- Klinik für Gynäkologie und Geburtshilfe, Marienhospital Bottrop, Bottrop
| | - D. Lüftner
- Medizinische Klinik und Poliklinik II, Campus Charité Mitte, Berlin
| | - M. Wallwiener
- Frauenklinik, Universitätsklinikum Heidelberg, Heidelberg
| | - M. P. Lux
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen
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177
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Stahel R, Bogaerts J, Ciardiello F, de Ruysscher D, Dubsky P, Ducreux M, Finn S, Laurent-Puig P, Peters S, Piccart M, Smit E, Sotiriou C, Tejpar S, Van Cutsem E, Tabernero J. Optimising translational oncology in clinical practice: Strategies to accelerate progress in drug development. Cancer Treat Rev 2015; 41:129-35. [DOI: 10.1016/j.ctrv.2014.12.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/08/2014] [Indexed: 02/05/2023]
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Vaca-Paniagua F, Oliver J, Nogueira da Costa A, Merle P, McKay J, Herceg Z, Holmila R. Targeted deep DNA methylation analysis of circulating cell-free DNA in plasma using massively parallel semiconductor sequencing. Epigenomics 2015; 7:353-62. [PMID: 26077425 DOI: 10.2217/epi.14.94] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
AIM To set up a targeted methylation analysis using semiconductor sequencing and evaluate the potential for studying methylation in circulating cell-free DNA (cfDNA). MATERIALS & METHODS Methylation of VIM, FBLN1, LTBP2, HINT2, h19 and IGF2 was analyzed in plasma cfDNA and white blood cell DNA obtained from eight hepatocellular carcinoma patients and eight controls using Ion Torrent™ PGM sequencer. RESULTS h19 and IGF2 showed consistent methylation levels and methylation was detected for VIM and FBLN1, whereas LTBP2 and HINT2 did not show methylation for target regions. VIM gene promoter methylation was higher in HCC cfDNA than in cfDNA of controls or white blood cell DNA. CONCLUSION Semiconductor sequencing is a suitable method for analyzing methylation profiles in cfDNA. Furthermore, differences in cfDNA methylation can be detected between controls and hepatocellular carcinoma cases, even though due to the small sample set these results need further validation.
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Affiliation(s)
- Felipe Vaca-Paniagua
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France
- Instituto Nacional de Cancerología, México DF, Mexico
- Unidad de Biomedicina, FES-Iztacala, Universidad Nacional Autónoma de México (UNAM), México DF, Mexico
| | - Javier Oliver
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France
- Instituto de Ciencias Básicas y Medicina Experimental del Hospital Italiano de Buenos Aires. Potosí 450, C1199ACL, Buenos Aires, Argentina
| | - Andre Nogueira da Costa
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France
- UCB BioPharma SPRL, Chemin du Foriest 1, B-1420 Braine L'Alleud, Belgium
| | - Philippe Merle
- Croix-Rousse Hospital, 103 grande place de la Croix-Rousse, 69004 Lyon, France
- Centre de Recherche en Cancérologie de Lyon (CRCL) UMR INSERM 1052, 151 Cours Albert Thomas, 69424 Lyon Cedex 03, France
| | - James McKay
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France
| | - Zdenko Herceg
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France
| | - Reetta Holmila
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372 Lyon CEDEX 08, France
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Ignatiadis M, Dawson SJ. Circulating tumor cells and circulating tumor DNA for precision medicine: dream or reality? Ann Oncol 2014; 25:2304-2313. [PMID: 25336116 DOI: 10.1093/annonc/mdu480] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Next-generation sequencing studies have provided further evidence to support the notion that cancer is a disease characterized by Darwinian evolution. Today, we often fail to capture this evolution and treatment decisions, even in the metastatic setting, are often based on analysis of primary tumor diagnosed years ago. Currently, this is considered a major reason for treatment failures in cancer care. Recent technological advances in the detection and characterization of circulating tumor cells and circulating tumor DNA might address this and allow for treatment tailoring based on real-time monitoring of tumor evolution. In this review, we summarize the most important recent findings in the field, focusing on challenges and opportunities in moving these tools forward in clinical practice.
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Affiliation(s)
- M Ignatiadis
- Department of Medical Oncology and Breast Cancer Translational Research Laboratory, J. C. Heuson, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium.
| | - S-J Dawson
- Division of Cancer Medicine; Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
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