Abstract 587: Genomic copy number profiling of single CTCs reveals clonal evolution in metastatic breast cancer and identifies actionable targets for informing treatment decisions

Introduction: Genomic profiling of circulating tumor cells (CTCs) is an approach to help to understand tumour heterogeneity and evolution in metastatic breast cancer (MBC) to inform prognosis and guide treatment options. We showed previously that single CTCs provide complementary information on hot spot mutations to those detected in circulating tumor DNA (ctDNA) and the primary tumour tissue, and now extend analyses to include genomic copy number changes. Herein, we report that identification of actionable targets through copy number profiling of single CTCs is achievable at any time point during metastatic progression and could be a valuable tool to guide treatment options.

Methods: Fourteen patients (13 12 progressing and 1 2 responding) who were receiving treatment for MBC (12 13 HR pos, 1 HER2 pos, I1 TNBC) were recruited to the study with ethical consent and followed up with a single blood sample. A 7.5ml blood sample was collected into a CellSave Preservative tube and processed and counted within 96 hours of collection using the CELLSEARCH® system and the Circulating Tumor Cell Kit (Menarini Silicon Biosystems). The DEPArray™ System was used to identify and recover individual, intact CTCs of epithelial origin (Cytokeratin 8, 18, 19 +ve, CD45 -ve) and white blood cells (WBCs) as single cells or as a small pool of cells. Whole genome amplification was performed using the Ampli1 WGA kit. Libraries were generated using the Ampli1 LowPass Kit (Menarini Silicon Biosystems) and samples passing QC were analysed f by next generation sequencing on an S5 platform (Thermo fFisher). Results were analysed using the MSBiosuite software and data was compared with in- house informatics workfows.

Results: From the 14 patients included in the study, we profiled a total of 97 samples using the Ampli1 LowPass sequencing workflow comprising 79 individual cells (across 14 patients) and 18 pools of approximately 10 cells. Successful genome- wide copy number profiles were generated in 12 of the 14 patients; samples from 2 patients had low QC scores and were inconclusive. In all, 12 patients individual CTCs from 12 patients showed similar copy number profiles, but with some heterogeneity, that revealed gene specific changes not detected by the cell pool. Moreover, 10 of the 12 patients had gene- specific changes (5 with CCND1 amplification, 2 with FGFR1 amplification, 1 with JAK2 amplification and 2 with STK11 deletion) that could have guided treatment decisions, for example offering an FGFR1 or JAK2 inhibitor.

Conclusion: This study highlights the genomic heterogeneity in CTCs seen in MBC and the potential of monitoring gene specific changes to identify actionable targets in order to inform treatment decisions. The work requires further evaluation and validation but it may offer a new approach to managing treatment decisions in MBC for those patients with detectable CTCs.

Citation Format: Daniel Fernandez Garcia, Georgios Nteliopoulos, Robert Hastings, Amelia Rushton, Karen Page, Luke J. Martinson, Molly Gray, David S. Guttery, Alberto Ferrarini, Nicolò Manaresi, Charles Coombes, Jacqui Shaw. Genomic copy number profiling of single CTCs reveals clonal evolution in metastatic breast cancer and identifies actionable targets for informing treatment decisions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 587.

Abstract 598: Resistance mechanisms to BRAF inhibition identified by single circulating tumor cell and cell-free tumor DNA molecular profiling in BRAF-mutant non-small cell lung cancer

Background: Combination therapy with dabrafenib + trametinib demonstrated robust activity in patients (pts) with BRAFV600E-mutant advanced non-small cell lung cancer (NSCLC), but its resistance mechanisms are poorly known. Liquid biopsy components such as circulating tumor cells (CTCs) and cell-free (cf) tumor DNA can provide a comprehensive genomic picture of tumor content. Molecular profiling of single CTCs from pts with BRAF-V600Emutant NSCLC was performed to carry out a pilot study to identify resistance mutations at failure to dabrafenib + trametinib and to compare the mutations detected on CTCs to the mutations found on cfDNA and tumor biopsies.

Patients and Methods: Eight pts with advanced BRAFV600E-mutant NSCLC at failure to dabrafenib + trametinib were prospectively enrolled between Jul 2018 and Mar 2019 at Gustave Roussy (IDRCB2008-A00585-50). Bloods samples were collected. Matched tissue-cfDNA and CTCs were available in 3 pts and matched tissue-CTCs for 4 pts. Single CTC isolation strategy included RosetteSep enrichment, immunofluorescent staining (Hoechst/CD45/cytokeratins) and fluorescence activated cell-sorting. The process to identify CTC mutations included Ampli1 whole-genome amplification, quality controls, multiplex targeted PCR with the Ampli1 CHPCustomBeta cancer panel developed by (Menarini Silicon Biosystems) and next-generation sequencing (NGS). The cfDNA was analyzed using InVisionFirst-Lung. Tissue samples were analyzed using targeted NGS in the MATCH-R trial (Recondo G; NPJ Precis Oncol 2020).

Results: Single CTCs were isolated from 7 pts. As baseline characteristics, the median age was 66 years, 5 (71%) were smoker; all the pts with adenocarcinoma histology. Most of the pts received dabrafenib + trametinib as 2nd line (86%). The median of CTCs isolated by patient was 20 (8-28). A wide spectrum of mutations in CTCs was observed at treatment failure that were involved in the main cancer pathways, including MAPK (n=1; NRAS), tyrosine kinase receptors (n=5; EGFR, ALK, FLT3, HER2,…), signal transduction (n=4; IDH1, EZH2,⋯), and DNA repair (n=2; AKT1, ATM,⋯). In the same CTC, several mutations were observed in 5/7 patients, commonly involving more than one cancer pathways. A higher degree of mutational diversity was observed in CTCs compared to tumor tissue biopsies and cfDNA. In the 3 patients with an available tumor/liquid biopsy, only 1 shared mutations between CTCs and matched tumor and cfDNA.

Conclusion: Single CTC profiling reveals a wide spectrum of therapeutic resistance mutations not detected by other analyses in pts with BRAFV600E-mutant NSCLC at failure to dabrafenib + trametinib. Integration of single CTC sequencing to tumor and cfDNA analysis, provides important perspectives to assess heterogeneous resistance mechanisms and to guide precision medicine in BRAFV600E- NSCLC.

Citation Format: Laura Mezquita, Marianne Oulhen, Agathe Aberlenc, Marc Deloger, Aurélie Honoré, Marianna Garonzi, Genny Buson, Claudio Forcato, Yann Lecluse, Mihaela Aldea, Maud NgoCamus, Claudio Nicotra, Karen Howarth, Ludovic Lacroix, Luc Friboulet, Benjamin Besse, Nicolò Manaresi, David Planchard, Françoise Farace. Resistance mechanisms to BRAF inhibition identified by single circulating tumor cell and cell-free tumor DNA molecular profiling in BRAF-mutant non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 598.

Genetic Characterization of Cancer of Unknown Primary Using Liquid Biopsy Approaches

Cancers of unknown primary (CUPs) comprise a heterogeneous group of rare metastatic tumors whose primary site cannot be identified after extensive clinical-pathological investigations. CUP patients are generally treated with empirical chemotherapy and have dismal prognosis. As recently reported, CUP genome presents potentially druggable alterations for which targeted therapies could be proposed. The paucity of tumor tissue, as well as the difficult DNA testing and the lack of dedicated panels for target gene sequencing are further relevant limitations. Here, we propose that circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) could be used to identify actionable mutations in CUP patients. Blood was longitudinally collected from two CUP patients. CTCs were isolated with CELLSEARCH® and DEPArrayTM NxT and Parsortix systems, immunophenotypically characterized and used for single-cell genomic characterization with Ampli1TM kits. Circulating cell-free DNA (ccfDNA), purified from plasma at different time points, was tested for tumor mutations with a CUP-dedicated, 92-gene custom panel using SureSelect Target Enrichment technology. In parallel, FFPE tumor tissue was analyzed with three different assays: FoundationOne CDx assay, DEPArray LibPrep and OncoSeek Panel, and the SureSelect custom panel. These approaches identified the same mutations, when the gene was covered by the panel, with the exception of an insertion in APC gene. which was detected by OncoSeek and SureSelect panels but not FoundationOne. FGFR2 and CCNE1 gene amplifications were detected in single CTCs, tumor tissue, and ccfDNAs in one patient. A somatic variant in ARID1A gene (p.R1276∗) was detected in the tumor tissue and ccfDNAs. The alterations were validated by Droplet Digital PCR in all ccfDNA samples collected during tumor evolution. CTCs from a second patient presented a pattern of recurrent amplifications in ASPM and SEPT9 genes and loss of FANCC. The 92-gene custom panel identified 16 non-synonymous somatic alterations in ccfDNA, including a deletion (I1485Rfs∗19) and a somatic mutation (p. A1487V) in ARID1A gene and a point mutation in FGFR2 gene (p.G384R). Our results support the feasibility of non-invasive liquid biopsy testing in CUP cases, either using ctDNA or CTCs, to identify CUP genetic alterations with broad NGS panels covering the most frequently mutated genes.

Abstract 5361: Isolation and genetic characterization of circulating tumor cells from cancer of unknown primary

Background Cancer of unknown primary (CUP) is a heterogeneous group of metastatic cancers whose primary site cannot be determined after standard clinical and pathological evaluation. CUP patients are generally treated with empirical chemotherapy and have poor prognosis. As reported in recent studies, CUPs present an average of 4 genetic alterations per tumor and these genetic alterations can be detected in circulating tumor DNA (Kato 2017). Thus, a potential improvement in CUP outcomes could derive from targeted therapies directed toward actionable mutations, and Circulating tumor cells (CTCs) can provide valuable information. Here, we describe a case of a 51-yr-old Caucasian female (Pt#71) with metastatic CUP. CTCs were detectable in her blood and analyzed for genetic alterations.

Methods Using CellSearch and DEPArray NxT, n=3 CTCs and n=1 leukocyte as a control were isolated from patient's peripheral blood. Single-cell whole genome amplification was obtained with Ampli1 WGA Kit and libraries were generated with Ampli1 OncoSeek Panel and Ampli1 LowPass kits. In parallel, formalin-fixed paraffin embedded (FFPE) tissue derived from a lymph node biopsy was analyzed with two different methods. One curl was sent for comprehensive genomic profile to FoundationOne assay testing (Roche). From another curl, DNA was extracted and directly processed with DEPArray LibPrep and DEPArray OncoSeek Panel kits. After sequencing on Illumina MiSeq platform, raw data were analyzed on MSBiosuite platform (Menarini Silicon Biosystems).

