Isolation of single circulating trophoblasts from maternal circulation for noninvasive fetal copy number variant profiling

OBJECTIVE

To develop a multi-step workflow for the isolation of circulating extravillous trophoblasts (cEVTs) by describing the key steps enabling a semi-automated process, including a proprietary algorithm for fetal cell origin genetic confirmation and copy number variant (CNV) detection.

METHODS

Determination of the limit of detection (LoD) for submicroscopic CNV was performed by serial experiments with genomic DNA and single cells from Coriell cell line biobank with known imbalances of different sizes. A pregnancy population of 372 women was prospectively enrolled and blindly analyzed to evaluate the current workflow.

RESULTS

An LoD of 800 Kb was demonstrated with Coriell cell lines. This level of resolution was confirmed in the clinical cohort with the identification of a pathogenic CNV of 800 Kb, also detected by chromosomal microarray. The mean number of recovered cEVTs was 3.5 cells per sample with a significant reverse linear trend between gestational age and cEVT recovery rate and number of recovered cEVTs. In twin pregnanices, evaluation of zygosity, fetal sex and copy number profiling was performed in each individual cell.

CONCLUSION

Our semi-automated methodology for the isolation and single-cell analysis of cEVTS supports the feasibility of a cell-based noninvasive prenatal test for fetal genomic profiling.

Recommendations and quality criteria for micronucleus studies with humans

Micronucleus (MN) analyses in peripheral blood lymphocytes and exfoliated cells from different organs (mouth, nose, bladder and cervix) are at present the most widely used approaches to detect damage of genetic material in humans. MN are extranuclear DNA-containing bodies, which can be identified microscopically. They reflect structural and numerical chromosomal aberrations and are formed as a consequence of exposure to occupational, environmental and lifestyle genotoxins. They are also induced as a consequence of inadequate intake of certain trace elements and vitamins. High MN rates are associated with increased risk of cancer and a range of non-cancer diseases in humans. Furthermore, evidence is accumulating that measurements of MN could be a useful tool for the diagnosis and prognosis of different forms of cancer and other diseases (inflammation, infections, metabolic disorders) and for the assessment of the therapeutic success of medical treatments. Recent reviews of the current state of knowledge suggest that many clinical studies have methodological shortcomings. This could lead to controversial findings and limits their usefulness in defining the impact of exposure concentrations of hazardous chemicals, for the judgment of remediation strategies, for the diagnosis of diseases and for the identification of protective or harmful dietary constituents. This article describes important quality criteria for human MN studies and contains recommendations for acceptable study designs. Important parameters that need more attention include sufficiently large group sizes, adequate duration of intervention studies, the exclusion of confounding factors which may affect the results (sex, age, body mass index, nutrition, etc.), the evaluation of appropriate cell numbers per sample according to established scoring criteria as well as the use of proper stains and adequate statistical analyses.

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 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.

Standardization of the Alkaline Elution Procedure Using X-Ray-Damaged Nuclear DNA

Structural modifications of DNA were induced by X-irradiation of crude hepatic nuclei at various dose ranges to standardize DNA damage evaluated by the alkaline elution technique. This quantitative assay can be used as reference for DNA damage induced by the in vivo administration of mutagens and/or carcinogens involved in the environment.

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 5607: Copy-number profiling of single, digitally-sorted PD-L1 positive cells in NSCLC FFPE tissues

Introduction:

Immune system strongly affects cancer cell fate; indeed, immune-checkpoint blockade is emerging as an effective therapeutic strategy in a broad range of tumor types. The effectiveness of these therapies depends on different aspects of tumor biology such as the expression of immune checkpoint proteins, the presence of infiltrating active immune cells and many others. To date, a robust biomarker to predict therapeutic response to these drugs has not been found yet.

Among all the strategies used to identify effective biomarkers, a single-cell level molecular profiling of tumor, stromal and infiltrating cells, has not been explored due to technical challenges. Here we present a method for the digital isolation of single PD-L1+ cells from FFPE tissues, along with their genetic characterization for the identification of novel biomarkers.

Methods:

FFPE tissue sections from two NSCLC patients, were independently tested for PD-L1 expression using IHC VENTANA PD-L1 (SP142) Assay and scored in terms of tumor content (30%, 85%), percentage of PD-L1 positive tumor cells (70%, 95%), PD-L1 intensity, and H-score (130, 175). From the same tissue blocks, additional FFPE sections were dissociated down to cell suspension, and immunofluorescently labelled using Keratin-AlexaFluor®488, Vimentin-AlexaFluor®647 and PD-L1 (clone SP263)-AlexaFluor®546. Four cell populations (Keratin+PD-L1-, Keratin+PD-L1+, Vimentin+PD-L1- and Vimentin+PD-L1+) were identified at the DEPArray™ platform and, for each, we isolated pools of precise number (range 43-121) of cells, along with pure single cells. Recovered cells were whole genome amplified (Ampli1™ WGA), and genome-wide copy-number aberrations (CNA) profiles were obtained by Ampli1™ LowPass kit and IonTorrent sequencing.

