Project 7

Development of MB based purification of biomarkers from liquid biopsy for early detection of cancer in BRCA+ subjects

The candidate should have preferably a M.Sc. in Biology or related topics

The innovative nanotechnological strategies proposed in STRIKE will address the early diagnosis and diagnosis-related therapy in BRCA+ mutation breast cancer (BC). Patients with germline mutations in the BRCA+ genes have unique features such as a high risk of developing tumors and, consequently, the need to be subjected to regular clinical follow-up visits and protocols. These subjects correspond to the ideal cohort of patients to test the feasibility of a “liquid biopsy” approach for an early diagnosis to anticipate the clinical detection of the disease.  Innovative magnetic beads (MBs) produced in STRIKE will be exploited to increase operating capture efficiency of DNA or exosome from complex biologic matrix (i.e blood, urine). Whole Exome Sequencing (WES) and MeDIP seq technology will be performed on the primary tumors (stored in paraffin) using the NGS platform and based on the identified mutational profiles, we will develop "customized" gene panels and methylation signatures for NGS and/or ddPCR analysis of cfDNA and exosomes from healthy subjects carry BRCA mutations.

Project 7 optimize the use MBs for the capture and analysis tumor biomarkers (tumor methylated DNA or tumoral exosome) from liquid biopsies from BRCA +subjects. Both activities are converging towards the industrial application of STRIKE results. In a first step using the technology developed by NTSOL (AC magnetometers) to monitor purification efficiency the purification of exosomes and methylated DNA will be optimized. Then, the purification procedure will be applied to complex matrixes and finally liquid biopsies from patients will be analyzed for the feasibility of the approach.

Project 7 will contribute to: a) have a better idea of how capturing agents (ie antibodies) can be linked to MB for optimal purification protocols; b) have determined the sensitivity and the specificity of thepurification protocol; c) teste the purification protocol in complex matrixes; d) teste the feasibility of the approach in liquid biopsies from BRCA+ subjects.

The project will be mainly carried out at Cogentech (Italy) under the supervision of Dr. Nina Offenhäuser. The PhD degree in “Applied Biology and Experimental Medicine” PhD programme (3 years) will be awarded at University of Messina under the supervision by Prof. Silvana Briuglia.

Cogentech is a benefit corporation providing cutting-edge technology services, integrating research, technology and healthcare (https://www.cogentech.it/scientific-services.php). Cogentech has its main site in Milan at the IFOM campus site (470 m2 laboratory space) 21 full time personal provide scientific services to IFOM researchers while also engaging actively in R&D. Cogentech’s second site is in Catania where 9 full time personal are involved in R&D focusing on the development of novel diagnostic devices for the early detection of tumors, minimal residual disease and personalized therapy.

Cogentech’s Laboratory in Catania (160 m²) is newly renovated and fully equipped with brand new instruments for:

• molecular analysis (Illumina Nextseq2000, Agilent Tapestation 4150, Biorad QX20 ddPCR system, C100 touch PCR, Diatech Labline Magcore Super Nuclei Acid extractor and QFX Denovix);
• protein analysis (Biorad gel electrophoresis, Turbo blot-transfer and Chemidoc);
• histological analysis (microtome, Leica DM44B Fluorescence microscope, LMD7 Laser capture microdissector, Olympus VS200 Slide Scanner);
• bioinformatics infrastructure (CPU, GPU).

Planned secondments:

❖ STEM Innovation (Italy), 1 week:  Complementary training meeting on IPR management and soft skill.

❖ Univerzita Palackeho V Olomouci, UP, (Czech Republic) 2 months: to be trained on development, synthesis and characterization of MagU.

❖ University of Messina (UNIME), 2 months: to be trained on development, synthesis and characterization of MNPs.

❖ Nanotech Solutions, NTSOL (Spain), 2 months: to characterize and improve the magnetic properties of MBs.