Results CTCs genome-wide characterization allowed the detection of sub-chromosomal losses, including a LOH region comprising the APC gene, and patterns of extensive gains. Moreover, amplification signals were detected in correspondence of FGFR2 and CCNE1 genes. Targeted sequencing on both CTCs and bulk tumor DNA confirmed the FGFR2 amplification in all the samples and detected a somatic variant in APC gene (APC:p.T1556Nfs*3). FoundationOne assay on FFPE biopsy reported the same amplification on FGFR2 and CCNE1 genes, along with a somatic variant in ARID1A gene (ARID1A:p.R1276*), a gene not present in the OncoSeek Panel. On the other hand, APC somatic variant was not identified by FoundationOne, probably due to contamination by normal cells and/or tumor heterogeneity.

Conclusions The comprehensive genomic profile of tumor FFPE tissue and CTCs was highly overlapping and allowed the characterization of genetic alterations in this CUP case, revealing potentially actionable mutations and copy number alterations. The advantage of isolating and analyzing single CTCs is clearly shown by the non-invasive procedure combined with a precise detection of druggable alterations due to cell purity.

Citation Format: Elisa Porcellini, Francesco Gelsomino, Noemi Laprovitera, Mattia Riefolo, Marianna Garonzi, Paola Tononi, Francesca Fontana, Antonia D'Errico, Maria Pantaleo, Nicolò Manaresi, Andrea Ardizzoni, Manuela Ferracin. Isolation and genetic characterization of circulating tumor cells from cancer of unknown primary [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5361.

DEPArray™ system: An automatic image-based sorter for isolation of pure circulating tumor cells

Circulating tumor cells (CTCs) are rare cells shed into the bloodstream by invasive tumors and their analysis offers a promising noninvasive tool to predict and monitor therapeutic responses. CTCs can be isolated from patient blood and their characterization at single‐cell level can inform on the genomic landscape of a tumor. All CTC enrichment methods bear a burden of contaminating normal cells, which mandate a further step of purification to enable reliable downstream genetic analysis. Here, we describe the DEPArray™ technology, a microchip‐based digital sorter, which combines precise microfluidic and microelectronic enabling precise, image‐based isolation of single CTCs, which can then be analyzed by Next Generation Sequencing (NGS) methods. © 2018 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.

Abstract 3190: Standardization and clinical implementation of liquid biopsy assays - IMI's CANCER-ID

The Innovative Medicines Initiative (IMI) project CANCER-ID (www.cancer-id.eu) is a 5 year (2015-2019) international public-private partnership of currently 40 partners from 14 countries with the aim to evaluate technologies for Circulating Tumor Cell (CTC), circulating free tumor DNA (ctDNA), microRNA (miRNA) and exosome enrichment, isolation and analysis. At the core of CANCER-ID’s activities are establishment of harmonized best practice protocols from patient sample collection, pre-analytical sample handling, sample and bioinformatics analyses down to the actionable information guiding patient selection and personalized treatment. CANCER-ID is furthermore testing and supporting development of standards for liquid biopsy as well as clinical implementation of liquid biopsy based protocols in the clinical setting. This includes interaction with regulatory bodies in Europe (EMA Innovation Task Force) and the US (FDA Public-Private Partnership liaison) to support future approval of liquid biopsies in multi-centered worldwide clinical studies.

During the clinical validation phase of the project, clinical-ready liquid biopsy protocols have been implemented in an observational study on the potential predictive value of monitoring treatment response towards Immune Checkpoint Inhibition (ICI) in 180 NSCLC patients at the UMC Groningen, The Netherlands, as well as in two ICI-chemotherapy combination studies in Triple-Negative Breast Cancer and Luminal B-type breast cancer, respectively, run by the University of Oslo, Norway (ALICE NCT03164993 and ICON NCT03409198). Within both studies, blood has been collected at baseline and at follow-up visits for ctDNA and CTC analysis, including technical evaluation of CTC PD-L1 protein expression. The aim is to assess whether the allelic frequency of mutations identified by plasma NGS as a potential measure for Tumor Mutational Burden or the number of PD-L1–positive/overall CTCs at different time points is indicative of treatment success. The studies aim at providing data to assess whether clinical predictive information could be inferred from baseline number of detected mutations and PD-L1 expressing CTCs. Preliminary data of these analyses will be presented.

As a follow-up activity of the IMI CANCER-ID program, the European Liquid Biopsy Society (ELBS) is currently being established by Prof. Pantel at UKE Hamburg, Germany. The ELBS will be open to all interested liquid biopsy stakeholders worldwide as a platform for scientific exchange, further efforts to standardize technologies and protocols in the field as well as for the initiation of new basic and clinical research projects with the aim to make liquid biopsies an integral part of clinical studies and patient care.

This work is supported by IMI JU & EFPIA (grant no. 115749, CANCER-ID). Samples from patients and healthy volunteers, respectively, were collected under signed informed consent.

Citation Format: Klaus Pantel, Leon W. Terstappen, Nicolò Manaresi, Harry J. Groen, Ed M. Schuuring, Ellen Heitzer, Michael Speicher, Bjørn Naume, Jon Amund Kyte, Thomas Schlange, for the IMI CANCER-ID consortium. Standardization and clinical implementation of liquid biopsy assays - IMI's CANCER-ID [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3190.

Abstract 3410: Hodgkin and Reed-Sternberg cells genome-wide copy number alteration analysis at single cell level by high-throughput automated platforms

Background: Classical Hodgkin Lymphoma (cHL) is generally highly curable with standard frontline therapies, although about 20% of the patients relapse or become refractory after initial treatment. cHL hallmark is the presence of morphologically characteristic malignant Hodgkin and Reed-Sternberg (HRS) cells that represent only a small fraction (about 1%) of the surrounding non-malignant environment. Genetic alterations of HRS cells are potentially a precious source of information to develop new treatments or prognostic biomarkers. In this perspective, low tumor cellularity, worsened by DNA degradation of FFPE samples, poses technical challenges to unravel malignant cells genetic alterations. Hereby we present new insights on purified HRS single cells obtained through highly automated platforms, providing precise observation of tumor genetic alterations.

Methods: FFPE tissue sections from 5 cHL patients were dissociated down to single cell suspensions. Cells were immunofluorescently labeled using anti-CD30-FITC and anti-PD-L1-PE antibodies. HRS cells, along with normal leukocytes, were selected on the basis of morphological and immunofluorescence criteria, and isolated using DEPArray™ NxT (Menarini Silicon Biosystems, MSB). Customized, high-throughput automated protocols were developed and implemented on STARLet liquid handler (Hamilton Life Sciences) to amplify isolated purified single cells genomic DNA and to generate genome-wide copy-number alterations (CNAs) profiles using Ampli1™ WGA and Ampli1™LowPass kits (MSB), respectively.

Results: More than 150 HRS cells were isolated from the 5 patient samples, from which CNA profiles were obtained. HRS cells presented extensive gains and losses across the whole genome, while leukocytes displayed flat profiles as expected. HRS cells clustered coherently with patients, revealing a high degree of heterogeneity of CNA profiles among different patients. However some commonalities across the patients genomes were identified. In particular, gains and amplification were detected in PD-L1, PD-L2 and JAK2 region (9p24), as well as gains and losses in regions where REL and other genes involved in NF-kB pathway map.

Conclusions: Leveraging on high throughput automated platforms and single cells isolation, the described method enabled cHL genome-wide genetic analysis at a single cell level, overcoming the intrinsic limitations of low-frequency of HRS and DNA degradation due to FFPE samples. Furthermore, unprecedented data on single HRS cells were described, opening up to a new approach to understand tumor diversity and to potentially develop personalized therapeutic strategies for cHL patients.

Citation Format: Andrea Raspadori, Paola Tononi, Chiara Mangano, Marianna Garonzi, Claudio Forcato, Chiara Bolognesi, Genny Buson, Francesca Fontana, Gianni Medoro, Nicolò Manaresi. Hodgkin and Reed-Sternberg cells genome-wide copy number alteration analysis at single cell level by high-throughput automated platforms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3410.

Abstract 2517: Validation of a targeted sequencing workflow for sequence variants and focal copy number alterations (CNAs) in single circulating tumor cells (CTCs)

Background

Characterization of individual CTCs helps investigating intra-tumour heterogeneity, and provides longitudinal information about temporal evolution of genomic lesions following therapeutic evolutionary pressure, missed by one-time, bulk, single-biopsy analysis. Here we present the validation of a complete workflow to detect hotspot mutations and CNAs in single cells. It combines ligation-mediated PCR (LM-PCR) Whole Genome Amplification (Ampli1™ WGA kit), best-in-class in terms of low allelic drop-out (ADO) and reproducibility of amplification bias, with a tailored, WGA-aware, next generation sequencing (NGS) targeted cancer panel (Ampli1™ OncoSeek) and a fully-automated cloud-based platform for bioinformatic analysis (MSBiosuite).

Methods

Single-cells (n=24) of breast, prostate, lung and neuroblastoma cancer cell lines spiked in healthy-donor blood, alongside 15 single White Blood Cells (WBCs) from 5 healthy donors and CTCs from prostate, lung and breast patients were enriched with CellSearch® System, sorted with DEPArray™ NxT technology and WGA’ed with Ampli1™ WGA kit (Menarini Silicon Biosystems). NGS reference materials (Seraseq™ Breast CNV and Seraseq™ Lung & Brain CNV) with known CNAs were also WGA’ed. WGA products were used as input for the Ampli1™ OncoSeek Panel assay (Menarini Silicon Biosystems), a single-tube, Illumina®-compatible kit that covers 60 clinically relevant genes including more than 1500 mutation hotspots and CNAs for a subset of 19 genes. WGA-tailored primer pairs design and their concentrations were optimized so that targeted amplicons for sequence variants are sufficiently represented. Redundant amplicons were included for robustness of focal CNA detection. Bioinformatic analysis was performed with an assay-specific, cloud-based pipeline (MSBiosuite, Menarini Silicon Biosystems).