Results:

The expression of PD-L1 on cell membrane was attributed -by means of co-expression of either keratin or vimentin- to tumor or stromal cells, respectively. For both patients, in the tumor populations numerous gains and losses were clearly identified along the genome; Keratin+PD-L1+ and Keratin+PD-L1- pooled cells displayed comparable profiles. Notably, in both patients copy gains were identified on chromosome 9 region including the PD-L1 gene. A variable range of alleles (3 to 6) on the same PD-L1 locus was detected on single tumor cells, along with a high inter-cell heterogeneity in terms of gain extent and genomic regions involved, suggestive of the presence of different tumor clones, hidden in pooled cells data. All the stromal (Vimentin+PD-L1+/-) cells showed flat profiles.

Conclusions:

This study demonstrates an innovative approach for isolation and genetic profiling of single pure PD-L1+ cells from FFPE tissue. DEPArray™ sorting combined with low-pass whole genome sequencing enables high quality genome-wide profiling of pure single cells and pools isolated from phenotypically distinct populations in FFPE tumor tissue.

Citation Format: Giulio Bassi, Chiara Bolognesi, Chiara Mangano, Claudio Forcato, Alberto Ferrarini, Valentina Del Monaco, Paola Tononi, Genny Buson, Gianni Medoro, Manaresi Nicolò, Francesca Fontana. Copy-number profiling of single, digitally-sorted PD-L1 positive cells in NSCLC FFPE tissues [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 5607. doi:10.1158/1538-7445.AM2017-5607

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 1675: Parallel genome and transcriptome-wide profiling of PD-L1 expressing tumor and infiltrating immune single cells in NSCLC

Introduction Targeting immune checkpoint has demonstrated contrasting clinical response in non-small cell lung cancer (NSCLC) due to the lack of robust biomarkers for patients stratification. This is partially due to a poor understanding of the role of the different cellular players (tumor, stromal, infiltrating immune cells) within the tumor microenvironment. Here we present an innovative workflow using the DEPArray™ sorting system, to isolate different classes of epithelial and hematopoietic viable single cells from fresh tissue biopsies for integrated genome and transcriptome sequencing analysis.

Methods Freshly resected NSCLC tissue was dissociated mechanically and enzymatically down to single cell suspension, and labelled with immunofluorescent antibodies targeting PD-L1 (28-8), EpCAM, CD8, CD45 along with Hoechst 33342 for nuclei detection. Distinct pure single cells, along with pools of precise number of cells were digitally isolated using DEPArray™ platform based on marker expression. For each cell recovery, mRNA was physically separated from genomic DNA and then amplified using the Ampli1™ WTA Kit to generate a library of high quality, full-length double stranded cDNA. Amplified cDNA is used for NGS library preparation and sequencing on Illumina® MiSeq System. In parallel, genomic DNA is collected with magnetic beads and eluted directly into the reaction mixture for whole genome amplification by Ampli1™ WGA kit. The WGA products were used to profile genome-wide copy-number aberrations (CNA) using Ampli1™ LowPass kit.

Results As a first step, we identified two main cell populations, the CD45+ infiltrating hematopoietic cells and the EpCAM+ epithelial cells. The hematopoietic fraction was further investigated to evaluate the presence of different subpopulations. Interestingly the PD-L1+ population, corresponding to immune suppressive hematopoietic cells, represented 47% of the total CD45+ fraction while CD8+ cells corresponding to cytotoxic T cells represented 9% of the total CD45. In the EpCAM+ population the PD-L1+ fraction represented 29% of the cells. Single viable cells along with matching pools of precise number of cells from each population were digitally isolated with DEPArray™ system for downstream analysis. Results of RNA-Seq and genomic DNA copy-number aberrations profiling will be presented at the conference.

Conclusion We show here a new approach to isolate pure, single PD-L1+/- tumor and tumor infiltrating hematopoietic cells from NSCLC tissue for integrated genome and transcriptome sequencing. The direct comparison of gene expression data to its corresponding genomic data in the same tumor cell, along with the transcriptomic profiling of immune infiltrate and stroma, may add a powerful tool to disentangle the tumor microenvironment biology. This will potentially offer a novel tool to develop new biomarkers and identify therapeutic leads.

