Blood Draw Predicts Breast Cancer Relapse

Friday, 04/09/2015  |   Breast Cancer  |  no comments

Untitled-1 Circulating tumor DNA (ctDNA) is a promising biomarker for noninvasive assessment of cancer burden, but existing ctDNA detection methods have insufficient sensitivity or patient coverage for broad clinical applicability. Here Newman et al., (2014) introduce cancer personalized profiling by deep sequencing (CAPP-Seq), an economical and ultrasensitive method for quantifying ctDNA. They implemented CAPP-Seq for non–small-cell lung cancer (NSCLC) with a design covering multiple classes of somatic alterations that identified mutations in >95% of tumors. They detected ctDNA in 100% of patients with stage II–IV NSCLC and in 50% of patients with stage I, with 96% specificity for mutant allele fractions down to ~0.02%. Levels of ctDNA were highly correlated with tumor volume and distinguished between residual disease and treatment-related imaging changes, and measurement of ctDNA levels allowed for earlier response assessment than radiographic approaches. Finally, we evaluated biopsy-free tumor screening and genotyping with CAPP-Seq. They envision that CAPP-Seq could be routinely applied clinically to detect and monitor diverse malignancies, thus facilitating personalized cancer therapy. Blood contains two types of cancer-derived materials that are susceptible to detailed molecular analysis: intact circulating tumor cells (CTC) and cell-free circulating tumor DNA (ctDNA). The former are shed from primary or metastatic tumor deposits, and although they are rare, they are thought to be enriched for metastatic precursors (Hater & Velculescu, 2014). Initially detected in an 1869 autopsy within the blood of a patient with widespread breast cancer (Ashworth, 1869), CTCs are now isolated with increasingly sophisticated technologies (Maheswaran & Haber, 2010; Pantel & Alix-Panabieres, 2010; Yu et al., 2011). However, the advantage of applying multiple DNA, RNA, and protein-based assays to study whole tumor cells in the circulation (so-called liquid biopsies) is currently restricted by the need for complex cellular isolation platforms. Recent advances in technologies to analyze circulating tumor cells and circulating tumor DNA are setting the stage for real-time, noninvasive monitoring of cancer and providing novel insights into cancer evolution, invasion, and metastasis. Source: Newman AM, Bratman SV, To J, et al. Nature Medicine. 20, 548–554 (2014) doi:10.1038/nm.3519 References: Ashworth TR. A case of cancer in which cells similar to those in the tumors were seen in the blood after death. Aust Med J 1869;14:146–9. Hater DA, Velculescu VE. Blood-Based Analyses of Cancer: Circulating Tumor Cells and Circulating Tumor DNA. Cancer Discovery June 2014 4; 650 doi: 10.1158/2159-8290.CD-13-1014 Maheswaran S, Haber DA. Circulating tumor cells: a window into cancer biology and metastasis. Curr Opin Genet Dev 2010;20:96–9. Pantel K, Alix-Panabieres C. Circulating tumour cells in cancer patients: challenges and perspectives. Trends Mol Med 2010;16:398–406. Pantel K, Alix-Panabieres M, Stott S, Toner M, Maheswaran S, Haber DA. Circulating tumor cells: approaches to isolation and characterization. J Cell Biol 2011;192:373–82. F1.large The management of metastatic breast cancer needs improvement. As clinical evaluation is not very accurate in determining the progression of disease, the analysis of circulating tumor DNA (ctDNA) has evolved to a promising noninvasive marker of disease evolution. Indeed, ctDNA was reported to represent a highly sensitive biomarker of metastatic cancer disease directly reflecting tumor burden and dynamics. However, at present little is known about the dynamic range of ctDNA in patients with metastatic breast cancer. In this study, 74 plasma DNA samples from 58 patients with metastasized breast cancer were analyzed with a microfluidic device to determine the plasma DNA size distribution and copy number changes in the plasma were identified by whole-genome sequencing (plasma-Seq). Furthermore, in an index patient we conducted whole-genome, exome, or targeted deep sequencing of the primary tumor, metastases, and circulating tumor cells (CTCs). Deep sequencing was done to accurately determine the allele fraction (AFs) of mutated DNA fragments. Although all patients had metastatic disease, plasma analyses demonstrated highly variable AFs of mutant fragments. analyzed an index patient with more than 100,000 CTCs in detail. Heidary et al., (2014) first conducted whole-genome, exome, or targeted deep sequencing of four different regions from the primary tumor and three metastatic lymph node regions, which enabled us to establish the phylogenetic relationships of these lesions, which were consistent with a genetically homogeneous cancer. Subsequent analyses of 551 CTCs confirmed the genetically homogeneous cancer in three serial blood analyses. However, the AFs of ctDNA were only 2% to 3% in each analysis, neither reflecting the tumor burden nor the dynamics of this progressive disease. These results together with high-resolution plasma DNA fragment sizing suggested that differences in phagocytosis and DNA degradation mechanisms likely explain the variable occurrence of mutated DNA fragments in the blood of patients with cancer. The