Results

Results on Seraseq NGS reference materials with known copy number gains (3, 6, 12) on 6 genes showed accurate detection of expected CNAs and high linearity of response (R2 = 0.97 ± 0.04). We observed low ADO rate (12.7% ± 4.2%). The Ampli1™ OncoSeek Panel assay detected known mutations and CNAs from cell lines at high sensitivity and the analysis of polymorphic variants in WBCs showed high agreement between biological replicates (overall agreement = 0.94 ± 0.06). Sequencing of CTCs from patients is ongoing and will be presented at the conference.

Conclusions

Here we presented a complete solution to detect hotspot mutations and focal CNAs that meets the need for accurate tumour characterization at single-cell level, suitable for individual CTC analysis.

Citation Format: Paola Tononi, Valentina del Monaco, Alberto Ferrarini, Genny Buson, Marianna Garonzi, Claudio Forcato, Andrea Raspadori, Nicolò Manaresi. Validation of a targeted sequencing workflow for sequence variants and focal copy number alterations (CNAs) in single circulating tumor cells (CTCs) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2517.

Abstract 2198: An integrated workflow for liquid biopsy of circulating multiple myeloma cells (CMMCs) with single cell resolution reveals tumor heterogeneity

Background: Multiple myeloma (MM) is a bone marrow derived cancer of plasma cells, which remains an incurable disease. Because of the invasive and painful nature of bone biopsy, an alternate tumor monitoring strategy is needed. We have previously shown that Circulating Multiple Myeloma Cells (CMMCs) isolated by CellSearch® (CS) are prognostic and indicative of disease burden through remission and relapse. Here we report, for the first time, the molecular characterization of pure single CMMCs isolated from a multiple myeloma patient, by integrating CS and DEPArray™ (DA) NxT systems, providing access to copy-number alteration (CNA) profiling. Methods: 4.0ml of peripheral blood from a patient with multiple myeloma was tested. On CS, target CMMCs were enriched using anti-CD138 for cell capture, and stained immunofluorescently with CD38-PE, CD19 and CD45-APC. Nuclei were stained with DAPI and detected target cells counted. The enriched sample was then analyzed using the DA NxT system: single CMMCs (CD38+/CD19- and CD45-/DAPI+), along with some single White Blood Cells (WBCs: CD38-/CD19+ or CD45+/DAPI+), were isolated. The DNA of each single cell was amplified using the Ampli1™ WGA kit and used for highly-multiplexed, genome-wide single-cell CNA analysis using a Ampli1™ LowPass kit (LPCNA) on Illumina® MiSeq. Results: CS identified 128 CMMCs. From DA NxT we harvested 20 individual CMMCs for LPCNA analysis. Copy-number profiles of CMMCs confirmed their tumor origin, showing a high-level of genome instability with several gains and few losses of chromosomal segments. Moreover, an unsupervised hierarchical cluster analysis highlighted a conserved pattern of alterations, enabling the separation between CMMCs and WBCs groups. A pattern of copy-number gains shared by all CMMCs, coupled with gains and losses shared by a subset of CMMCs, suggests a branched evolution of different tumor subclones. WBC profiles were flat as expected. Conclusions: Cell enrichment by CS followed by individual cell sorting using DA NxT, enabled the isolation of single CMMCs with 100% purity. Ampli1™ single-cell analysis demonstrated CMMC molecular heterogeneity suggestive of tumor subclones presence. This platform combination provides a reliable and non-invasive method for MM characterization enabling translational research and future clinical application.

Citation Format: Mario Terracciano, Claudio Forcato, Edoardo Petrini, Alberto Ferrarini, Valentina del Monaco, Andrea Raspadori, Carrie Morano, Steven Gross, Chiara Bolognesi, Genny Buson, Thai Bui, Francesca Fontana, Gianni Medoro, Mark Connelly, Nicolò Manaresi. An integrated workflow for liquid biopsy of circulating multiple myeloma cells (CMMCs) with single cell resolution reveals tumor heterogeneity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2198.

Abstract 4579: The genetic heterogeneity and the molecular evolution of systemic metastatic castration resistant prostate cancer during therapy

Background: Circulating tumour cells (CTCs) have a significant prognostic impact in metastatic castration-resistant prostate cancer (mCRPC) and provide direct access to the systemic disease. Here, we performed genome-wide copy number analysis of CellSearchTM detected CTCs to follow the genomic evolution of mCRPC during systemic therapy.

Methods: Blood samples were collected from 13 patients with mCRPC before, during and after two different targeted therapy regimes. Single CTCs were isolated from CellSearchTM cartridges using the DEPArray™ system and the MoFlo XDP cell sorter. Genomes of sorted single cells were amplified using Ampli1™ WGA kit. Amplification products were analysed by array-based comparative genomic hybridization (aCGH) and low-pass sequencing (LPS) using Ampli1™ LowPass kit to detect somatic chromosomal copy number aberrations (CNAs) and explore the degree of genomic heterogeneity.

Results: We analysed >300 CTCs for CNAs by aCGH and/or LPS. Although most CTCs displayed CNAs typical for mCRPC, we identified three genomic CTC-groups across all cells with the EpCAMpos/CKpos/DAPIpos/CD45neg phenotype: CTCs with typical mCRPC CNAs (Type A; 80%), extremely aberrant CTCs (Type B; 11%), CNA-negative/low CTCs (Type C; 9%). The occurrence of Type B and C was almost mutually exclusive. At baseline, we noted different levels of CTC-heterogeneity and different CTC-aberration levels between the different patients. Interestingly, CTCs of patients with a relevant decrease in CTC-count under PARP-inhibition (CTC-responder) displayed significantly elevated CNAs at baseline compared to CTC-non-responders. During therapy, we could observe clonal changes among all patients.

Conclusions: Our data show that CTC-analysis enables the dissection of clinical relevant intra-patient heterogeneity and clonal evolution under therapy in mCRPC patients. Comprehensive genomic monitoring during therapy might help to tailor therapies more effectively and may pinpoint to molecular mechanism of therapeutic resistance.

Citation Format: Rui PL Neves, Streit LRF Anna, Katharina Raba, Elina-Katharina Bongers, Bianca Behrens, Guus van Dalum, Penny Flohr, Joaquin Mateo, Semini Sumanasuriya, Mateus Crespo, Berni Ebbs, Gemma Fowler, Pasquale Rescigno, Suzanne Carreira, Maryou Lambros, Edoardo Petrini, Marianna Garonzi, Nicolò Manaresi, Johann de Bono, Nikolas H. Stoecklein. The genetic heterogeneity and the molecular evolution of systemic metastatic castration resistant prostate cancer during therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4579.

Abstract 3654: Identification of resistance mutations to crizotinib through circulating tumor cell (CTC) analysis in ALK-rearranged non-small-cell lung cancer (NSCLC)

Background

Non-invasive methods including CTCs are crucial to develop for the implementation of precision medicine in the treatment of NSCLC. We recently reported how CTCs with abnormal ALK FISH-patterns monitored on treatment can stratify patients at risk of early-resistance to crizotinib (Pailler et al., Cancer Res, 2017). ALK-rearranged NSCLC patients treated with crizotinib develop resistance which manifest by the upregulation of bypass signaling pathways in two-thirds of cases. Here, we evaluated whether individual CTCs could identify resistance mutations to crizotinib and represent tumor diversity compared to single-site tumor-biopsies.

Methods

Individual CTCs were isolated from seven ALK-rearranged patients at resistance to crizotinib. Matched tumor-biopsies were available for three. Two isolation strategies were used: (i) ISET-filtration, immunofluorescence (Hoescht/CD45/epithelial-markers/mesenchymal-marker), scanning, laser-microdissection; (ii) RosetteSep, immunofluorescence (Hoescht/CD45/ALK/cytokeratins), cell-sorting. A process including Ampli1 whole-genome amplification, quality controls, multiplex PCR with two panels (Ampli1 CHPCustomBeta cancer panel developed by Silicon Biosystems and a home-made panel targeting all ALK mutations) and Ion Torrent next-generation sequencing (NGS) was established. Ten to 17 pools with 1-5 CTCs and one CD45+ cell pool were analyzed for each patient. A bioinformatic workflow was developed including determination of allele drop-out (ADO), false-positive rate (FPR) and positive predicted value (PPV).

Results

By comparing germline variants present in constitutional and CD45+ pool DNA, we calculated for each sample the statistics of mean ADO, FPR and PPV which were respectively 19%, 2.6x10-4 and 69%. When variants were present into two pools, the PPV and FPR were 96% and 2.39 10-5 respectively. In the three patients with an available tumor-biopsy, a limited number of shared mutations between CTC and matched tumor-biopsies were identified. In contrast, CTC-private mutations (exclusively present in CTCs and not in matched biopsies) present in at least two CTC pools were identified including in FLT3, SMAD4, KIT, PI3KCA, EGFR, KRAS, PDGFRA genes among which several were COSMIC mutations. A higher degree of mutational diversity was observed in CTCs compared to tumor-biopsies.

Conclusion

Using a rigorously qualified workflow, we reported for the first time the identification of resistance mutations in individually isolated CTCs of ALK-rearranged patients. In accordance with published series from tumor-biopsies, our CTC results highlighted the role of bypass signaling pathways in resistance to crizotinib. Our study provides important perspectives on using CTCs for precision medicine and informing on tumor heterogeneity in NSCLC patients.

Citation Format: Emma Pailler, Vincent Faugeroux, Marianne Oulhen, Claudio Forcato, Mélanie Laporte, Yann Lecluse, Ludovic Lacroix, Maud NgoCamus, Claudio Nicotra, Jordi Remon, Laura Mezquita, David Planchard, Jean-Charles Soria, Nicolò Manaresi, Benjamin Besse, Françoise Farace. Identification of resistance mutations to crizotinib through circulating tumor cell (CTC) analysis in ALK-rearranged non-small-cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3654.