Citation Format: Stefano Casonato, Giulio Bassi, Chiara Bolognesi, Chiara Mangano, Valentina del Monaco, Genny Buson, Claudio Forcato, Alberto Ferrarini, Farideh Bischoff, Gianni Medoro, Nicolò Menaresi, Francesca Fontana. Parallel genome and transcriptome-wide profiling of PD-L1 expressing tumor and infiltrating immune single cells in NSCLC [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 1675. doi:10.1158/1538-7445.AM2017-1675

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 2730: Image-based single cell-sorting to separate and recover distinct cell populations from complex heterogeneous mixed tissue: precise sample preparation upstream of FISH

Fluorescent in Situ Hybridization (FISH) is commonly used for assessment of chromosomal alterations. Guidelines for determining FISH-based classification of clinical biomarkers exist but are based on pre-analytical factors, including fixation/sectioning/thickness/age, that can greatly influence biomarker status determination. Here, we use single-cell image-based cell sorting by DEPArrayTM for the separation and recovery of pure distinct cell populations prior to FISH.

Methods: A multi-center study to evaluate HER2-FISH based analysis on FFPE with and without DEPArrayTM pre-processing was conducted using breast tumors classified as infiltrating ductal carcinoma (n=12), metastatic (n=1) and ductal carcinoma (n=1). From each block, four 50-micron thick curls were sectioned. One curl from each sample was sent to each of four centers (3 US; 1 EU). Each site performed disassociation of curls to generate a single cell suspension. Cells were then stained and sorted using the DEPArrayTM platform for recovery of tumor (cytokeratin+/vimentin-/DAPI+) and stromal (cytokeratin-/vimentin+/DAPI+) cells. Dual-probe FISH for HER2 and centromere 17 was performed on the sorted cells and compared with conventional tissue section FISH.

Results: Overall, ≥ 90% concordance between the sorted tumor cells and the conventional HER2 FISH result was observed. Among the 7 HER2+ cases, HER2 ratio scores for the sorted tumor cells ranged slightly higher, from 2.60 to 8.95, as compared to the conventional method (from 2.10 to 5.14). In all cases in which stromal cells were also recovered, an expected normal ratio was observed, thus verifying that the populations were efficiently separated. Discordance can be attributed to intra-tumoral heterogeneity and the fact that conventional FISH on FFPE requires only a 4-micron section for analysis.

Conclusion: Today, a percentage of patients are likely misclassified for the biomarker of interest as result of pre-analytical factors. We demonstrate here the ability to overcome these pre-analytic factors and ultimately improve the accuracy in determining biomarker status using the DEPArrayTM

Note: This abstract was not presented at the meeting.

Citation Format: Amanda Gerber, Aditi Khurana, Lisa Koenig, Lindsay Strotoman, Lori Millner, Valeria Sero, Chiara Bolognesi, Sabine Kasimir-bauer, Gianni Medoro, Matthew Moore, Philip Cotter, Nicolo Manaresi, Farideh Bischoff. Image-based single cell-sorting to separate and recover distinct cell populations from complex heterogeneous mixed tissue: precise sample preparation upstream of FISH [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 2730. doi:10.1158/1538-7445.AM2017-2730

CLIA validation workflow of a novel tumor cell isolation platform

e23161

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.

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.

Abstract 371: Longitudinal genetic characterization of circulating tumor cells in metastatic breast cancer patients

Background:

Little is known about the evolution of genetic aberrations during metastatic cancer progression and in response to systemic treatment. Obtaining repeated tissue biopsies is often impractical. On the other hand, it has been shown that circulating tumor cells (CTCs) can be easily followed during disease course and genetic characterization at the single cell level is possible with high reliability [1].

Methods:

Individual CTCs of a ER+ and HER2- de novo metastatic breast cancer patient treated with weekly paclitaxel/gemcitabine as first line therapy, were collected at three different time points (before start, after one and two cycles of treatment). Whole peripheral blood was enriched using the CellSearch® system and CTCs were sorted by DEPArray™ device. The whole genome of single CTCs was amplified with Ampli1™ WGA kit and WGA quality was assessed by Ampli1™ QC Kit. Genome wide single cell copy number variation (CNV) profile was evaluated with Agilent SurePrint 180k array comparative genomic hybridization (aCGH).

Results:

CTCs count at CellSearch was 22, 75 and 15 at three time points respectively.