dynamic range of ctDNA varies substantially in patients with metastatic breast cancer. This has important implications for the use of ctDNA as a predictive and prognostic biomarker. Clinical response evaluation of patients with cancer is often not accurate. Therefore, the use of ctDNA has been proposed as a biomarker for monitoring tumor burden and treatment response. Indeed, several studies have suggested that ctDNA analysis is an effective indicator of tumor load, allowing more accurate monitoring of tumor dynamics (Diehl et al., 2008; Leary et al., 2010; McBride et al., 2010). Circulating tumor DNA was successfully detected in 29 of the 30 women (97%) in whom somatic genomic alterations were identified; CA 15-3 and circulating tumor cells were detected in 21 of 27 women (78%) and 26 of 30 women (87%), respectively. Circulating tumor DNA levels showed a greater dynamic range, and greater correlation with changes in tumor burden, than did CA 15-3 or circulating tumor cells. Among the measures tested, circulating tumor DNA provided the earliest measure of treatment response in 10 of 19 women (53%). In breast cancer, a recent study has provided evidence that ctDNA levels had a greater dynamic range and greater correlation with changes in tumor burden than CA 15-3 or CTCs (Dawson et al., 2013). Source Heidary M, Auer M, Ulz P, et al. The dynamic range of circulating tumor DNA in metastatic breast cancer. Breast Cancer Research 2014, 16:421 http://breast-cancer-research.com/content/16/4/421 References Dawson SJ, Tsui DW, Murtaza M, et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med 2013, 368:1199–1209. Diehl F, Schmidt K, Choti MA, et al. Circulating mutant DNA to assess tumor dynamics. Nat Med 2008, 14:985–990. Leary RJ, Kinde I, Diehl F, et al. Development of personalized tumor biomarkers using massively parallel sequencing. Sci Transl Med 2010, 2:20ra14. McBride DJ, Orpana AK, Sotiriou C, et al. Use of cancer-specific genomic rearrangements to quantify disease burden in plasma from patients with solid tumors. Gene Chromosome Canc 2010, 49:1062–1069. Tracking tumor DNA in the blood of early breast cancer patients after surgery can detect relapse 7.9 months earlier than conventional imaging, according to the results of a study published in Science Translational Medicine. Using a non-invasive circulating tumor DNA (ctDNA) analysis, Isaac Garcia-Murillas, PhD, of the Institute of Cancer Research in London, and colleagues tracked breast tumor–specific mutations in 55 patients who had undergone surgery and chemotherapy as a potentially curative treatment. The results of the prospective study suggest that patients at risk for relapse may be identified earlier and given more aggressive treatment to prevent metastasis. Of the 15 patients who relapsed on study, the presence of ctDNA predicted the relapse of 12 patients. Among the patients who did not relapse, 96% had no detectable ctDNA in either the post-surgery sample (24 of 25; P = .0038) or during temporal tracking of tumor mutations (27 of 28; P < .0001). One patient, with triple-negative disease, had detectable ctDNA after surgery but did not relapse on study. All metastatic tumors were detectable by ctDNA except for three patients who had recurrence in the brain. The study also showed that ctDNA analysis could identify the genetic events that define minimal residual disease among breast cancer patients. This genetic analysis of minimal residual disease also predicted the genetics of the relapsed tumor better than sequencing analysis of the primary breast tumor. The study authors concluded that tracking of ctDNA linked to cancer relapse could facilitate the tailoring of adjuvant therapies based on the mutations captured in patients’ blood samples. The utility of ctDNA analysis in late-stage cancer patients has already been demonstrated in previous research studies, although the technique is not yet ready to be used in the clinical setting. The current study, however, is among the first to demonstrate the ability to capture ctDNA from blood samples of earlier stage cancer patients. Tumor DNA circulates in the blood in minute amounts, and whether these molecules can be consistently detected using current technologies has been an open question. Garcia-Murillas and his colleagues first sequenced each patient’s primary tumor, identifying tumor-specific somatic mutations to track in the ctDNA following surgery. ctDNA detected at baseline, prior to any therapy, was not associated with early relapse. ctDNA detected at 2 to 4 weeks after surgery was indicative of early relapse—those who had detectable ctDNA (19%; 7 of 37 patients) had a median disease-free survival (DFS) of 6.5 months; median DFS among patients with no detectable ctDNA was not reached. “In addition to confirming the feasibility of ctDNA detection in non-metastatic breast cancer, Garcia-Murillas et al have extended these findings in a prospective study, demonstrating that longitudinal monitoring of ctDNA is more reliable than single baseline measurements in predicting recurrence in women treated with neoadjuvant chemotherapy for localized breast cancer,” stated Tilak Sundaresan, MD, and Daniel Haber, MD, PhD, of the Massachusetts General Hospital Cancer Center in Boston.

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