LIQUID BIOPSY

Transcription

1 LIQUID BIOPSY Miguel Abal Investigador I3SNS Oncoloxía Médica Traslacional Instituto de Investigación Sanitaria de Santiago (IDIS) Complexo Hospitalario Universitario de Santiago/SERGAS

2 A major reason for treatment failures is our inability to monitor tumor evolution and adapt treatment accordingly. Recent technological advances have enabled the detection and detailed characterization of circulating tumor cells (CTC) and circulating tumor DNA (ctdna) in blood samples from patients with cancer. Often referred to as a "liquid biopsy," CTCs and ctdna are expected to provide real-time monitoring of tumor evolution and therapeutic efficacy, with the potential for improved cancer diagnosis and treatment.

3 Liquid biopsy Solid biopsy

4 Pantel K, and Alix-Panabières C Cancer Res 2013;73:

5 Circulating Tumor Cell (CTC) liquid biopsy (clinical tool) new therapeutic target to prevent and/or eradicate metastasis

6 We need high sensitive and specific techniques to isolate and quantify CTC

7 Schematic view of CTC enrichment methods Pantel & Alix-Panabières. Circulating tumour cells in cancer patients: challenges and perspectives. Trends Mol Med Sep;16(9):

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9 The EPISPOT assay procedure.

10 The microfluidic circulating tumor cell (CTC) chip Efficient and selective separation of viable CTCs from peripheral whole blood samples, mediated by the interaction of target CTCs with antibody (EpCAM)- coated microposts under precisely controlled laminar flow conditions.

11 Microfluidic devices for CTC capture and characterisation A circulating tumor cell (CTC) selection microfluidic device integrated to an electrokinetic enrichment device for preconcentrating CTCs directly from whole blood to allow for molecular profiling.

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13 Tools:

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15 7.5mL CellTracks AutoPrep System CD45 Ferrofluid-nanoparticules/EpCAM CYTOKERATINE DAPI CellTracks Analyzer II CK+/CD45 - CK-/CD45 +

16 The CellSearch Circulating Tumor Cell Kit is intended for the enumeration of circulating tumor cells (CTC) of epithelial origin (CD45-, EpCAM+, and cytokeratins8, 18+, and/or 19+) in whole blood.

17 FDA APPROVAL FOR CLINICAL USE (Cristofanilli et al., N Engl J Med 2004) (Cohen et al., J Clin Oncol 2008) (de Bono et al., Clin Cancer Res 2008)

18 (Cristofanilli et al., N Engl J Med 2004) (Cohen et al., J Clin Oncol 2008) (de Bono et al., Clin Cancer Res 2008)

19 Progression-free survival (PFS) and overall survival (OS) of metastatic colorectal cancer patients with < three and three circulating tumor cells (CTCs) in 7.5 ml of blood (A, B) before therapy, (C, D) 1 to 2, 3 to 5, 6 to 12, and 13 to 20 weeks after initiation of therapy, and (E, F) by circulating tumor cell status at baseline and 3 to 5 weeks. Cohen S J et al. JCO 2008;26:

20 mcrc (n=50) Prediction of therapy response based on CTC-biomarker analysis Cycle 1 Cycle 2 Cycle 3 Cycle 4 1 month Staging CT Baseline 4-weeks Anti EpCAM 12-weeks CT Preamplification RNA extraction qpcr for selected transcripts

21 vs CTC-markers can predict therapy response more accurately and earlier than CT imaging 21

22 For any technology to be used in the clinic, demonstration of analytic validity (the accuracy of the test to measure the target of interest), clinical validity (the value of the test to predict the clinical outcome), and ultimately clinical utility (ability of the test to lead to improved clinical outcome when treatment choice is informed by test results) is required. A recent study assessed the clinical validity of circulating tumour cell (CTC) quantification for prognostication of patients with metastatic breast cancer by undertaking a pooled analysis of individual patient data (20 studies; approx patients). The data confirmed the independent prognostic effect of CTC count on progression-free survival and overall survival. CTC count also improved the prognostication of metastatic breast cancer when added to full clinicopathological predictive models, whereas serum tumour markers do not. (Bidard et al., Clinical validity of circulating tumour cells in patients with metastatic breast cancer: a pooled analysis of individual patient data. Lancet Oncol. 2014;15(4):406-14).

