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A liquid biopsy platform combining a high fundamental frequency QCM device with dynamic chemistry for detecting mutations in circulating DNA

Authors: A. Grammoustianou, G. Papadakis, M. Tabraue, J.J. Díaz-Mochon, R. Fernández, J.V. García, A. Arnau, E. Gizeli. AWSensors S.L., Institute of Molecular Biology and Biotechnology- FORTH, University of Crete, Destina Genomics S.L., Centro de Investigación e Innovación en Bioingeniería – Universidad Politécnica de Valencia

Event:  5th International Conference on Bio-sensing Technology, Riva del Garda, Italy (2017)

In the past decade, the analysis of circulating tumour DNA (ctDNA) in blood has been a major breakthrough; ctDNA has been proposed as a priceless source for cancer diagnostic, prognostic and treatment monitoring through a new methodology known as “Liquid Biopsy”. This study presents a novel diagnostic method for the acoustic detection of KRAS mutations in ctDNAs based on: (1) DNA analysis by “dynamic chemistry” that utilizes aldehyde modified nucleobases (SMART) and abasic peptide nucleic acids (DGL probes) capable for the errorfree detection of nucleic acids and their mutations; and, (2) a high fundamental frequency (100 MHz) acoustic wave microsensor (AWS HFF-QCM) that allows the accurate, inexpensive, label-free and real time monitoring of the “dynamic chemistry”. Surface-immobilized DGL probes on the AWS HFF-QCM device are used to detect ctDNAs of wild type and mutated KRAS variants. Upon hybridization of the DGL probe with its target ssDNA, a duplex is formed where biotin- tagged SMART bases can lock in front of the position under interrogation; streptavidin binding detected in a follow-up step confirms the presence of the SMART bases. The use of DGL probes in combination with an isothermal DNA amplification step RPA) have allowed the sensitive and specific recognition of single mismatches in KRAS genes in less than 1 hour. This work presents a unique and novel technology that can emerge as a promising tool in the field of cancer diagnostics.

Liquid Biopsy detection protocol

Schema for complete detection protocol:

(A) Extracted DNA containing mutant (red) and wild type DNA fragments (black) are enzymatically amplified.

(B) Denatured amplicons are hybridized on surface immobilized DGL probes. Chemical locking of a specific tagged SMART base takes place only in the appropriate position.

(C) Incorporated SMART bases are recognized by streptavidin and monitored in real-time during an acoustic measurement.

DNA

H2020 Project LiqBiopSens: A new liquid biopsy platform for early detection of colorrectal cancer

We are proud to announce that the European Comission awarded a grant of a total value of 2’7M euros to our project LIQBIOPSENS for early detection of colorectal cancer by carrying out liquid biopsy. The grant was awarded within Horizon2020 and specifically in the call entitled “ICT-28-2015: Cross cutting ICT Key Enabling Technologies”.

 

AWSensors will coordinate this H2020 project during the next 3 years (2016-2018). The overall aim of this project is the further development and validation in real settings of a novel diagnostic platform for the early and fast detection of circulating tumor DNA (ctDNA) and their KRAS and BRAF mutations associated to colorectal cancer through blood samples.

Liquid Biopsy platform LiqBiopSens features

The main features of LiqBiopSens are:

  1. Reliability (detection rates vary from 95-100 %)
  2. Low-Cost
  3. Sensitivity (in the zM range)
  4. Multiplexing capabilities (analysis of 27 KRAS and BRAF mutations simultaneously)
  5. Short analysis time (30-60 min.)
  6. User-friendly interface
  7. Flexibility

LIQBIOPSENS platform is based on the integration of two novel complementary technologies:

  • DGL© technology property of DestiNA Genomics Ltd, capable of delivering faster, more error-free detection of DNA and their mutations than current enzyme-based detection systems, making ‘false positive’ results a thing of the past.
  • A novel high resolution acoustic wave microsensor technology property of AWSensors, that allows an accurate, inexpensive, label-free, direct and real-time transduction method to quantitatively evaluate the results of the application of the mentioned DGL© technique.

However, solution proposed by the LIQBIOPSENS project relies on the multidisciplinary integration of different key enabled technologies. Accordingly, LiqBiopSens will be accomplished by AWSensors and Destina Genomics in collaboration with the following partners:

Liquid Biopsy platform LiqBiopSens concept

The operating concept of our project is described in the following representative scheme:

Early detection of colorrectal cancer by liquid biopsy

ctDNA amplicons produced in chamber (1) are denatured and transferred to the sensors surface via   microfluidics (2) where hybridization with DGL probes takes place; mutation‐discrimination is carried out during the injection (3) of novel probes which click selectively on the target DNA (4) while acoustic detection exploits functionalized nanoparticles (5).

Colorectal cancer, the second most common cause of cancer death

The most frequently occurring forms of cancer in the EU are colorectal, breast, prostate and lung cancers. In men, lung cancer is the most frequent cause of cancer death, while in women, it is breast cancer. In both men and women, colorectal cancer is the second most common cause of cancer death.

The “gold standard” for identifying the type and extent of a cancer is a tissue biopsy, in which a small sample of tissue is taken from the suspected tumour and histologically examined. While this procedure can provide important information about the patient disease, tissue biopsy can be painful, represents a single snap-shot in time, is subjected to significant selection bias and if the tumour tested was first detected by palpation or imaging, it may already be so large that the disease is well advanced. Furthermore, when the tumour tissue is removed or it is inaccessible, these genotyping techniques are impossible. Therefore, cancer remains a ghost disease when primary tumours are removed through surgery, meaning that there are not tools to assess the efficiency of treatments or prevent metastasis.

Liquid Biopsy, a revolution in the fight against cancer

It has long been known that solid tumors release DNA in the blood and the load of circulating tumor DNA (ctDNA) has been correlated to staging and prognosis. However, only recent advances in the sensitivity and accuracy of DNA analysis have allowed for genotyping of somatic changes found in tumors by interrogating ctDNA. This technique is known as ‘Liquid Biopsy’ and it is based on the analysis of a biomarker that can be easily isolated from many body fluids (blood, saliva, urine, ascites, pleural effusion, etc.).

 

Successful implementations of liquid biopsy techniques to track tumor dynamics in real time and for the early detection, such as LIQBIOPSENS, are going to revolutionise how clinicians fight against cancer.