A total of 25 single CTCs were collected and 23 (92%) showed high Genome Integrity Index (GII) as measured by Ampli1™ QC kit (GII = 3 or 4). For each time point multiple CTCs (3, 6 and 3 respectively) were selected for single cell aCGH analysis. The genomic profile was strikingly similar (1q gain, 12p, 13p, 16q and 17p losses) across individual cells of the same blood sample and throughout different time points evaluated. After 3 cycles of therapy a disease progression was documented by CAT-scan.

Discussion:

The observed high GII, low genetic heterogeneity and stable genome across different time points suggests the presence of an aggressive clone resistant to the treatment and cancer-associated genes analysis for sequence variants by NGS targeted sequencing is ongoing. Further patients with longitudinal follow-up will be enrolled in order to evaluate if the heterogeneity between aCGH profile at a given time point and longitudinal evolution of aCGH profiles can be associated with early treatment response. Results will be presented at the conference.

[1] Polzer B, Medoro G, et al, EMBO Mol Med. 2014 Oct 30;6(11):1371-86.

Citation Format: Valeria Sero, Francesca De Luca, Anna Doffini, Francesca Galardi, Marta Pestrin, Zbignew T. Czyz, Genny Buson, Giulia Bregola, Chiara Bolognesi, Francesca Fontana, Gianni Medoro, Bernhard Polzer, Angelo Di Leo, Christoph A. Klein, Nicolo Manaresi. Longitudinal genetic characterization of circulating tumor cells in metastatic breast cancer patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 371. doi:10.1158/1538-7445.AM2015-371

Abstract 1552: Image-based microchip sorting of pure, immuno-phenotypically defined subpopulations of tumor cells from tiny formalin-fixed paraffin embedded (FFPE) samples reveals their distinct genetic features

Background: We provide a solution of pressing needs in preparation of FFPE samples for genomic analysis: small sample size, unwanted admixture of normal cells, analysis of tumor rare-cell subpopulations present at low percentages in the tumor fraction.

Methods: We disaggregated into cell suspensions archival FFPE samples from 12 ovarian, pancreatic and lung cancer patients, staining for Vimentin, Keratin and DNA. We sorted by DEPArray™ precise numbers (mean = 107, median 58, range = 5-600) of pure homogenous cells from the major population of tumor cells, the contaminant diploid stromal cells, and other minority tumor cell types indicative of epithelial-to-mesenchymal transition (EMT). Using IonTorrent AmpliSeq CHPv2, we generated sequencing libraries, after lysis of the pure cells recovered by DEPArray™ (n = 54), or unsorted samples (either QIAmp DNA columns or disaggregated cells). Libraries were sequenced with IonTorrent PGM (mean depth>2,000x), and analyzed using IonTorrent software.

Results: On several loci, we detected somatic mutations with 100% variant frequency, only observable as heterozygous in the unsorted samples and as wild-type in stromal cells of same patient, confirming 100% purity of sorted cells. Moreover, in the EMT-phenotype subpopulations we identified clear somatic mutations, different from tumor cells majority and undetectable in unsorted samples. Frequently, for loci harboring germ-line heterozygous SNPs with variant frequency around 50% for pure stromal cells, we readily detected loss-of-heterozygosis in tumor cells subpopulations as binary (0%/100%) variants. Quantitative traits such as copy number gains and losses were also reproducibly identified in tumor cell replicates as deviations from the 50% variant frequency of germline SNPs of pure stromal cells. Furthermore, we observed an excellent coverage uniformity (mean = 96%) for recoveries (n = 27) in the range of 81-600 cells, even higher than the uniformity obtained with (n = 2) QIAmp-purified DNA (92%). Mean uniformity gradually decreased to 89% for cell recoveries (n = 13) in the range 21-80, and further decreased to 70% for lower cell numbers (n = 14).

Highlights: Sorting tumor rare-cell subpopulations reveals their genetic characteristics, undetectable in unsorted samples. Analyzing homogenous cell subpopulations boosts signal-to-noise ratio working around inherent sensitivity/specifitiy trade-offs of rare-variant calls. The proposed workflow further enables reliable detection of quantitative traits such as CNVs. Sorting pure stromal cells yields internal controls for archival samples.

Citation Format: Chiara Bolognesi, Anna Doffini, Genny Buson, Rossana Lanzellotto, Giulio Signorini, Valeria Sero, Alex Calanca, Francesca Fontana, Rita Romano, Stefano Gianni, Giulia Bregola, Gianni Medoro, Raimo Tanzi, Giuseppe Giorgini, Hans Morreau, Massimo Barberis, Willem E. Corver, Nicolo Manaresi. Image-based microchip sorting of pure, immuno-phenotypically defined subpopulations of tumor cells from tiny formalin-fixed paraffin embedded (FFPE) samples reveals their distinct genetic features. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1552. doi:10.1158/1538-7445.AM2015-1552

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.

