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Single molecule bio-electronic smart system array for clinical testing

Periodic Reporting for period 1 - SiMBiT (Single molecule bio-electronic smart system array for clinical testing)

Reporting period: 2019-01-01 to 2019-12-31

The general objective of the SiMBiT project is to develop a bio-electronic smart system that can perform single-molecule detection of both proteins and DNA bio-markers. Specifically, the SiMBiT activities will develop a lab-based device into a cost-effective portable multiplexing array prototype with extremely fast time-to-results. During the first year, the programme of activities, described in the Annex 1 of the Grant Agreement, has been successfully carried out, meeting what foreseen besides few minor deviations (some foreseen and some not foreseen) that have been successfully tackled. The deliverables and the milestones have been completed and submitted on time. Only in one case a small delay was incurred and justified. Overall the SiMBiT Consortium has successfully reached the end of year one via a systematic cooperative work involving an intensive inter-sectorial research effort from academia and industrial partners, accomplishing all planned steps towards the development of a cost-effective bio-electronic smart system array.
W1: In the T1.1 the hardware and software specifications for the SiMBiT prototype have been prepared. All partners have defined the main requirements related to the functionality of the bio-sensor physical architecture for usability inside a point of care platform. This activity has been completed.
In the T1.2 standard procedures for QC/QA have been analized and a check list tool was prepared, the QC check list is produced on the partner by partner basis every three months. The T1.2 activity has been completed.
In the T1.3 the monitoring activity is performed using the QC check list tool designed in the T1.2. Every three months the partner check lists are compiled and controlled. The T1.3 will be completed at M42.

W2: we developed and submitted two deliverables in due time:
D2.1: Printed EG-TFT comprising the nanostructured organic semiconductor, stably operates in pure water for at least 7 days. The gate is the reference gate. It was monitored the behavior of the poly(3-hexylthiophene-2,5-diyl) (P3HT) when is used as channel material in EG-TFT. The effects of a prolonged interaction between P3HT and water were characterized using surface techniques as X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM), and it was studied how these changes in the semiconductor morphology and composition affects the EG-TFT performances. The P3HT processing parameters were optimize. Part of these results have been published (https://www.frontiersin.org/articles/10.3389/fchem.2019.00667/full).
D2.2: Report on design and development of “3D arrays of gates”. In this document we report the design, fabrication process flow and the development of 3D arrays of gates. The activity performed aims at the demonstration and validation of a 3D printed gate structure suitable for the development of the final gate cover plate that will fit the standard ELISA plate geometries.

W3: The evaluation of the figures of merit and device physics of the electrolyte-gated thin-film transistors (EG-TFTs) have been achieved. The impact of the geometrical, physical and chemical characteristics of the semiconductor, electrolyte and gate on the EG-TFTs electrical characteristics and stability have been analyzed both experimentally and theoretically. A quasi-two-dimensional EG-TFT model able to reproduce the electrical characteristics of bio-functionalized EG-TFTs as a function of the ligand concentration has been developed and validated. This model provided insight on the bio-functionalized EG-TFTs and it is currently exploited in order to obtain an analytical formulation. Various tools for the EG-TFTs simulation and optimization are currently under implementation.

W4: IIT optimized and validated a process flow for the fabrication of single Electrolyte-Gated Thin Film Transistors (EG-TFTs) compatible with the realization of the final array. As planned, an array of 4x4 devices was also developed with the same process.
Owing to the better results obtained with photolithography, especially in terms of reproducibility, and to an expected easier implementation at an industrial level, contact pads for both single devices and 4x4 arrays were successfully realized with good reproducibility.
The deposition of a dielectric layer has been carried out by inkjet-printing an insulator only in the areas required. Careful optimization of the process parameters allowed to exploit the inkjet printing technique to design the matrix layout with all contacts presented only on one side of the array.
The deposition of the semiconducting layer was carried on via inkjet printing as well. The optimization of the process parameters and of the substrate cleaning and preparation protocols allowed the realization of devices through a large area and scalable technique.

W5: The objective to complete the system design for the first 4x4 well array SiMBiT prototype has been achieved. A high level system design overview has been defined and discussed in a deliverable report. More detailed designs of each component has been realised, including the bio-electronic sensor array, addressing electronics exploiting organic TFTs on foil, the frontend Si chip and the non-disposable readout PCB. A critical aspect of the first SiMBiT prototype design is the mechanical implementation, more specifically, the interfaces between each component. This has been discussed between project partners and defined, with any associated risks and risk mitigation options identified. The process flow in which the first SiMBiT prototype will be created has also been determined.

W6:First, we established functional logistics for clinical sample collection with two clinical collaborators. All collaborators have been informed about the criteria of study inclusion and ethical requirements for each patient. Aliquots from incoming samples have been stored for later testing with SiMBiT. Simultaneously, all clinical samples have been analyzed by Next Generation Sequencing (NGS).
The screening for additional biomarkers has been focused on expression of the protein MUC1 and of several miRNAs. If sample volumes allowed, expression of MUC1 has been determined by ELISA and expression of miR-21-5p and miR-221-3p has been determined by qPCR. To screen for more potential miRNA candidates, miRNA-sequencing on pancreatic cystic tumor tissue has been performed.
For this first year, we can report a clinical collective of 37 patients. All samples have been analyzed by NGS, in 18 samples ELISA was performed. As a result of the biomarker screening, we can outline MUC1, miR-21 & miR-221 as promising biomarker candidates, as they are upregulated in PDAC and mucinous lesions.

W7: A set of public communication tools was developed during the first months of the project and updated throughout the project duration. SiMBiT partners attended to several workshops, international conferences and other relevant events presented good opportunities to disseminate and discuss
Deliverables D7.1 : Report on the public Website and Social Media profile Setup and D7.2: SiMBiT leaflet and poster, were submitted online in due time
The information on section 2.1 of the Annex 1 is still relevant for CSGI, UDUS, UNIBS, ABO, IIT, TU/e, FE, MASMEC and Efficient Innovation.