A streamlined workflow for single-cells genome-wide copy-number profiling by low-pass sequencing of LM-PCR whole-genome amplification products

Chromosomal instability and associated chromosomal aberrations are hallmarks of cancer and play a critical role in disease progression and development of resistance to drugs. Single-cell genome analysis has gained interest in latest years as a source of biomarkers for targeted-therapy selection and drug resistance, and several methods have been developed to amplify the genomic DNA and to produce libraries suitable for Whole Genome Sequencing (WGS). However, most protocols require several enzymatic and cleanup steps, thus increasing the complexity and length of protocols, while robustness and speed are key factors for clinical applications. To tackle this issue, we developed a single-tube, single-step, streamlined protocol, exploiting ligation mediated PCR (LM-PCR) Whole Genome Amplification (WGA) method, for low-pass genome sequencing with the Ion Torrent^™ platform and copy number alterations (CNAs) calling from single cells. The method was evaluated on single cells isolated from 6 aberrant cell lines of the NCI-H series. In addition, to demonstrate the feasibility of the workflow on clinical samples, we analyzed single circulating tumor cells (CTCs) and white blood cells (WBCs) isolated from the blood of patients affected by prostate cancer or lung adenocarcinoma. The results obtained show that the developed workflow generates data accurately representing whole genome absolute copy number profiles of single cell and allows alterations calling at resolutions down to 100 Kbp with as few as 200,000 reads. The presented data demonstrate the feasibility of the Ampli1^™ WGA-based low-pass workflow for detection of CNAs in single tumor cells which would be of particular interest for genome-driven targeted therapy selection and for monitoring of disease progression.

Abstract 5345: Complementary NGS approaches on digitally sorted pure tumor cells reveal hidden molecular characteristics in low tumor content FFPE specimens

Introduction:

Precise characterization of tumor cell populations is an essential requirement for guiding the cancer care, allowing patients to receive personalized therapies. Poor biopsies with low-tumor content represent a significant barrier for sample enrollment in clinical trials. Here we describe a multi-level approach for precisely characterizing the genetic mutation landscape of pure tumor cell populations sorted by the DEPArray™ technology from low-cellularity FFPE samples.

Methods:

50μm sections of FFPE from breast infiltrating ductal adenocarcinoma with 10% tumor content were processed by DEPArray sorting protocol. Illumina-compatible libraries were prepared from sorted stromal (n=497) and tumor (n=419) cell pools, and from the unsorted sample. An aliquot of these libraries was processed using SeqCap EZ MedExome enrichment kit (Roche) for whole-exome sequencing (WES) with a HiSeq 2500, reaching a mean coverage of 27x for tumor and 25x for stromal libraries. A second aliquot was used for low-pass (≈1M fragments per sample) whole-genome sequencing (WGS) on a MiSeq to analyze copy-number alterations (CNA). Other cell lysates from stromal (n=104, n=112) and pure tumor (n=75) populations were used in DEPArray OncoSeek amplicon-based assay for focused analysis of clinically relevant somatic variants and copy-number alterations.

Results:

In sorted pure tumor populations, WES analysis of B-allele frequencies of germline heterozygous SNPs clearly outlined an aberrant profile, precisely revealing several Loss-of-Heterozygosity (LOH) and copy-altered regions. Conversely, unsorted gDNA showed a flat profile non-distinguishable from sorted stromal cells, as expected for a low-cellularity tumor sample. Similar results were obtained by low-pass WGS, where the huge number of copy number aberrations (≈1.2 Gbp) in tumor is contrasted by lack of gains and losses in stromal cells and unsorted gDNA. Noteworthy, WES, low-pass and targeted sequencing by OncoSeek panel highlighted a focal amplification of ERBB2 gene (>13 copies), which was just barely detectable as a 1-copy gain in bulk gDNA. Genetic analyses showed a high concordance between WES and targeted panel data, with two non-synonymous homozygous somatic mutations found in TP53 (p.L111R) and ERBB2 (p.D769Y). In the unsorted sample, the TP53 mutation was missed because allelic frequency was below the limit of detection due to normal-cell dilution, while the ERBB2 mutation was still detectable only because of the high-level amplification.

Conclusions:

DEPArray sorting technology is an indispensable tool for accurately investigating cancer genomes, enabling multi-level applications for obtaining a fine-grain characterization of copy-numbers, LOH, and tumor-specific variants, independent of original tumor content.

Citation Format: Claudio Forcato, Alberto Ferrarini, Genny Buson, Cassie Schumacher, Chiara Bolognesi, Paola Tononi, Valentina del Monaco, Chiara Mangano, Francesca Fontana, Gianni Medoro, Timothy Harkins, Nicolò Manaresi. Complementary NGS approaches on digitally sorted pure tumor cells reveal hidden molecular characteristics in low tumor content FFPE specimens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5345. doi:10.1158/1538-7445.AM2017-5345

Abstract 5349: Accurate molecular profiling of sequence and copy number alterations from sub-nanogram FFPE DNA amounts

Introduction: Formalin-fixed paraffin-embedded (FFPE) specimens represent an invaluable source of material for precision oncology. However, FFPE samples pose significant challenges for molecular assays, such as targeted Next-Generation Sequencing (NGS), because of the highly variable DNA quality and often limited sample size. Here we present a complete workflow from sample quality control to targeted library preparation to reliably detect sequence and copy number alterations (CNA) through targeted NGS from extremely low input FFPE samples.

Materials & methods: Three FFPE specimens from patients with breast (BrCa) or pancreatic cancer, with DNA quality varying over a broad range and with low tumor cellularity (down to 10%) were selected for targeted NGS profiling. The DNA quality was determined using the DEPArray™ FFPE QC Kit, a qPCR-based assay yielding a QC score defined as the ratio between the quantification of a 132 bp amplicon, corresponding approximately to the average length (116bp) of DEPArray OncoSeek amplicons, and a shorter amplicon of 54 bp. The QC scores of the 3 FFPE specimens ranged between 0.23 to 0.74. We then used QC score, multiplied by the ploidy (assessed on DEPArray during cell sorting) and by the number of cells recovered, to estimate the effectively amplifiable template (EAT). Thirty two pure cell populations (21 stromal and 11 tumor), with different EATs (80-300), corresponding to a wide range of number of cells per pool (31-214), were collected with the DEPArray digital sorter. Libraries were prepared from each cell pool, using the single-tube, Illumina-compatible DEPArray OncoSeek panel comprising 63 oncology relevant genes (average 740,000 sequenced amplicons per sample).

Results: Variant calling showed sensitivity comprised between 93% and 99% and specificity > 99% for EATs ≥ 80 equivalent to as low as ≈250 pg of DNA. Analysis of CNAs in stromal cells was highly specific (zero false positive at 1.5 fold-change threshold). Moreover, analysis allowed to highly reproducibly identify CNAs in CCND1 (3x), ERBB2 (8x), MYC (3x) and PIK3KA (2x) in both replicates of one BrCa sample. Similarly, ERBB2 amplification (7x) was found in the other BrCa sample (10% tumor cellularity) across two replicates at different EATs (80, 120) corresponding to as low as 59 and 75 cells. As expected by the low tumor content, in the corresponding unsorted sample ERBB2 was below the 2-fold gain threshold with respect to the stromal control, which would not qualify a sample as Her2-amplified.

Highlights: Starting from pure intact cells with well characterized DNA quality and ploidy, our workflow allows reliable molecular profiling of sub-nanogram DNA samples by determining with precision the extremely-low minimum amount of cells necessary to obtain highly reproducible sequence variant calling and CNAs detection by targeted NGS.

Citation Format: Paola Tononi, Alberto Ferrarini, Genny Buson, Valentina del Monaco, Giulio Bassi, Chiara Mangano, Claudio Forcato, Chiara Bolognesi, Francesca Fontana, Gianni Medoro, Nicolò Manaresi. Accurate molecular profiling of sequence and copy number alterations from sub-nanogram FFPE DNA amounts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5349. doi:10.1158/1538-7445.AM2017-5349

Abstract 3945: Precise copy-number profiling of single cells isolated from FFPE tissues by low-pass whole-genome sequencing

Introduction

Chromosome instability (CIN) is a hallmark of cancer, acting by boosting genetic alterations responsible of tumorigenesis, progression and heterogeneity. Whole-genome sequencing (WGS) protocols are established methods for studying copy-number alterations (CNA) in single-cells, following a necessary whole-genome amplification (WGA) step. We previously presented a method for single-cell CNA profiling of CTCs based on shallow WGS of LM-PCR based WGA products. Here for the first time, we show that the same method may be employed even on single FFPE cells, overcoming the challenges of DNA degradation and damage linked to this type of samples.

Methods

Two 50μm thick FFPE sections from pancreas ductal adenocarcinoma with <20% tumor content were processed following DEPArray™ sample preparation protocol, including cell dissociation and staining with vimentin, keratin and DAPI, and DNA quality was assessed using the DEPArray FFPE QC kit (QC=0.7). Cell pools (n=15, range=6-213 cells) and single-cells (n=11) from pure tumor and stromal populations were recovered in separate tubes and lysed. A pool of 86 tumor cells and a pool of 213 stromal cells were used for low-pass WGS on MiSeq, obtaining ≈2M paired-end reads on average. By contrast, other cell pools and single cells were firstly whole-genome amplified using the Ampli1™ WGA kit and then sequenced at shallow coverage using Ampli1 LowPass kit and IonTorrent PGM, with ≈500k single-end reads as mean throughput per library. The genome integrity (GI) of WGA samples was evaluated by Ampli1 QC, a PCR-assay based on 4 amplicons of different lengths.

Results

The purity of DEPArray sorting was confirmed by the large number of chromosome alterations in sorted tumor and the parallel lack of gains and losses in sorted stromal pools and single-cells. A titration test was conducted measuring the consistency of CNA profiles of tumor WGA products starting from different number of cells, ranging from 117 down to single cells. For the purpose, we employed a Receiver Operating Characteristic (ROC) curve using the non-amplified tumor population as reference. Results showed an excellent performance level with a mean Area Under Curve (AUC) equals to 0.93. Interestingly, lower AUCs (0.87) were observed for single-cells, due to some level of inter-cell heterogeneity. Moreover, the proposed low-pass WGS method demonstrated a high resiliency to DNA degradation as quality of CNA profiles, measured by Derivative Log Ratio Spread (DLRS), only showed a weak correlation with GI level, with high-quality CNA profiles obtained also with the lowest GI value.