Biomonitoring of genotoxic risk in agricultural workers from five colombian regions: association to occupational exposure to glyphosate

In order to assess possible human effects associated with glyphosate formulations used in the Colombian aerial spray program for control of illicit crops, a cytogenetic biomonitoring study was carried out in subjects from five Colombian regions, characterized by different exposure to glyphosate and other pesticides. Women of reproductive age (137 persons 15-49 yr old) and their spouses (137 persons) were interviewed to obtain data on current health status, history, lifestyle, including past and current occupational exposure to pesticides, and factors including those known to be associated with increased frequency of micronuclei (MN). In regions where glyphosate was being sprayed, blood samples were taken prior to spraying (indicative of baseline exposure), 5 d after spraying, and 4 mo after spraying. Lymphocytes were cultured and a cytokinesis-block micronucleus cytome assay was applied to evaluate chromosomal damage and cytotoxicity. Compared with Santa Marta, where organic coffee is grown without pesticides, the baseline frequency of binucleated cells with micronuclei (BNMN) was significantly greater in subjects from the other four regions. The highest frequency of BNMN was in Boyaca, where no aerial eradication spraying of glyphosate was conducted, and in Valle del Cauca, where glyphosate was used for maturation of sugar cane. Region, gender, and older age (> or =35 yr) were the only variables associated with the frequency of BNMN measured before spraying. A significant increase in frequency of BNMN between first and second sampling was observed in Narino, Putumayo, and Valle immediately (<5 d) after spraying. In the post-spray sample, those who reported direct contact with the eradication spray showed a higher quantitative frequency of BNMN compared to those without glyphosate exposure. The increase in frequency of BNMN observed immediately after the glyphosate spraying was not consistent with the rates of application used in the regions and there was no association between self-reported direct contact with eradication sprays and frequency of BNMN. Four months after spraying, a statistically significant decrease in the mean frequency of BNMN compared with the second sampling was observed in Narino, but not in Putumayo and Valle del Cauca. Overall, data suggest that genotoxic damage associated with glyphosate spraying for control of illicit crops as evidenced by MN test is small and appears to be transient. Evidence indicates that the genotoxic risk potentially associated with exposure to glyphosate in the areas where the herbicide is applied for coca and poppy eradication is low.

Gene-environment interactions in ocular diseases

Degenerative ocular diseases are widespread in the population and represent a major cause of reversible and irreversible blindness. Scientific evidences have been accumulating supporting the role of genotoxic damage and gene environment interactions in the pathogenesis of these diseases mainly including glaucoma, age-related macular degeneration, and cataract. Glaucoma, in its degenerative form, is characterized by the degeneration of the trabecular meshwork, the tissue of the anterior chamber of the eye devoted to aqueous-humour outflow. Such a degenerative process results in intra-ocular pressure increase and progressive damage of optic nerve head. Oxidative stress and DNA damage play an important role in inducing the degeneration of these well differentiated target tissues in which DNA damage results in a progressive cell loss. Macular degeneration is a common age-related disease affecting the central regions of the retina inducing progressive accumulation of oxidized lipoproteins and neovascularization. Environmental genotoxic risk factors include diet, light, and cigarette smoke paralleled by individual susceptibility as determined by adverse genetic assets. Cataract is a progressive opacity of the crystalline lens resulting from molecular damages induced by various risk factors including UV-containing light. This disease has been related to a failure in antioxidant defences. Experimental study provides evidence that cataract patients possess higher basal level of DNA damage, as evaluated by Comet test, in lymphocytes than controls. This finding is paralleled by the higher susceptibility to oxidative stress observed in the same patients. These novel experimental data further support the role of DNA damage as a main factor contributing to cataract onset. In conclusion, the examined degenerative ocular diseases recognise environmental risk factors often displaying genotoxic attitudes. Whenever these factors target individuals who are susceptible due their genetic assets the results is the onset of a specific eye disease depending on the affected ocular tissue.