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24 The value of CTC enumeration for treatment decision making in metastatic breast cancer was prospectively tested in the Southwest Oncology Group (SWOG) S0500 clinical trial. The SWOG trial evaluated the benefit of an early change in chemotherapy for patients with persistently increased CTCs at first follow-up after starting first-line chemotherapy. Of 595 evaluable patients, 123 patients with persistently elevated CTCs on day 21 of therapy were randomized to either continue the same treatment or to switch to an alternative chemotherapy of physician's choice. In this trial, an early switch to an alternative chemotherapy did not increase overall survival (OS). Although CTCs were strongly prognostic, the absence of a survival benefit from changing treatment based on elevated CTC counts suggests that earlier detection of relapse can only be important when a more effective treatment is available: Switching from one ineffective therapy to another ineffective therapy does not change outcome. Instead, changing treatment based on CTC molecular characterization might be a more promising approach to test.

25 DEP Array semi-conductor chip

26 Silicon Biosystems Patented Technology: Moving DEP Cages Non-uniform electric field generated by the chip electrodes (cross section) Cell trapping by DEP cages cage-move ndep Cage ndep Cage

27 Moving DEP Cages Enables Outstanding Performance in Single-Cell Sorting Recovery Parking 1. Inject, trap and image all cells 2. Move all cells of interest into Parking chamber 3. Move separately to Recovery chamber and flush Main chamber

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29 Homogeneous pools of cells from FFPE 300 pure cells tumor vs. stromal from FFPE tissue Direct multiplex PCR Deep Sequencing data analysis

30 100% purity

31 3100.d.4 50_50F_E03_09.ab1 50_50F Lane 9 Signal G:515 A:390 T:445 C:290 DT3100POP6{BD}v2.mob Points 592 to Base 1: 592 Fri Tu A G G AC TAA TG GG AA AA TTTA AA G TGCAAC CA G T CT GAG T CAA CA G AT TT CT T CCAA T TA NGT T GAC AG GT GTAGG T C C TAC TA A TAC T GT AC C T Digitalization improves resolution C T GAT CA TA C T GT C TTAC T T TG ATAA A AC C T CCAANT C CCNC T AT CA T T T T T GGT T TC CAT C T T CC T GGC AA AC T CA T T TC TT C TA A TA C T GT Quantitation 230 T T TA GT T GC C C CC C T AT C TT TA T T GT GA C GA GG GGT C GT T GC CA A AGA GT GA TC T GA GGGA A GT TAA A GG ATAC A GT T C C T TGT CTAT C GGC T Sequencing CC AGA CC T GAA GC T CT C T T C TGGT GGG GC T GT TG GC T CT GGT C T GC TC T GAA GAA A AT T CC C T GGC C T TC C C TT GT AGGAA GGC CA G AT C T

32 Cancer Mutation Panel for CTCs Ampli1- WGA

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34 CTC Characterization by DEPArray and Ampli1 yield Actionable Information Gene CTC WBC pool MU27 PIK3CA Ex 9 mut wt wt wt wt wt wt wt DO wt wt wt wt wt wt wt Ex 20 mut mut mut mut mut mut mut mut mut mut DO wt DO wt wt wt Her2 CNV+ NA n n n n n n DO n n n n NA n n pool MU22 PIK3CA Ex 9 mut wt wt wt wt wt wt wt wt wt wt DO wt wt wt Ex 20 mut mut mut mut mut mut mut mut mut mut mut mut wt wt wt Her2 CNV+ NA n n n n n n n n DO DO NA n n pool MU28 PIK3CA Ex 9 mut wt wt wt DO DO wt wt wt wt wt wt Ex 20 mut wt wt wt wt wt wt wt wt wt wt wt Her2 CNV+ NA n n DO n n n DO NA n NA MU09 PIK3CA Ex 9 mut wt wt wt wt wt wt wt wt wt Ex 20 mut mut mut mut mut wt wt wt wt wt Her2 CNV+ a a a a a a NA NA NA pool MU18 PIK3CA Ex 9 mut wt mut wt wt wt wt wt Ex 20 mut mut wt wt wt wt wt wt Her2 CNV+ DO NA n n DO NA n MU37 PIK3CA Ex 9 mut mut mut wt wt wt wt Ex 20 mut wt wt wt wt wt wt Her2 CNV+ a a a a NA n MU23 PIK3CA Ex 9 mut mut mut wt DO wt wt wt Ex 20 mut wt wt wt DO wt wt wt Her2 CNV+ n DO n n NA n n MU21 PIK3CA Ex 9 mut wt wt wt wt wt wt Ex 20 mut wt wt wt wt wt wt Her2 CNV+ a a a NA n n MU29 PIK3CA Ex 9 mut wt wt wt DO DO Ex 20 mut wt wt wt wt wt Her2 CNV+ n n n n NA MU05 PIK3CA Ex 9 mut wt wt wt Ex 20 mut wt wt wt Her2 CNV+ a NA NA PI3Kinhibitor Lapatinib Herceptin Source: Division of Oncogenomics, Pathology Dept., Uni Regensburg