Conclusions

Presented approach for copy-number profiling of tumor single-cells isolated by DEPArray digital sorter and processed with Ampli1 workflow has proven to be a reliable and valuable application for the molecular characterization of tumor clones in degraded samples as FFPE tissues.

Citation Format: Alberto Ferrarini, Genny Buson, Chiara Bolognesi, Claudio Forcato, Paola Tononi, Valentina del Monaco, Chiara Mangano, Francesca Fontana, Gianni Medoro, Nicolò Manaresi. Precise copy-number profiling of single cells isolated from FFPE tissues by low-pass whole-genome sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3945. doi:10.1158/1538-7445.AM2017-3945

Abstract 1717: Orthogonal identification of circulating tumor cells (CTCs) using single cell low pass whole-genome sequencing (WGS) and copy-number alteration (CNA) analysis

Introduction: Presence of circulating tumor cells has prognostic value in multiple malignancies, and molecular analysis of CTCs is currently ongoing in numerous clinical trials. Most CTC enrichment methods rely on standard epithelial and leukocyte markers (CK+CD45-), so recovered cells are assumed to be of epithelial origin but never shown to be bona fide tumor cells. Conversely, atypical cells lacking the characteristic marker profile may not be analyzed, even though they may represent important tumor subpopulations. Here we evaluate a rapid, non-exhaustive, and cost-effective first-pass genomic analysis of individual candidate CTCs. This approach allows efficient upfront CNA-based confirmation that a given cell is of tumor origin, while leaving abundant DNA for deeper subsequent analysis in cells of interest.

Methods: Whole peripheral blood of metastatic prostate cancer patients was enriched for CTCs using the CellSearch® system (Janssen Diagnostics) under an IRB-approved protocol, and 5 samples with >5 CTCs were selected for further study. Next, the DEPArray™ v2 system (Menarini Silicon Biosystems) was used to identify and isolate single CTCs (CK+CD45-DAPI+) and paired white blood cells (WBCs; CK-CD45+DAPI+) from the enriched samples. In addition, cells negative for both cytokeratin and CD45 but with characteristic malignant morphology (large with high nuclear-cytoplasmic ratio) were isolated. Recovered single cells were whole-genome amplified with Ampli1™ WGA and quality controlled by Ampli1 QC. Ampli1 LowPass kit was then used to prepare NGS libraries for absolute CNA profiling by low-pass WGS.

Results: Thirty-three single CTCs (CK+CD45-DAPI+) and 30 WBCs (CK-CD45+DAPI+), as well as 47 putative CTCs with non-conventional phenotype (CK-CD45-DAPI+) were isolated. Single-cell WGA products with high Genome-Integrity Index (QC score ≥3) were prioritized for CNA analysis. Ampli1 LowPass data demonstrated copy number gains/losses confirming tumor origin of the CK+ cells, while WBCs showed a normal profile. In addition, a portion of the cells having non-conventional phenotype also demonstrated copy number alterations consistent with tumor origin.

Discussion: We demonstrate a WGA and low-pass WGS approach on single CTCs sorted from enriched peripheral blood, which offers a dual benefit: i) it allows rapid, non-exhaustive upfront identification of bona fide tumor cells for further study, and ii) it reveals genetic similarities and diversities (vis a vis copy number alteration) across CTCs of classical as well as non-conventional phenotypes, which may better represent clonal diversity. In a clinical setting, this molecular approach may be more effective for reliably identifying and characterizing heterogeneous CTCs, yielding profiles that more accurately reflect disease evolution and inform treatment strategies.

Citation Format: Gareth Morrison, Valeria Sero, Yucheng Xu, Jacek Pinski, Sue Ingles, David Quinn, Claudio Forcato, Genny Buson, Chiu-Ho Webb, Kyle Horvath, Aditi Khurana, Gianni Medoro, Suman Verma, Matthew Moore, Philip Cotter, Nicolò Manaresi, Farideh Bischoff, Amir Goldkorn. Orthogonal identification of circulating tumor cells (CTCs) using single cell low pass whole-genome sequencing (WGS) and copy-number alteration (CNA) analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1717. doi:10.1158/1538-7445.AM2017-1717

CLIA validation workflow of a novel tumor cell isolation platform

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Background: DEPArray™ technology is based on Dielectrophoresis (DEP). High quality image-based cell selection enables users to identify, isolate and recover intact specific individual rare cells of interest from complex, heterogeneous tissues such as live or fixed cell suspensions. Here we demonstrate a validation workflow for application of molecular sequencing technologies and FISH downstream of rare cell recovery. Methods: FFPE scrolls (n = 93) were dissociated and stained with markers to distinguish putative stromal and tumor populations. DNA integrity was tested using a qPCR technique to predict the amount of DNA required for a successful downstream sequencing metrics. DEPArray™ recovered stromal and tumor cells underwent NGS analysis on an Illumina platform based DEPArray™ OncoSeek Panel. Separately, recovered stromal and tumor cells were also utilized for targeted HER2 FISH. CellSearch® cartridges (19 Breast and 5 Bladder Cancers) were processed through the DEPArray to isolate WBCs (CK-/CD45+/DAPI+; n = 30), CTCs (CK+/CD45-/DAPI+; n = 33) and atypical (CK-/CD45-/DAPI+; n = 47) cells. Recovered cells underwent whole-genome amplification with Ampli1™ WGA and quality controlled by Ampli1 QC. Ampli1 LowPass kit was then used to prepare NGS libraries for absolute CNA profiling by low-pass WGS. Results: Reproducibility and reliability was reported as 100% for instrument performance. For FFPE, the OncoSeek panel simultaneously detected SNPs, indels and CNAs of 63actionable and oncology relevant genes. For FISH, 95% concordance with conventional HER2 results was observed. For CTCs, Ampli1 LowPass detected copy number gains/losses confirming tumor origin of the CK+ cells. A portion of non-conventional cells also demonstrated copy number alterations consistent with tumor origin. Conclusions: The isolation of pure single or pooled tumor cells with the DEPArray™ technology can be used as a method to improve downstream MDx analysis using different techniques, thus to inform treatment decisions and provide valuable prognostic information.

Digital sorting and copy number profiling of purified, PD-L1 positive, Reed Sternberg cells in classical Hodgkin lymphoma

7528

Background: Classical Hodgkin Lymphoma (cHL) is one of the disease in which the check-point inhibitors have been demonstrated to be more successful. Lately, it has been reported that in malignant Reed-Sternberg Cells (RSCs), PD-1 ligands (PD-Ls) are overexpressed and that chr.9 amplification correlates with advanced stages of the disease, when the standard therapy have already failed. Unfortunately, the detection of the genetic alterations in RSCs is challenging, as one of the hallmark of cHL is the presence of a small number of malignant cells sparse in an abundant and heterogeneous immune infiltrate. Here we present a method for the isolation and the genetic characterization of purified RSCs, which overcomes the limitations posed by the low-cellularity of cHL biopsies, and could be helpful for earlier detection of genetic alterations and adoption of immunotherapy. Methods: FFPE tissue sections from cHL patients were dissociated down to single-cell suspension and stained using anti-CD30 and anti-PD-L1 antibodies. Beyond the positivity to CD30 and PD-L1, RSCs were selected according to morphological criteria such as cell size and the presence of polylobate nuclei compared to surrounding lymphocytes. Target cells were isolated using the DEPArray™ cell sorter, as single cells or in small pools of cells. Recovered cells were whole genome amplified ( Ampli1™ WGA), and genome-wide copy-number aberrations (CNAs) profiles were obtained using Ampli1™ LowPass kit on IonTorrent platform. Results: After the dissociation, RSCs maintained cell morphology and therefore, we were able to discriminate them from the heterogeneous immune infiltrate. RSCs appeared as large multinucleated cells with a big central nucleolus surrounded by a clear halo; cell diameter and ploidy were computed from the images. Pools of lymphocytes and pools of CD30+/ PD-L1+ RSCs were isolated. Sequencing results confirmed the expected flat profile for lymphocytes, while RSCs showed an aberrant profile with multiple losses and gains. Conclusions: The analysis of purified RSCs, could offer a valuable tool to uncover genetic alterations hidden by cHL immune infiltrate, for earlier adoption of more effective treatment regimens.

Inter-laboratory evaluation of a novel DEPArray-HER2 FISH assay

e12506

Background: Fluorescent in Situ Hybridization (FISH) is a method currently used for detection and assessment of HER2 gene amplification. Although clinical guidelines set forth by CAP/ASCO exist to ensure accuracy, limitations in HER2test results due to sample preparation, assay-conditions and tumor heterogeneity remain unresolved. We have successfully demonstrated analytical confidence in performing HER2 FISH on DEPArray™ sorted and recovered tumor cells. In this study, we aimed to evaluate inter-laboratory concordance of the DEPArray™ HER2-FISH assay. Methods: Three laboratories equipped with the DEPArray™ were designated as testing sites for this study. Positive control SKBr3 cells embedded in paraffin as well as 20 invasive breast carcinoma FFPE samples were blinded and evaluated by each of the three labs. Control and patient samples were processed through the DEPArray™ beginning with dissociation of the FFPE curls followed by single-cell image-based cell sorting to separate and recover pure distinct tumor cell populations prior to HER2 FISH analysis. Data was only obtained when ∼200 intact cytokeratin+/vimentin-/DAPI+ tumor cells from each sample were recovered and used for subsequent FISH using a standard dual-color HER2/CEP17 FISH procedure. Results: Overall, 80% concordance between DEPArray™-HER2 and conventional HER2 (6 HER2 negative and 10 HER2 positive) was observed between lab(s) and the conventional HER2 method. In each of 4 cases, a discordant HER2 result was reported by one of three sites. In three of these discordant cases, the DEPArray™ HER2 ratio was reported as amplified while the conventional result was negative. In the remaining discordant case, the converse was observed by one site; however, this case was initially evaluated 15 years ago. All three sites correctly scored the SKBr3 positive control cells. Conclusions: The results showed a high concordance rate of correct HER2 status classification. This data further supports the understanding that tissue heterogeneity can indeed give rise to discordant results that may consequently affect treatment options for patients. We demonstrate that sample preparation by DEPArray™ may aid in a more precise classification for tumor biomarker status.