A biomonitoring study assessing the residual biological effects of pollution caused by the HAVEN wreck on marine organisms in the Ligurian Sea (Italy)

Residual biological effects of the 1991 HAVEN oil spill off the Ligurian (Arenzano) coast were assessed in this study. Samples of the fish species Boops boops, Mullus barbatus, and Uranoscupus scaber were collected from two polluted sites near the HAVEN wreck and from an uncontaminated area. In addition to this, mussels were caged along the coast affected by the HAVEN disaster. The physiological status of fish and mussels was assessed using a battery of stress and exposure biomarkers. The PAH content of mussel and fish tissues was also analyzed. Significant biological responses were observed in lysosomal membrane stability, neutral lipid and lipofuscin accumulation and micronucleus frequency for mussels caged at two sites close to the HAVEN wreck. Chemical analyses indicated, however, that these effects are not caused by aromatic hydrocarbons. For this reason, we suggest that the aftermath of the HAVEN disaster contributes very little to coastal ecosystem pollution. This was also confirmed by the few biological effects observed in fish specimens (Boops boops) collected from surface waters. Nevertheless, it is important to point out that benthic fish displayed a stress syndrome potentially caused by aromatic hydrocarbons released from the oil tanker, as witnessed by an enhanced EROD activity and increased lipofuscin and neutral lipid lysosomal contents.

The use of biomarkers in biomonitoring: a 2-tier approach assessing the level of pollutant-induced stress syndrome in sentinel organisms

The paper outlines a 2-tier approach for wide-scale biomonitoring programmes. To obtain a high level of standardization, we suggest the use of caged organisms (mussels or fish). An "early warning", highly sensitive, low-cost biomarker is employed in tier 1 (i.e. lysosomal membrane stability (LMS) and survival rate, a marker for highly polluted sites). Tier 2 is used only for animals sampled at sites in which LMS changes are evident and there is no mortality, with a complete battery of biomarkers assessing the levels of pollutant-induced stress syndrome. Possible approaches for integrating biomarker data in a synthetic index are discussed, along with our proposal to use a recently developed Expert System. The latter system allows a correct selection of biomarkers at different levels of biological organisation (molecular/cellular/tissue/organism) taking into account trends in pollutant-induced biomarker changes (increasing, decreasing, bell-shape). A selection of biomarkers of stress, genotoxicity and exposure usually employed in biomonitoring programmes is presented, together with a brief overview of new biomolecular approaches.

Lack of mutagenicity and clastogenicity of PNAEmu-NLS targeted to a regulatory sequence of the translocated c-myc oncogene in Burkitt's lymphoma

Peptide nucleic acids (PNAs) are synthetic homolog of nucleic acids in which the phosphate-sugar polynucleotide backbone is replaced by a flexible polyamide. They bind complementary polynucleotide sequences with higher affinity and specificity than their natural counterparts. PNAs linked to the appropriate nuclear localization signal (NLS) peptide have been used to selectively down-regulate the expression of several genes in viable cells. For example in Burkitt's lymphoma (BL) cells the c-myc oncogene is translocated in proximity to the Emu enhancer of the Ig gene locus and upregulated. PNAs complementary to the second exon of c-myc or to the Emu enhancer sequence (PNAEmu-NLS), selectively and specifically block the expression of the c-myc oncogene and inhibit cell growth in vitro and in vivo. PNAEmu-NLS administration to mice did not exhibit toxic effects even at the highest concentration allowed by the experimental conditions. Because of the accumulating data confirming PNAEmu-NLS potential therapeutic value, PNAEmu-NLS was evaluated for the inability to induce mutations in tester strains of Salmonella typhimurium, Escherichia coli, and at the hprt locus in Chinese hamster ovary cells (CHO). Moreover, the induction of chromosomal aberrations in CHO cells and of micronuclei in human lymphocytes were investigated. We may conclude that PNAEmu-NLS neither induces mutations nor has clastogenic effects as detectable by treatment under the standard test conditions.

Genotoxicity biomarkers and acetylcholinesterase activity in natural populations of Mytilus galloprovincialis along a pollution gradient in the Gulf of Oristano (Sardinia, western Mediterranean)

A year-round biomonitoring study on blue mussels (Mytilus galloprovincialis) was carried out in 4 selected sites along the Gulf of Oristano (Sardinia, Italy): a commercial port (Port), the outlet of the S'Ena Arrubia and Marceddì lagoons (in the catchment area of intensive agricultural and diary activities, and abandoned mining), and a reference site (North). Heavy metal concentrations in sediments from Marceddì were 2-3 to 10-20 times higher in Pb, Cd and Zn, respectively, than those found at North and S'Ena Arrubia. Higher values (P<0.05) of micronuclei frequency were detected in mussels from Marceddì and Port compared to those detected in mussels from North and S'Ena Arrubia. DNA damage in animals from North was significantly lower than that at the other sites. Results of acetylcholinesterase inhibition consistently showed the strongest effects in mussels from Port and Marceddì. Our results suggest that these biomarkers can be used in coastal marine biomonitoring as early signals of exposure and adverse effects along a pollution gradient.

