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Conference Agenda

Overview and details of the sessions of this conference. Please select a date or location to show only sessions at that day or location. Please select a single session for detailed view (with abstracts and downloads if available).

 
Session Overview
Session
LB1: Liquid Biopsies & Exosomes
Time:
Monday, 03/Apr/2017:
10:30am - 12:30pm

Session Chair: Michael W Pfaffl, TUM, Germany
Session Chair: Stephen Andrew Bustin, Anglia Ruskin University, United Kingdom
Location: Lecture hall 14
650 participants, TUM Weihenstephan

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Presentations

Extracellular Vesicles and their Potential as Biomarkers and Therapeutics

Jan O Lötvall

University of Gothenburg, Sweden

All cells in the body release multiple types of extracellular vesicles (EVs), including exosomes, microvesicles and beyond. In 2007 we discovered that exosomes contain both mRNA and microRNA that can be shuttled from one cell to another (Valadi, Ekström et al., 2007), which was a very surprising finding at the time.

Different cells release EVs with different molecular cargos, and each cell type can even change their EV cargo under diffierent conditions, such as stress or cancer transformation. This important feature of EVs has made them very interesting candidates as biomarkers in disease. Indeed, both RNA and DNA EV cargo, as well as EV proteins, can be utilized as diagnostics, and to monitor disease, which will be reviewed in the presentation.

The ability of EVs to shuttle RNA and other molecules from one cell to the cytoplasm of another cell has also open up the opportunity to highjack this natural system to deliver therapeutic molecules to diseased cells, where current biological treatments such as antibodies are unable to reach. This opens up the opportunity todevelop treatments for different diseases, for example targeting oncogenes with microRNA or siRNA molecules, that otherwise cannot easily penetrate the cell membrane. This new category of biological treatments has the opportunity to open up a totally new way to reach previously unreachable disease targets, with molecules that otherwise would not reach the ideal disease target. This part of the presentation will thus describe the possibilities of EV-based therapeutics in different diseases, and give examples of models where this approach has been successful in experimental models.


Ultrasensitive mutation detection in liquid biopsies using SiMSen-Seq

Anders Ståhlberg

University of Gothenburg, Sweden

Detection of cell-free DNA in liquid biopsies offers great potential for use in non-invasive diagnostics and to monitor treatment. However, the allele frequencies are often low in liquid biopsies and challenging to analyze, since standard next-generation sequencing suffers from insufficient sensitivity and digital PCR is not suitable to analyze multiple allele variants. Hence, we have developed SiMSen-Seq:“Simple, Multiplexed, PCR-based barcoding of DNA for Sensitive mutation detection using Sequencing’’ that allows allele frequencies < 0.1% to be detected, using several kilobases of DNA. Several barcoding strategies have been reported, but all require long and complex library preparation protocols. SiMSen-Seq was developed to generate barcoded libraries with minimal DNA input (< 5ng), flexible target selection and a very simple (~3 hour) library construction protocol. SiMSen-Seq allows detection of variant alleles with easy customization of library content and a protocol that can be implemented in any molecular biology laboratory. In this presentation we will discuss assay development and bioinformatics that are used in SiMSen-Seq. In addition, we show data from several applications, focusing on cancer.


Droplet-based digital PCR for cancer patient follow up’

Valerie Taly

Université Paris Descartes/ INSERM/ CNRS, France

Tumor-specific genomic alterations can be used to detect circulating tumor DNA circulating (ctDNA). They represent specific biomarkers that distinguish cancer cells and normal cells. They are likely to be useful for the diagnosis, prognosis, treatment, and follow-up of cancer patients, but their use in clinical oncology requires a highly sensitive strategy that discriminates modified sequences in a large excess of DNA coming from normal cells [1, 2].

Picoliter droplet-based digital PCR allows performing millions of single molecule PCR reactions in parallel to detect and quantify a minority of mutant sequences in a complex mixture of DNA [3]. It enables direct counting of the number of copies of a target sequences present in the sample and the multiplex detection of several sequences including rare mutations and hypermethylated regions [4,5]. Newly developed optimized NGS strategies can now also reach relevant sensitivity and allow the screening of a wide range of mutations in circulating DNA [6].