A new method for gene expression analysis of pure lymphocytes recovered from heterogeneous fixed mouse tissue

e23089

Background: Tumor infiltrating lymphocytes (TILs) are biomarkers that play a critical role in cancer diseases, including differential diagnosis, determination of prognosis, prediction of response to treatment, and evaluation of disease progression. Gene expression analysis in TILs derived from fresh tissue may not accurately depict the gene profile of the tissue microenvironment as it can change aggressively during lymphocyte isolation and RNA extraction. In addition, tissue sample size can limit the isolation of TILs with current technologies. In this study, we demonstrate the use of the DEPArray™platform to isolate pure populations of lymphocytes from a fixed mouse tissue for RNA analysi. Methods: Mouse splenocytes were activated in vitro with anti-CD3 and -CD28 for 72hs. Cells were harvested, fixed with 2% paraformaldehyde (PFA) for 20 min at RT, and stained for either CD4 or CD8 expression. Gene expression analysis of CD45, ADORA2A, GLS and GAPDH was performed in CD4+ and CD8+ DEPArray™sorted cells using the TaqMan PreAmp Cells-to-Ct kit. Results: The table below summarizes the Ct values for CD45, ADORA2A, GLS and GAPDH expression in 300 fixed unsorted control and DEPArray™sorted lymphocytes. Conclusions: We have demonstrated the feasibility of gene expression analysis on pure populations of CD4+ and CD8+ cells isolated from a fixed tissue using the DEPArray™ platform. The advantage of this approach is the DEPArray’s ability to identify and isolate subpopulations of cells from complex heterogeneous samples and/or specimens that are limited by size or content. This methodology will be applied for isolation of TILs in syngeneic and xenograft models of cancers for downstream RNA applications. [Table: see text]

CLIA validation of a novel HER2 FISH test involving image-based cell-sorting to recover pure tumor cell populations from formalin fixed paraffin embedded tissue

e12519

Background: The use of the DEPArray™ system to prepare pure tumor cell populations for more reliable and accurate downstream molecular sequence analysis has been previously demonstrated. To formally evaluate the utility of the DEPArray™ for sample preparation prior to molecular testing, we conducted a CLIA validation study to investigate the analytical performance of the instrument as well as accuracy in determining HER2 status in FFPE tumor specimens using a standard FISH assay. Methods: An initial cohort consisting of 93 FFPE samples (68 from Breast and 25 from Stomach) were selected based on defined inclusion criteria (tumor type and tumor content). For each sample, a single 50µm FFPE scroll was dissociated and then stained using fluorescently labeled Vimentin and Cytokeratin markers to distinguish between putative stromal and tumor populations, respectively. Following separation of these populations on the DEPArray™, a minimum of 100 single cells from each population was recovered and used for subsequent HER2 FISH testing. In addition, an H&E of each sample was evaluated by a Pathologist to confirm the presence of tumor content. Single-cell HER2-FISH analysis was then performed on the DEPArray™ processed samples to assess the number of signals present for each of the chromosome 17 and HER2 loci. Results were compared to the conventional tissue section FISH score. Results: Of the 93 specimens, 80 samples met pre-analytical acceptability criteria that were also confirmed by conventional methods to be either HER2-positive (n = 43) or HER2-negative (n = 37). Overall, a 95% concordance between HER2 results derived from the conventional as compared to the DEPArray™ method was observed. In addition, the instrument performance in terms of reproducibility and reliability was reported as 100%. Conclusions: DEPArray™ for preparation of FFPE-derived tumor cells was analytically validated and shown to yield high confidence in performing HER2-FISH analysis on recovered pure tumor cells. Current strategies to establish clinical utility and efficacy of this approach are underway for cases characterized as equivocal for HER2 or indeterminate by FISH.

Isolation and genetic analysis of pure cells from forensic biological mixtures: The precision of a digital approach

Latest genotyping technologies allow to achieve a reliable genetic profile for the offender identification even from extremely minute biological evidence. The ultimate challenge occurs when genetic profiles need to be retrieved from a mixture, which is composed of biological material from two or more individuals. In this case, DNA profiling will often result in a complex genetic profile, which is then subject matter for statistical analysis. In principle, when more individuals contribute to a mixture with different biological fluids, their single genetic profiles can be obtained by separating the distinct cell types (e.g. epithelial cells, blood cells, sperm), prior to genotyping. Different approaches have been investigated for this purpose, such as fluorescent-activated cell sorting (FACS) or laser capture microdissection (LCM), but currently none of these methods can guarantee the complete separation of different type of cells present in a mixture. In other fields of application, such as oncology, DEPArray™ technology, an image-based, microfluidic digital sorter, has been widely proven to enable the separation of pure cells, with single-cell precision. This study investigates the applicability of DEPArray™ technology to forensic samples analysis, focusing on the resolution of the forensic mixture problem. For the first time, we report here the development of an application-specific DEPArray™ workflow enabling the detection and recovery of pure homogeneous cell pools from simulated blood/saliva and semen/saliva mixtures, providing full genetic match with genetic profiles of corresponding donors. In addition, we assess the performance of standard forensic methods for DNA quantitation and genotyping on low-count, DEPArray™-isolated cells, showing that pure, almost complete profiles can be obtained from as few as ten haploid cells. Finally, we explore the applicability in real casework samples, demonstrating that the described approach provides complete separation of cells with outstanding precision. In all examined cases, DEPArray™ technology proves to be a groundbreaking technology for the resolution of forensic biological mixtures, through the precise isolation of pure cells for an incontrovertible attribution of the obtained genetic profiles.

Abstract 2394: Scalable, rapid and affordable low-pass whole genome sequencing method for single-cell copy-number profiling on LM-PCR based WGA products

Introduction: Genome-wide profiling of copy-number alterations (CNA) in single cells enables the characterization and investigation of genomic heterogeneity and evolution in tumor cell populations such as individual circulating tumor cells (CTCs), or disaggregated solid tumors. Ampli1™ WGA is a commercially available kit for whole-genome amplification from single cells suitable for array comparative genomic hybridization (aCGH), which is currently the gold standard for genetic diagnosis of CNA. However, labor and reagent costs limit aCGH applicability. Here we introduce for the first time a rapid, high-throughput low-pass Whole Genome Sequencing (WGS)-based method for CNA analysis (LPCNA) on single cells, enabling simultaneous profiling of multiple cells at lower cost and effort.

Methods: Six single cells from NCI-H23, NCI-H661 and NCI-H1650 cell lines and 19 white blood cells (WBCs) were amplified using Ampli1™ WGA Kit. Only 5μl (1/10th of total WGA product) were used as sample input for LPCNA. Purified WGA products were processed for each sample in a single-tube, one-step reaction resulting in IonTorrent-compatible indexed libraries. Samples were pooled and size-selected to recover fragments with a length ranging from 300 to 400 bp. Following purification and template preparation, pools were sequenced on Ion 318™v2 Chips. Array CGH was performed for comparison, using Agilent SurePrint 4×180k arrays as previously reported. CNA analysis was performed using Control-FREEC for low-pass WGS data, or Agilent Genome Workbench for aCGH.

Results: By exploiting the deterministic nature of Ampli1™ whole genome amplification, we devised a method to generate IonTorrent compatible libraries in a single reaction, drastically reducing time of bench work and cost.

Method accuracy has been assessed by comparing the copy number profiles generated by our approach with about 870,000 reads/sample (average genome coverage of 0.064x, range 0.051-0.073) with those obtained by a validated aCGH method. Very good agreement in gain and loss profiles was achieved for all single tumor cells analyzed. As expected WBC analysis resulted in normal copy-number profiles with autosomes copy number = 2, with minimal false-positive rate (<0.6% at a resolution of 760kb with 618k reads).

Highlights: This innovative low-pass sequencing approach for CNA detection on single cells enables high level multiplexing on different NGS platforms. The approach is highly scalable and flexible. From few (6-8) samples (IonTorrent PGM, 318™v2 Chip), up to 96 samples (Ion Proton, Ion PI™ Chip v3) can be processed in a single run. This approach meets the need for rapid results (<7h turnaround time for library preparation) and affordable cost required for massively parallel single-cell analysis such as multiple tumor cells or CTCs.

This work has been carried out within IMI CANCER-ID consortium (www.cancer-id.eu).

Citation Format: Genny Buson, Paola Tononi, Claudio Forcato, Francesca Fontana, Gianni Medoro, Rui Neves, Birte Möhlendick, Nikolas Stoecklein, Nicolò Manaresi. Scalable, rapid and affordable low-pass whole genome sequencing method for single-cell copy-number profiling on LM-PCR based WGA products. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2394.

Abstract 2417: Efficiency in recovery of pure tumor cell populations from limited tumor tissue specimens intended for clinical application

Introduction: We have previously shown reliability in isolating pure populations of rare cells from complex tissues using the DEPArray™ system. Several molecular techniques can be applied to a variety of histological samples, for example Macrodissection is the gross manual dissection of FFPE samples used to isolate areas of interest within a specimen for optimal downstream analysis, while Fine Needle Aspiration (FNA) is a safe procedure routinely used to examine a lesion helping to make a diagnosis. These techniques are also used to assess the effect of treatment. Here we demonstrate preliminary results showing 100% efficiency in recovering pure tumor cell populations from different samples using the DEPArray™ platform to overcome the issue of tumor heterogeneity. Method: FFPE macrodissected sections (n = 9;) and FNA (n = 5;) originating from prostate, breast, pancreatic and lung tumors were evaluated. Each was processed using a tissue disassociation and staining procedure followed by DEPArray™ sorting based on cytokeratin (Ker), vimentin (Vim) and nuclear staining. The recovered cell populations were lysed in the collection tube prior to PCR-based target enrichment for next generation sequencing using IonTorrent™ AmpliSeq CHPv2. Results: DEPArray™ analysis allowed identification of well separated cell populations, including Tumor (Vim-/Ker+) and Stromal (Vim+/Ker-) cells in all the samples analyzed. In the Macrodissection samples we were able to estimate the% of tumor cells (mean 23% range 4-54%), demonstrating an unexpected low frequency of tumor cells remaining following macrodissection. In FNA specimens analyzed only 21% (4.3% to 42.7% range) of the total (mean of 6335) cells analyzed were of tumor (KER+) origin. For subsequent NGS analysis, groups of pure cells (mean 174 cells, range from 37 to 280) for each population were recovered. Among the tumor cells isolated from the macrodissected and FNA specimens, we observed non-synonymous somatic variants and LOH events for different genes. This situation can not be highlighted in unsorted population. Conclusions: DEPArray™ technology can be used to isolate pure tumor cells from heterogeneous FFPE samples used in diagnostic application, such as Macrodissection or FNA specimens. Thus, the DEPArray™ platform brings digital precision to detection, quantification and recovery of pure target cells for subsequent downstream molecular analysis that can improve cancer diagnosis and treatment decisions.