Basal activation of the P2X7 ATP receptor elevates mitochondrial calcium and potential, increases cellular ATP levels, and promotes serum-independent growth

P2X7 is a bifunctional receptor (P2X7R) for extracellular ATP that, depending on the level of activation, forms a cation-selective channel or a large conductance nonselective pore. The P2X7R has a strong proapoptotic activity but can also support growth. Here, we describe the mechanism involved in growth stimulation. Transfection of P2X7R increases resting mitochondrial potential (delta psi(mt)), basal mitochondrial Ca2+ ([Ca2+]mt), intracellular ATP content, and confers ability to grow in the absence of serum. These changes require a full pore-forming function, because they are abolished in cells transfected with a mutated P2X7R that retains channel activity but cannot form the nonselective pore, and depend on an autocrine/paracrine tonic stimulation by secreted ATP. On the other hand, sustained stimulation of P2X7R causes a delta psi(mt) drop, a large increase in [Ca2+]mt, mitochondrial fragmentation, and cell death. These findings reveal a hitherto undescribed mechanism for growth stimulation by a plasma membrane pore.

Effects of a beverage containing an enzymatically induced-viscosity dietary fiber, with or without fructose, on the postprandial glycemic response to a high glycemic index food in humans

OBJECTIVE

Dietary supplementation with guar gum or fructose has been reported to reduce the postprandial glycemic response to an oral glucose challenge. As a result of the poor palatability of most foods containing guar gum, a novel low-viscosity beverage with guar gum was developed that becomes viscous in vivo through an enzymatic induction. The primary study objective was to determine the effect of an amylase-induced viscosity (I-V) product, with or without supplemental fructose, on the postprandial glycemic response to a high glycemic index test meal in healthy nondiabetic subjects.

DESIGN

The study was a four-treatment, placebo-controlled, double-blind, randomized block protocol.

SETTING

The study was performed at Glycaemic Index Testing, Inc., Toronto, Ontario, Canada.

SUBJECTS

A total of 30 healthy nondiabetic volunteers (13 male, 17 female, mean+/-s.e.m. age of 51+/-3 y and body mass index of 24.2+/-0.4 kg/m(2)) participated in the study.

INTERVENTION

In the morning after an overnight fast, subjects participated in four 3-h meal glucose tolerance tests on separate occasions. The test meals contained 50 g of available carbohydrate from maltodextrin and white bread (control) or the same meal with either 5 g of guar gum (3.6 g galactomannan), 5 g of fructose, or 5 g of guar gum +5 g of fructose.

RESULTS

Treatments containing guar gum had a reduced (P<0.01) baseline-adjusted peak glucose response and incremental area under the glucose curve. In contrast to previous studies, fructose increased (P<0.05) the baseline-adjusted peak glucose concentration.

CONCLUSIONS

Guar gum incorporated into an amylase I-V product provided a means to stabilize blood glucose levels by reducing the early phase excursion and then by appropriately maintaining the later phase excursion in healthy nondiabetic humans.

[European multicenter cross-sectional study on exposure to low doses of benzene]

A cross-sectional multicenter european study has been carried out to evacuate the relations between exposure to low level of benzene and biological markers of internal dose (t,t-MA, S-PMA) and early biological effect (DNA-SSB). The research has shown significantly increased levels (adjusted for smoking habits) of the urinary excretion of t,t-MA, S-PMA and DNA-SSB in petrochemical workers (mean benzene level = 5,694 micrograms/m3) but not in filling station attendants, traffic police officers, and bus drivers compared to referent workers. Dose-response relations were detected between benzene air levels, t,t-MA, S-PMA and DNA-SSB in petrochemical workers, with significantly increased levels of DNA-SSB detected for benzene exposure levels in the range 391-1,800 micrograms/m3 (0.12-0.58 ppm).