We will illustrate how, by allowing non invasive highly sensitive and quantitative analysis of ctDNA within blood patient samples, these methods are used for follow-up of cancer progression and tumor response to treatment. We will present results of prospective clinical trials highlighting pertinence of these approaches in pancreatic [7], lung [8] and colon cancer.

Refs:

[1] Taly, V., Pekin, D, El Abed A. and Laurent-Puig, P. (2012). Trends in Molecular Medicine, 18(7):405-16.

[2] Perkins G., Lu, H., Garlan, F. and Taly V. (2017). Adv clin chem, 79: in press.

[3] Pekin, D., Skhiri, Y., Baret, J.-C., Le Corre, D., Mazutis, L., Ben Salem, C., Millot, F., El Harrak, A., Hutchison, J.B., Larson, J.W., Link, D.R., Laurent-Puig, P., Griffiths, A.D., and Taly, V. (2011). Lab chip, 11(13): 2156-66.

[4] Taly, V., Pekin, D., Benhaim, L., Kotsopoulos, SK, Le Corre, D., Li X., Atochin, I., Link, D.R., Griffiths, A.D., Pallier, K., Blons, H., Bouche, O., Landi, B., Hutchison, J.B. and Laurent-Puig, P. (2013). Clin Chem, 59(12): 1722-31.

[5] S. Garrigou, G. Perkins, F. Garlan, C. Normand, A. Didelot, D. Le Corre, S. Peyvandi, C. Mulot, R. Niarra, P. Aucouturier, G. Chatellier, P. Nizard, K. Perez-Toralla, E. Zonta, C. Charpy, A. Pujals, C. Barau, O. Bouché, J.-F. Emile, D. Pezet, F. Bibeau, J. B. Hutchison, D. R. Link, A. Zaanan, P. Laurent-Puig, I. Sobhani and V. Taly. Clin Chem, 62(8):1129-39.

[6] Pecuchet, N., Rozenholc, Y., Zonta, E., Pietraz, D., Didelot, A., Combe, P., Gibault, L., Bachet, JB, Taly, V., Laurent-Puig, P. Blons, H and Fabre, E. (2016). Clin Chem, 62(11):1492-1503.

[7] Pietraz, D., Pecuchet, N., Garlan, F., Didelot, A., Dubreuil, O., Doat, S., Imbert-Bismut, F., Karoui, M., Vaillant, JC, Taly, V., Laurent-Puig, P. and Bachet, JB. (2017). Clin Cancer Res, 23(1):116-23.

[8] Pecuchet, N., Zonta, E., Didelot, A., Combe, P., Thibault, C., Gibault, L., Rozenholc, Y., Taly, V., Fabre, E., Blons, H and Laurent-Puig, P. (2016). Plos Med, 13(12): e1002199.


Exosomes - Advancing Liquid Biopsy Diagnostics

Mikkel Noerholm

Exosome Diagnostics, Germany

The field of liquid biopsy has gained enormous interest in recent years. An important goal of personalized medicine has been being able to detect tumor derived genetic profiles and tracking the evolution of tumor mutations over time. Utilizing cell free tumor DNA (ctDNA) for detection of mutations in plasma has shown some promise in late stage cancer patients, but can only be used to track genetic changes. A more complete picture can be seen by combining the mutations in ctDNA with the mutations and RNA profiles from exosomes. Exosome Diagnostics have validated and launched the world’s first clinical tests using exosomal RNA (exoRNA). We have also developed a single step isolation platform for exoRNA and ctDNA from biofluids, which increases the available mutant copies from the tumor available for analysis. In a blinded head to head analysis, this platform had better sensitivity when compared to ctDNA alone. Exosomes are especially interesting because they are released as an active process from not only cancer cells, but also other cells, such as tumor stroma and immune cells. This enables us to access RNA profiles when monitoring response to more complex processes, such as immunotherapy response, where monitoring mutations may not be sufficient.



 
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