Citation Format: Valeria Sero, Claudio Forcato, Chiara Bolognesi, Genny Buson, Giulio Signorini, Paola Tononi, Gianni Medoro, Nicolò Manaresi, Farideh Z Bischoff. Efficiency in recovery of pure tumor cell populations from limited tumor tissue specimens intended for clinical application. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2417.

Abstract 1374: Isolation and analysis of pure intact tumor cell populations from FFPE: Implications for more precise HER2 FISH testing in breast cancer

Body: Guidelines worldwide focus on the importance of precise, reproducible, and quality assurance of Fluorescent In Situ Hybridization (FISH) methods for testing companion diagnostic markers, including Human Epidermal Growth Factor Receptor 2 (HER2) gene amplification in breast cancer. Despite these guidelines, variations in test results due to pre-analytical sampling and tissue processing are observed. In this study, we demonstrate a unique approach to isolating pure and intact tumor cells from breast cancer Formalin-Fixed, Paraffin-Embedded (FFPE) samples for precise subsequent FISH analysis.

Methods: Fifty-micron thick FFPE curls from both HER2 non-amplified breast cancer tumors (n = 4; each with a reported HER2/CEP17 ratio 1.8) and positive control SKBr3 breast cancer cells were tested. Isolation of ∼250 pure and intact cytokeratin-positive/vimentin-negative/DAPI positive tumor cells from each sample was achieved using the DEPArray™ platform, an automated system enabling image-based cell sorting with single-cell resolution for pure cell population isolation and collection. Recovered cells were then cyto-spun onto poly-L coated glass slides prior to standard dual-color HER2/CEP17 FISH (Path Vysion Abbott/Vysis) analysis.

Results: Positive HER2 amplification levels for the FFPE derived control SKBr3 cells were observed (HER2/CEP17 ratio >4.4) and consistent with levels reported in the literature. Among the patient samples, ≥75% of the DEPArray™ isolated tumor cells were recovered onto slides prior to FISH. Through routine FISH scoring, an expected non-amplified result was observed for each patient sample, with observed HER2/CEP17 ratios only ranging from 1.1 to 1.4.

Conclusion: We demonstrate feasibility in performing FISH for HER2/CEP17 on pure and intact tumor cells isolated from breast cancer derived FFPE using the DEPArray™ platform. Using a 50-micron section permitted recovery of whole, intact, tumor cells based on immunostaining for cytokeratin, vimentin, and DAPI. Efficient recovery of the DEPArray™ sorted cells onto slides further permitted routine FISH analysis of only tumor cells. These preliminary results imply the possibility of more precise FISH analysis when standard FISH results are inconclusive or when insufficient tumor content prohibits downstream analysis. Evaluation of larger numbers of patient samples is underway.

Citation Format: Amanda Gerber, Trisky Clarin, Ambica Bhandari, Valeria Sero, Chiara Bolognesi, Gianni Medoro, Nicolò Manaresi, Mathew Moore, Philip D. Cotter, Farideh Bischoff. Isolation and analysis of pure intact tumor cell populations from FFPE: Implications for more precise HER2 FISH testing in breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1374.

Abstract 2253: Digital sorting and single-cell genomic profile comparison of lung adenocarcinoma CTCs between EpCAM and size-based enrichment methods

Introduction

Several methods are currently available for Circulating Tumor Cells (CTCs) enrichment. Many studies compared CTC counts between FDA-approved CellSearch® system (based on EpCAM enrichment) and size-based selection methods. However, little is known about genomic differences across CTCs obtained from different platforms. For the first time, we report here a genomic characterization of copy-number and sequence variants in single CTCs enriched with different methods from the same patient.

Methods

Peripheral blood (PB) and FFPE tissue from a pelvis bone metastasis were collected from an advanced lung adenocarcinoma patient, treated with cisplatin-pemetrexed-necitumumab as first line therapy and with carboplatin-gentamicin as second-line. Two PB samples were collected at the same time: one was enriched with CellSearch® System, and one with Parsortix PR1 (size-based selection), followed by Cytokeratin-APC, CD45-PerCp and DAPI staining.

Both samples were analyzed with DEPArray™ system and single CTCs along with single WBCs as controls, were isolated.

Collected cells were whole genome amplified with Ampli1™ WGA kit and their Genome Integrity Index (GII) was assessed. On IonTorrent™ PGM Platform, we profiled Genome-wide copy-number alterations (CNA) by low-pass whole-genome sequencing with Ampli1™ LowPass Kit, and analyzed cancer-gene sequence variants with Ampli1™ CHP Custom Beta targeted panel.

FFPE tissue was disaggregated down to single-cell suspension and labelled with Keratin and Vimentin to distinguish tumor from stromal cells. Aliquots of pure cells were recovered with DEPArray™ system; the analysis of CNVs and mutations on tissue-derived samples is in progress.

Results

Single CTCs (CK+, CD45-,DAPI), showing GII≥3, either isolated from CellSearch®-enriched or PR1-enriched blood, along with WBC, were selected for NGS.

Ampli1™ LowPass Kit data showed several aberrations confirming tumor origin of all CTCs, while WBCs (n = 6) produced balanced profiles. Unsupervised hierarchical clustering segregated PR1-derived (n = 6) from CellSearch®-derived (n = 4) single CTCs in two separate branches. PR1-derived CTCs were very similar to each other, whereas CellSearch®-derived CTCs were more heterogeneous, although certain aberrations were common to all CTCs across platforms. At the sequence level, the targeted panel revealed somatic mutations shared by all CTCs (FLT3), a PTPN11 subclonal mutation (in 3/6 PR1 and 1/4 CellSearch), and other private mutations in single CTCs.

Discussion

The combination of low-pass whole-genome sequencing and targeted sequencing on single-CTCs sorted from PB enriched with different platforms reveals genetic similarities and diversities.

Integration of results with genetic analysis of pure tumor cells isolated from the tumor tissue, will provide further insight of tumor diversity in different compartments.

Citation Format: Francesca Fontana, Francesco Gelsomino, Claudio Forcato, Mario Terracciano, Chiara Bolognesi, Annalisa Altimari, Genny Buson, Chiara Mangano, Paola Tononi, Francesco Bacchi, Gianni Medoro, Michelangelo Fiorentino, Nicolò Manaresi, Michele Tognetto, Andrea Ardizzoni. Digital sorting and single-cell genomic profile comparison of lung adenocarcinoma CTCs between EpCAM and size-based enrichment methods. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2253.

Abstract 3617: Digital sorting rescues low-cellularity tumor FFPE samples for genome-wide copy-number profiling

Introduction: The analysis of formalin-fixed paraffin embedded (FFPE) cancer specimens is particularly challenging due to minute amount of tissue, low-tumor cellularity and heterogeneity, associated with low quality DNA. This results in an imprecise characterization of somatic variants and copy-number alterations (CNA). Here we show how digital sorting combined with low-pass whole genome sequencing (WGS) can resolve genome-wide copy-number profiling even for the more challenging FFPE samples.

Methods: An archival FFPE sample from one pancreatic cancer patient, rejected by the International Cancer Genome Consortium (ICGC) criteria due to low tumor content (<25%), was dissociated into a single cell suspension. Using the DEPArray™ digital sorter, tumor and normal stromal cell subpopulations (range = 70-77) were recovered using Keratin/Vimentin immunofluorescence and DNA ploidy, from which 0.4-0.5ng DNA was obtained. After lysis, Illumina®-compatible libraries were prepared from one pool of pseudo-diploid sorted tumor cells, one pool of stromal cells and one unsorted sample (1500 cells, i.e. about 10ng gDNA) using the Accel-NGS® 2S DNA Library Kit from Swift Biosciences. Libraries were used for low-pass whole genome sequencing on Illumina® MiSeq. Paired-end (2×100) reads were aligned to hg19 human reference using BWA software and copy-number profiles were generated with Control-FREEC.

Results: A total of 11M paired-end reads and a mean coverage of 0.12x were obtained from low-pass WGS, enabling the detection of CNAs at good resolution. The resulting copy-number profiles clearly show the difference between the stromal and tumor populations, with the first characterized by a flat profile (0 gains, 0 losses) and the second presenting several somatic copy-number alterations (6 gains, 22 losses). As expected due to dilution by normal cells, CNA profiles of unsorted samples missed most of the gains and losses (only 5/28 = 18% of aberrant genomic regions were detected). At a single base level, the difference between unsorted and sorted samples was more significant as the unsorted fraction missed >99% of CNA bases found in the sorted tumor population.

Conclusions: DEPArray™ sorting combined with Accel-NGS® 2S kits and Illumina® low-pass whole genome sequencing enables high quality genome-wide profiling of pure tumor and stromal populations. The capacity of this method to deal with low DNA input (0.5ng) from archival FFPE samples characterized by low cancer cell content (<25%) makes it a valuable and easily accessible tool for studying tumor CNA profiles.

Citation Format: Claudio Forcato, Julie Lalibertè, Chiara Bolognesi, Ivana Cataldo, Genny Buson, Chiara Mangano, Cinzia Cantù, Francesca Fontana, Paola Tononi, Gianni Medoro, Tim Harkins, Rita T. Lawlor, Aldo Scarpa, Nicolò Manaresi. Digital sorting rescues low-cellularity tumor FFPE samples for genome-wide copy-number profiling. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3617.

Abstract P6-05-11: DEPArray™ enables recovery of pure tumor cells from heterogeneous fine needle aspirates for routine downstream NGS analysis

Introduction: We have previously shown reliability in isolating pure populations of cells from complex tissues using the DEPArray™. Fine Needle Aspiration (FNA) is a quick and simple procedure often performed to make a diagnosis or rule out conditions such as cancer. Although FNA is also used to assess response to treatment, the procedure is often deemed insufficient in yield and purity of tumor cells. Here we provide preliminary results showing 100% efficiency in recovering pure tumor cell populations from FNA samples of patients affected by Metastatic Breast Cancer and known to have low tumor burden (<20%) prior to using the DEPArray™ platform.