Carcinogenic risk of toluene diisocyanate and 4,4'-methylenediphenyl diisocyanate: epidemiological and experimental evidence

Diisocyanates are highly reactive compounds widely used, for example, in the production of polyurethane foams, elastomers, paints, and adhesives. The high chemical reactivity of these compounds is also reflected in their toxicity: diisocyanates are one of the most important causes of occupational asthma but also other adverse effects, such as irritation and toxic reactions, have been described in exposed subjects. One of the open questions is whether occupational isocyanate exposure is a carcinogenic hazard. The few epidemiological studies available have been based on young cohorts and short follow-up and are not conclusive. Toluene diisocyanate (TDI) has been classified as carcinogenic in animals on the basis of gavage administration studies, but no conclusions are available on inhalation exposure. For 4,4'-methylene diphenyldiisocyanate (MDI) there is suggestive evidence for carcinogenicity in rats. The possible carcinogenic mechanism of TDI and MDI is not clear. Both chemicals have been positive in a number of short-term tests inducing gene mutations and chromosomal damage. The reactive form could be either the diisocyanate itself or may derive from the metabolic activation of the aromatic diamine derivatives formed by hydrolysis. TDI and MDI react with DNA in vivo and in vitro. However, the structure of the adducts has not been identified. Especially from the in vivo experiment it is not known if the adducts are a product from the reaction with the isocyanate or the corresponding amine. In conclusion, both TDI and MDI are highly reactive chemicals that bind to DNA and are probably genotoxic. The alleged animal carcinogenicity of TDI and MDI would suggest that occupational exposure to these compounds is a carcinogenic risk. The few epidemiological studies available have not, however, been able to clarify if TDI and MDI are occupational carcinogens.

Glycemic response to a food starch esterified by 1-octenyl succinic anhydride in humans

To evaluate the glycemic response to a food starch esterified by 1-octenyl succinic anhydride (OSA), 30 healthy nondiabetic adult subjects were studied in a double-blind crossover design. After an overnight fast, subjects consumed a product containing either 25 g of glucose or 25 g of OSA-substituted starch. Finger-prick capillary blood was obtained at baseline and 15, 30, 45, 60, 90, and 120 min postprandial for glucose measurement. After OSA treatment, the rise in blood glucose was reduced (P < 0.05) at 15 and 30 min and tended (P < 0.08) to be lower at 45 min. Mean peak rise in glucose was reduced 19% (P < 0.01) by OSA (3.30 +/- 0.19 versus 2.66 +/- 0.16 mmol/L) compared to glucose, but time to peak did not differ between treatments. Net incremental area under the curve was also lower (P < 0.05) on OSA compared to glucose. Minimal effects on gastrointestinal symptoms (intensity and frequency of nausea, cramping, distention, and flatulence) were noted for both products, with no clinically significant difference between products. In conclusion, starch substitution with OSA attenuated the postprandial glycemic excursion compared to an equivalent glucose challenge and was well tolerated by fasting healthy adult subjects.

HUman MicroNucleus project: international database comparison for results with the cytokinesis-block micronucleus assay in human lymphocytes: I. Effect of laboratory protocol, scoring criteria, and host factors on the frequency of micronuclei

Micronucleus (MN) expression in peripheral blood lymphocytes is well established as a standard method for monitoring chromosome damage in human populations. The first results of an analysis of pooled data from laboratories using the cytokinesis-block micronucleus (CBMN) assay and participating in the HUMN (HUman MicroNucleus project) international collaborative study are presented. The effects of laboratory protocol, scoring criteria, and host factors on baseline micronucleated binucleate cell (MNC) frequency are evaluated, and a reference range of "normal" values against which future studies may be compared is provided. Primary data from historical records were submitted by 25 laboratories distributed in 16 countries. This resulted in a database of nearly 7000 subjects. Potentially significant differences were present in the methods used by participating laboratories, such as in the type of culture medium, the concentration of cytochalasin-B, the percentage of fetal calf serum, and in the culture method. Differences in criteria for scoring micronuclei were also evident. The overall median MNC frequency in nonexposed (i.e., normal) subjects was 6.5 per thousand and the interquartile range was between 3 and 12 per thousand. An increase in MNC frequency with age was evident in all but two laboratories. The effect of gender, although not so evident in all databases, was also present, with females having a 19% higher level of MNC frequency (95% confidence interval: 14-24%). Statistical analyses were performed using random-effects models for correlated data. Our best model, which included exposure to genotoxic factors, host factors, methods, and scoring criteria, explained 75% of the total variance, with the largest contribution attributable to laboratory methods.

Networking and expert-system analysis: next frontier in biomonitoring

The extensive use of biomarkers in environment biomonitoring programmes has raised the problem of data management and intercomparison. A research project (Pollution Effect Network, PEN) is proposed here, consisting of the realisation of an on-line warehouse for biomarker data (http://www.muf.unipmn.it/pen). The web site will contain repository sections and expert system procedures able to integrate information from different biomarkers and provide ranking of the organism health status in terms of synthetic stress syndrome indexes. Researchers accessing the site will be able to submit and process their own data. This will allow common criteria in the evaluation of the biological effects of pollutants, and an intercomparison of biomonitoring data among different geographic areas and sentinel species.