ESCHILO: Early Stage Cancer diagnosis via HIghly sensitive Lab- On-chip multitarget systems
Responsible:
Contribution from Regione Lombardia
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Start date: 2013-10-01
Length: 36 months
Project abstract
Goal of the project:
Eschilo project aims to provide the health system with a technological product for the early diagnosis of tumors that is innovative, low-cost yet very sensitive. Starting from a small drop of blood or urine and applying proprietary techniques developed by partners in the fields of spintronics, silicon photonics and very high sensitivity electronic circuits, the project aims to realize a miniaturized lab-on-chip platform that can identify the genetic mutations which give rise to cancerous tumors.
The lab-on-chip platform will contain all the functionalities traditionally present in a biomedical analysis laboratory, from the capture and extraction of DNA from the biological sample to the detection of the significant genetic mutations and their classification.
This transfer of the diagnosis technology from the biological lab to the clinical bed has a threefold advantages: (i) provide a quick response to the diagnosis, (ii) improve the risk management by avoiding the transfer of the samples to the laboratory and the correlated errors and finally (iii) reduce the analysis costs.
The identification of the sequences of interest will be achieved through suitable highly selective biological probes grafted to the surface of the sensor, in a matrix architecture that will enable the analysis across a broad spectrum of genes with a single measurement protocol. The expected sensitivity of the system, of about a few fM as already demonstrated in laboratory experiments, will place the instrument in a category of excellence perfectly suited to the application and would likely define it as a gold standard reference device for the international community.
Motivation of the project:
The reference scenario in which the project is placed consists of the molecular diagnostics in medicine, focused on the search for mutations in the genes that cause a specific disease. One example is that of breast cancer : Italian women have an average of 12 out of 100 chance of developing the disease throughout life , but the risk rises to 80 % in those who are carriers of an anomaly borne by the genes BRCA 1 or BRCA 2 . Therefore, the execution of a "genetic diagnosis" able to identify hereditary predisposition is configured as the first of a series of interventions that can prevent or reduce the risk of becoming ill.
State of the art:
Currently the molecular study of genetic diseases requires as a first step PCR (Polymerase Chain Reaction), an enzymatic reaction that allows in vitro amplification of a specific region of DNA (the one that, if changed, would cause the disease), copying up to obtain millions of copies. Although this is a simple technique , it is not without the introduction of artifacts and still requires a considerable time. In the case of diseases caused by gene alteration, the subsequent analytical phase is represented by automatic sequencing of the amplified fragment in PCR. The search for mutations is then performed by comparing the sequence obtained with a reference sequence (Re-sequencing). This technique represents the best existing approach for the search of mutations and single nucleotide polymorphisms and is well developed in the laboratories of IFOM. By providing the results in 48 hours, this analysis is adopted for those diagnostic tests that IFOM currently provides to the healthcare system of the Lombardy region.
Novelty of the project:
The ESCHILO project aims to develop a new methodology for the detection of gene mutations, based on the integration of two modules lab-on -chip:
(i) a first module for the capture and extraction of DNA from the biological sample (blood or urine of individuals potentially carrying mutations ) by "immunoaffinity capture" of magnetic nanoparticles suitably functionalised;
(ii) a microchip biosensors with high sensitivity (up to fM) based on the detection of the resistance variation in a magnetic resistor as a function of the number of magnetic nanoparticles (i.e. DNA strains) captured by the magnetic resistor itself. The high sensitivity will allows to avoid the chemical amplification by PCR.
In particular, if the detector array will have 216 sensitive points, the system will be able to reveal in one shot all 12 relevant gene mutations in oncology in a time of screening reduced (about 24 hours) with a low cost device for the order of 20 €.
Eschilo project aims to provide the health system with a technological product for the early diagnosis of tumors that is innovative, low-cost yet very sensitive. Starting from a small drop of blood or urine and applying proprietary techniques developed by partners in the fields of spintronics, silicon photonics and very high sensitivity electronic circuits, the project aims to realize a miniaturized lab-on-chip platform that can identify the genetic mutations which give rise to cancerous tumors.
The lab-on-chip platform will contain all the functionalities traditionally present in a biomedical analysis laboratory, from the capture and extraction of DNA from the biological sample to the detection of the significant genetic mutations and their classification.