Method: FNA paraffin embedded sections (50 microns thickness) from metastases originating from breast (n=3) primary tumors were evaluated. Each FFPE curl was processed to yield single cells followed by DEPArray™ sorting based on cytokeratin (Ker), vimentin (Vim) and nuclear staining. The recovered cell populations were directly lysed in the collection tube prior to PCR-based target enrichment for next generation sequencing using Ion AmpliSeq™ CHPv2.

Results: DEPArray™ analysis allowed identification of 3 well separated cell populations, including tumor (Ker+/Vim-), stromal (Vim+/Ker) and putative EMT (Ker+/Vim+) cells. Overall, only 21% (4.3% to 42.7% range) of the total (mean of 6335) cells analyzed were of tumor (KER+/Vim-) origin. Groups of pure cells (mean 105 cells, range 15-200) for each population were recovered for sequence analysis. In one breast cancer FNA sample, we observed TP53 LoH but only in the recovered tumor (KER+) cells and not in the unsorted, stromal (VIM+), or EMT (KER+/VIM+) populations. In addition, a PIK3CA missense somatic heterozygous variant was identified in both the tumor and putative EMT populations but not in stromal cells, confirming this as a somatic mutation.

Conclusion: DEPArray™ allows resolution of two main limitations associated with FNA samples obtained for genomic analysis: too few target cells and unwanted admixture of normal cells. DEPArray™ allows for phenotypic distinction between the sorted cells prior to recovery; thus, enabling sequence analysis that is suitable for detecting genomic aberrations such as CNVs and LoH, which cannot be evaluated as precisely in an unsorted sample. Clearly, the DEPArray™ platform brings precision to detection, quantification and recovery of pure target cells that are suitable for subsequent downstream molecular analysis that can improve cancer diagnosis and personalized treatment strategies for breast cancer patients.

Citation Format: Sero V, Forcato C, Bolognesi C, Buson G, Medoro G, Yazdani M, Blevins A, Manaresi N, Bischoff FZ. DEPArray™ enables recovery of pure tumor cells from heterogeneous fine needle aspirates for routine downstream NGS analysis. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-05-11.

Digital Sorting of Pure Cell Populations Enables Unambiguous Genetic Analysis of Heterogeneous Formalin-Fixed Paraffin-Embedded Tumors by Next Generation Sequencing

Precision medicine in oncology requires an accurate characterization of a tumor molecular profile for patient stratification. Though targeted deep sequencing is an effective tool to detect the presence of somatic sequence variants, a significant number of patient specimens do not meet the requirements needed for routine clinical application. Analysis is hindered by contamination of normal cells and inherent tumor heterogeneity, compounded with challenges of dealing with minute amounts of tissue and DNA damages common in formalin-fixed paraffin-embedded (FFPE) specimens. Here we present an innovative workflow using DEPArray™ system, a microchip-based digital sorter to achieve 100%-pure, homogenous subpopulations of cells from FFPE samples. Cells are distinguished by fluorescently labeled antibodies and DNA content. The ability to address tumor heterogeneity enables unambiguous determination of true-positive sequence variants, loss-of-heterozygosity as well as copy number variants. The proposed strategy overcomes the inherent trade-offs made between sensitivity and specificity in detecting genetic variants from a mixed population, thus rescuing for analysis even the smaller clinical samples with low tumor cellularity.

Molecular profiling of single circulating tumor cells with diagnostic intention

Several hundred clinical trials currently explore the role of circulating tumor cell (CTC) analysis for therapy decisions, but assays are lacking for comprehensive molecular characterization of CTCs with diagnostic precision. We therefore combined a workflow for enrichment and isolation of pure CTCs with a non-random whole genome amplification method for single cells and applied it to 510 single CTCs and 189 leukocytes of 66 CTC-positive breast cancer patients. We defined a genome integrity index (GII) to identify single cells suited for molecular characterization by different molecular assays, such as diagnostic profiling of point mutations, gene amplifications and whole genomes of single cells. The reliability of > 90% for successful molecular analysis of high-quality clinical samples selected by the GII enabled assessing the molecular heterogeneity of single CTCs of metastatic breast cancer patients. We readily identified genomic disparity of potentially high relevance between primary tumors and CTCs. Microheterogeneity analysis among individual CTCs uncovered pre-existing cells resistant to ERBB2-targeted therapies suggesting ongoing microevolution at late-stage disease whose exploration may provide essential information for personalized treatment decisions and shed light into mechanisms of acquired drug resistance.

Programmable interactions of functionalized single bioparticles in a dielectrophoresis-based microarray chip

Manipulating single biological objects is a major unmet challenge of biomedicine. Herein, we describe a lab-on-a-chip platform based on dielectrophoresis (DEP). The DEParray is a prototypal version consisting of 320 × 320 arrayed electrodes generating >10,000 spherical DEP cages. It allows the capture and software-guided movement to predetermined spatial coordinates of single biological objects. With the DEParray we demonstrate (a) forced interaction between a single, preselected target cell and a programmable number of either microspheres or natural killer (NK) cells, (b) on-chip immunophenotypic discrimination of individual cells based on differential rosetting with microspheres functionalized with monoclonal antibodies to an inhibitory NK cell ligand (HLA-G), (c) on-chip, real-time (few minutes) assessment of immune lysis by either visual inspection or semiautomated, time-lapse reading of a fluorescent dye released from NK cell-sensitive targets, and (d) manipulation and immunophenotyping with limiting amounts (about 500) cells. To our knowledge, this is the first report describing a DEP-based lab-on-a-chip platform for the quick, arrayed, software-guided binding of individually moved biological objects, the targeting of single cells with microspheres, and the real-time characterization of immunophenotypes. The DEParray candidates as a discovery tool for novel cell:cell interactions with no prior (immuno)phenotypic knowledge.

Dielectrophoresis-based 'Lab-on-a-chip' devices for programmable binding of microspheres to target cells

There is a general agreement on the fact that the Laboratory on chip (Lab-on-a-chip) technology will enable laboratory testing to move from laboratories employing complex equipments into non-laboratory settings. In this respect, dielectrophoresis (DEP) is a very valuable approach to design and produce Lab-on-a-chip devices able to manipulate microparticles and cells. In this study, we report the application of DEP-based devices for facilitating programmable interactions between microspheres and target tumor cells. We used two Lab-on-a-chip devices, one (the SmartSlide) carrying 193 parallel electrodes and generating up to 50 cylinder-shaped DEP cages, the other (the DEP array) carrying 102,400 arrayed electrodes and generating more than 10,000 spherical DEP cages. We determined whether these devices can be used to levitate and move microspheres and cells in order to obtain a forced interaction between microspheres and target cells. The first major point of this manuscript is that the DEP-based SmartSlide can be used for transfection experiments in which microspheres and target cells are forced to share the same DEP cage, leading to efficient binding of the microspheres to target cells. The data obtained using the DEP array show that this system allows the sequential, software-controlled binding of individually and independently moved single microspheres to a single target tumor cell. To our knowledge, this is the first report on the possible use of a DEP-based Lab-on-a-chip device for guided multiple binding of singularly moved microspheres to a single tumor cell. This approach can be of interest in the field of drug discovery, delivery and diagnosis.

Microfluidic channel fabrication in dry film resist for production and prototyping of hybrid chips

Microfluidic networks are patterned in a dry film resist (Ordyl SY300/550) that is sandwiched in between two substrates. The technique enables fabrication of complex biochips with active elements both in the bottom and the top substrate (hybrid chips). The resist can be double bonded at relatively low temperatures without the use of extra adhesives. A postbake transfers the resist into a rigid structure. The resist is qualified in terms of resolution, biocompatibility and fluidic sealing. Fabrication in both a fully equipped cleanroom setting as well as a minimally equipped laboratory is described. The technique is applied for dielectrophoresis-based cell separation systems and a fuel cell reaction chamber with micropillars. The dry film resist can be considered a cheap and fast alternative to SU-8.

Levitation and movement of human tumor cells using a printed circuit board device based on software-controlled dielectrophoresis

In this study we describe an original, efficient, and innovative printed circuit board (PCB) device able to generate dielectrophoresis-based, software-controlled cages that can be moved to any place inside a microchamber. Depending on their dielectrophoretic properties, eukaryotic cells can be "entrapped" in cages and moved under software control. The main conclusion gathered from the experimental data reported is that the PCB device based on dielectrophoresis permits levitation and movement of different tumor cells at different dielectrophoresis conditions. The results presented herein are therefore the basis for experiments aimed at forced interactions or separation of eukaryotic cells using "lab-on-a-chip." In fact, because many cages can be controlled at the same time, and two or more cages can be forced to share the same or a different location, it is possible, in principle, either to bring in contact cells of a differing histotype or to separate them.

Applications to cancer research of "lab-on-a-chip" devices based on dielectrophoresis (DEP)

The recent development of advanced analytical and bioseparation methodologies based on microarrays and biosensors is one of the strategic objectives of the so-called post-genomic. In this field, the development of microfabricated devices could bring new opportunities in several application fields, such as predictive oncology, diagnostics and anti-tumor drug research. The so called "Laboratory-on-a-chip technology", involving miniaturisation of analytical procedures, is expected to enable highly complex laboratory testing to move from the central laboratory into non-laboratory settings. The main advantages of Lab-on-a-chip devices are integration of multiple steps of different analytical procedures, large variety of applications, sub-microliter consumption of reagents and samples, and portability. One of the requirement for new generation Lab-on-a-chip devices is the possibility to be independent from additional preparative/analytical instruments. Ideally, Lab-on-a-chip devices should be able to perform with high efficiency and reproducibility both actuating and sensing procedures. In this review, we discuss applications of dielectrophoretic(DEP)-based Lab-on-a-chip devices to cancer research. The theory of dielectrophoresis as well as the description of several devices, based on spiral-shaped, parallel and arrayed electrodes are here presented. In addition, in this review we describe manipulation of cancer cells using advanced DEP-based Lab-on-a-chip devices in the absence of fluid flow and with the integration of both actuating and sensing procedures.