Copy Number Alteration Profiling of Single Circulating Tumor Cells which May Be used to Predict Response to Therapy

Scientists reported the development of a robust and streamlined procedure for whole-genome copy number profiling of circulating tumor cells (CTCs) from a simple blood test. In contrast to existing methods that are complex and costly, the single-tube, single-step protocol is able to detect absolute Copy Number Alterations (CNA) in single cells and maintain accuracy at a lower cost than conventional genomic analysis procedure, opening up to the possibility for genome-driven targeted therapy selection and monitoring of disease progression in liquid biopsy.

The genome of tumor cells goes through multiple aberration events which are intimately connected to the underlying tumor biology and are reflected in the CNA profile of the entire genome. Multiple recent findings across several cancer types have pointed to the fact that these pattern of aberrations are linked to increased response or resistance to different classes of drugs, ranging from classical chemotherapy, to PARP-inhibitors and Immune checkpoint inhibitors. “A variety of analytical techniques have been developed to analyze copy-number alterations in the research lab,” explained Nicolò Manaresi, Ph.D., lead author of the study. “However, they are not well suited for clinical application on CTCs where reproducibility, robustness and scalability are required. Our approach offers a streamlined, less expensive method for genome-wide CNA profiling of single cancer cells.” Dr. Manaresi also serves as Chief Scientific Officer at Menarini-Silicon Biosystems, based in Bologna and Huntingdon Valley, PA. (U.S.)

The study, published in the online scientific journal PLOS ONE, presents the characterization of an innovative workflow — developed and commercialized by Menarini Silicon Biosystems as Ampli1™ LowPass kit. The method exploits the characteristics of Ampli1 WGA, which is based on ligation mediated-PCR WGA of fragments obtained by digestion on specific restriction sites, to produce, in a single amplification step, sequencing-ready, barcoded DNA libraries suitable for genome-wide CNA profiling by low-pass whole genome sequencing. This allowed to decrease workflow time and efforts, allowing higher throughput while reducing the cost. The approach is also demonstrated on patient CTCs, isolated by DEPArray™ technology following enrichment from blood using the CELLSEARCH^® system*.

“In comparison to aCGH, a widely used and accepted method for screening CNAs in clinical diagnostic, our approach allowed us to decrease the cost of analysis while providing comparable or superior performances” said Dr. Manaresi. “Moreover Ampli1 LowPass has the advantage to determine absolute copy numbers changes and this has important implications for the biological inter­pretation of cancer samples. As sequencing cost per base is decreasing with advances in NGS technologies, our streamlined workflow will further decrease the cost of copy number analysis in the future and pave the way to simpler blood test to study cancer heterogeneity in liquid biopsy.”

Researchers from the University Hospital of the Heinrich-Heine-University of Dusseldorf, the Medical Oncology Unit of the University Hospital of Bologna, The Institute of Cancer Research, London, and The Royal Marsden NHS Foundation Trust (London) also participated in the study.

About Menarini Silicon Biosystems

Menarini Silicon Biosystems, based in Bologna, Italy, and Huntingdon Valley (PA), USA, develops technologies and products that help researchers understand the biological complexity of disease through the study of single cells. The company manufactures and markets the DEPArray NxT, the only image-based digital cell-sorting and isolation platform that enables clinical researchers to conduct molecular analyses on live or fixed cells with single-cell precision. In 2017 Menarini Silicon Biosystems purchased all the assets and relevant business related to the CELLSEARCH® Circulating Tumor Cell (CTC) System. The integration of CELLSEARCH and DEPArray provides an end-to-end workflow solution* for the enumeration, isolation, and molecular characterization of CTCs from a simple blood test in the clinical research setting. This will help drive the clinical utility and correlation of CTCs with the effectiveness of specific therapies. Menarini Silicon Biosystems is a wholly owned subsidiary of the Menarini Group, a multinational pharmaceutical, biotechnology and diagnostics company headquartered in Florence, Italy, with a heritage of over 130 years and over 16,000 employees in more than 100 countries.

*The workflow described is for research use only. Not for use in diagnostic procedures. The performance characteristics and safety and effectiveness of the workflow have not been established and are not cleared or approved by the FDA.

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The research was supported by CANCER-ID, a project funded by the Innovative Medicines Joint Undertaking (IMI JU) [Grant Agreement #115749] and Menarini Silicon Biosystems, which commercialize the CELLSEARCH® system, the DEPArray™ system and the Ampli1™ product line.

COI: Ferrarini, Forcato, Buson, Tononi, del Monaco, Terracciano, Bolognesi, Fontana, Medoro and Manaresi are employee of Menarini Silicon Biosystems. Buson, Tononi and Manaresi are co-inventors on the patent “Method and kit for the generation of dna libraries for massively parallel sequencing” (WO 2017178655 A1). The method presented has been implemented as a kit called Ampli1™ LowPass, commercially available from Menarini Silicon Biosystems.

Citation: Ferrarini A, Forcato C, Buson G, Tononi P, del Monaco V, Terracciano M, et al. (2018) A streamlined workflow for single-cells genome-wide copy-number profiling by low-pass sequencing of LM-PCR whole-genome amplification products. PLoS ONE 13(3): e0193689. https://doi.org/10.1371/journal.pone.0193689