This transfer of the diagnosis technology from the biological lab to the clinical bed has a threefold advantages: (i) provide a quick response to the diagnosis, (ii) improve the risk management by avoiding the transfer of the samples to the laboratory and the correlated errors and finally (iii) reduce the analysis costs.
The identification of the sequences of interest will be achieved through suitable highly selective biological probes grafted to the surface of the sensor, in a matrix architecture that will enable the analysis across a broad spectrum of genes with a single measurement protocol. The expected sensitivity of the system, of about a few fM as already demonstrated in laboratory experiments, will place the instrument in a category of excellence perfectly suited to the application and would likely define it as a gold standard reference device for the international community.
Motivation of the project:
The reference scenario in which the project is placed consists of the molecular diagnostics in medicine, focused on the search for mutations in the genes that cause a specific disease. One example is that of breast cancer : Italian women have an average of 12 out of 100 chance of developing the disease throughout life , but the risk rises to 80 % in those who are carriers of an anomaly borne by the genes BRCA 1 or BRCA 2 . Therefore, the execution of a "genetic diagnosis" able to identify hereditary predisposition is configured as the first of a series of interventions that can prevent or reduce the risk of becoming ill.
State of the art:
Currently the molecular study of genetic diseases requires as a first step PCR (Polymerase Chain Reaction), an enzymatic reaction that allows in vitro amplification of a specific region of DNA (the one that, if changed, would cause the disease), copying up to obtain millions of copies. Although this is a simple technique , it is not without the introduction of artifacts and still requires a considerable time. In the case of diseases caused by gene alteration, the subsequent analytical phase is represented by automatic sequencing of the amplified fragment in PCR. The search for mutations is then performed by comparing the sequence obtained with a reference sequence (Re-sequencing). This technique represents the best existing approach for the search of mutations and single nucleotide polymorphisms and is well developed in the laboratories of IFOM. By providing the results in 48 hours, this analysis is adopted for those diagnostic tests that IFOM currently provides to the healthcare system of the Lombardy region.
Novelty of the project:
The ESCHILO project aims to develop a new methodology for the detection of gene mutations, based on the integration of two modules lab-on -chip:
(i) a first module for the capture and extraction of DNA from the biological sample (blood or urine of individuals potentially carrying mutations ) by "immunoaffinity capture" of magnetic nanoparticles suitably functionalised;
(ii) a microchip biosensors with high sensitivity (up to fM) based on the detection of the resistance variation in a magnetic resistor as a function of the number of magnetic nanoparticles (i.e. DNA strains) captured by the magnetic resistor itself. The high sensitivity will allows to avoid the chemical amplification by PCR.
In particular, if the detector array will have 216 sensitive points, the system will be able to reveal in one shot all 12 relevant gene mutations in oncology in a time of screening reduced (about 24 hours) with a low cost device for the order of 20 €.
Project results
Publications:
- G. Gervasoni, M. Carminati, G. Ferrari, M. Sampietro, E. Albisetti, D. Petti, P. Sharma, R. Bertacco, "A 12-channel dual-lock-in platform for magneto-resistive DNA detection with ppm resolution", 2014 IEEE Biomedical Circuits and Systems Conference (BioCAS), 22-24 October 2014, Lausanne, p. 316-319, DOI: 10.1109/BioCAS.2014.6981726.
- A. Laurent, M. Calabrese, H-J. Warnatz, M-L. Yaspo, V. Tkachuk, M. Torres, F. Blasi and D. Penkov, “ChIPSeq and RNA-Seq Analyses Identify Components of the Wnt and Fgf Signaling Pathways as Prep1 Target Genes in Mouse Embryonic Stem Cells” (2015). PLoS ONE 10(4): e0122518. doi:10.1371/journal.pone.0122518.
- M. Monticelli, D. Petti, E. Albisetti, M. Cantoni, E. Guerriero, R. Sordan, M.Carminati, G. Ferrari, M. Sampietro, R. Bertacco, “Closed loop microfluidic platform based on domain wall magnetic conduits: a novel tool for biology and medicine”, MRS Online Proceedings Library, Volume 1686, 2014, mrss14-1686-v02-06 doi: 10.1557/opl.2014.925, Published online by Cambridge University Press 21 Nov. 2014.