35 if CTCs can be isolated from cancer patients as viable cells that can be genotyped and functionally characterized over the course of therapy, they have the potential to identify treatments that most effectively target the evolving mutational profile of the primary tumor (Yu et al., Ex vivo culture of circulating breast tumor cells for individualized testing of drug susceptibility. Science July 11; 345(6193): ).

36 The isolation of viable CTCs is technically challenging, success associated with unmanipulated CTCs. CTCs proliferated best as tumor spheres when cultured in serumfree media supplemented with epidermal growth factor (EGF) and basic fibroblast growth factor (FGF) under hypoxic conditions (4% O2). Nonadherent culture conditions were critical, because CTCs senesced after a few cell divisions in adherent monolayer culture

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39 CONCLUSION single-cell analyses have provided higher-resolution evidence of intratumor heterogeneity with the finding of substantial clonal diversity and subclonal heterogeneity, such that no two individual tumor cells are genetically identical. Beyond spatial heterogeneity, solid tumors also exhibit temporal heterogeneity, evolving over time under selection pressure from treatment. Thus, there is an increased appreciation that the management of metastatic disease should rely on analysis of contemporary tumor tissue rather than on the primary tumor diagnosed years ago. However, obtaining serial samples of metastatic tissue is impractical and complicated by spatial heterogeneity and sampling bias. Analysis of circulating tumor cells (CTC) and circulating tumor DNA (ctdna) thus holds appeal and promise for noninvasive real-time assessment of tumor molecular profiles during the course of disease. Evaluation of CTCs and ctdna may enable more sensitive monitoring of treatment efficacy and thereby guide drug selection, even potentially in the adjuvant setting where no such tools exist today.

40 Miguel Abal Translational Medical Oncology (IDIS) Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS) Trav. Choupana s/n Santiago de Compostela (Spain) phone

41 Fragments of DNA are shed into the bloodstream from dying cells during cellular turnover or other forms of cell death. More than 90% of healthy individuals having less than 25 ng cfdna per ml. cfdna in the circulation is typically fragmented to 160 to 180 bp in length, corresponding to nucleosome-protected DNA observed in apoptotic cells. In certain conditions, including inflammation, exercise, or tissue injury, cfdna levels can be substantially higher.

42 ctdna ctdna may be derived from primary tumors, metastatic lesions, or CTCs. The fraction of ctdna that is tumor derived in patients with cancer has a variable contribution ranging from <0.1% to >10% of the DNA molecules. The variability in levels of ctdna is not well understood and is thought to be affected by tumor burden, stage, cellular turnover, accessibility to the circulation, and factors affecting blood volume. Although patients with similar tumor types may have varying absolute levels of ctdna at the time of diagnosis, the relative levels of ctdna within an individual have been shown to correlate with tumor burden and response to therapy.

43 Subject 11 had a sigmoid adenocarcinoma and two liver metastases that were treated with systemic chemotherapy before surgery (Chemotherapy 1). The subject underwent a sigmoid colectomy, left hepatic lobectomy and RFA of a solitary right hepatic lesion (Surgery 1). Imaging studies at 2 months showed recurrence in the liver, and the subject underwent a right hepatectomy (Surgery 2). Given the high risk of recurrence, chemotherapy was reinitiated (Chemotherapy 2). At 8 months, imaging showed three recurrent liver lesions and a suspicious celiac lymph node. The subject underwent RFA of these lesions and resection of the celiac node (Surgery 3). After surgery, the subject received additional chemotherapy (Chemotherapy 3); however, later imaging revealed multiple pulmonary metastases.

44 Technologies for ctdna analysis

45 BEAMing Up Personalized Medicine: Detecting Cancer-Driving Mutations in Circulating DNA BEAMing (Beads, Emulsification, Amplification, and Magnetics)

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