Periodic Reporting for period 3 - SiMBiT (Single molecule bio-electronic smart system array for clinical testing)
Okres sprawozdawczy: 2021-07-01 do 2022-12-31
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 of pancreatic cyst lesions. Specifically, the SiMBiT activities have been focused on the development of a cost-effective portable multiplexing array prototype with time-to-results within 1 hour allowing early diagnosis of pancreatic cancer directly in blood serum. The SiMBiT final prototype performance were assessed in real samples such as cyst fluid, and blood serum. A machine learning based classifier, allowing to reliably discriminate negative/control samples from high-grade and low-grade cysts has been developed, demonstrating diagnostic specificity and sensitivity of 100 %. Benchmarking against Simoa, ELISA and Ion-Torrent NGS gold standard diagnostic procedures have been carried out too. Overall, the SiMBiT Consortium has successfully reached the end of the third period 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 the bio-electronic smart system array. The SiMBiT assay can be seen as a label-free ELISA system that has the potential to acquire a dominant position in the field of label-free biosensors, with a disruptive effect in the immunoassays market and in the hi-throughput diagnostic system. The SiMBiT platform is capable of timely, non-invasive and reliable identification of pancreatic cancer precursor cysts, with tremendous impact on the currently used diagnostic procedures. Indeed, a faster diagnostic technique to identify neoplastic diseases in a pre-malignant (or pre-invasive) state represents the only chance to proceed with effective cure. This is true especially for pancreatic-biliary cancer, which are otherwise identified at later stages and treated only using palliative methods. The technological progress derived from the SiMBiT device can mostly affect secondary prevention: the detection of the disease can be achieved in the earliest possible stage, taking advantage of the high sensitivity of the technique. The availability of such a system, capable of single-molecule detection, represents one of the best chances for clinicians to get progress in existing clinical practices, not only for the early diagnosis but also for the etiology of progressive diseases.
W1: After the conclusion of first and second Task of the WP1 (T1.1 on technical specifications of the SiMBiT bio-electronic smart system and T1.2 on the standard operating procedures) with the preparation of two deliverables: D1.1 (M3) and D1.2 (M4), the work package activity has continued with the task T1.3 on the quality control data reporting and the preparation of the first (intermediate) version of the Exploitation Plan. The conclusion of the quality control data reporting is due at the conclusion of the project (D1.3) and the final version of the Exploitation Plan has been delivered at M48.
W2: WP2 is dedicated to the fabrication, characterization and optimization of the sensing device. During the third reporting period of the project, the efforts were focused on the optimization of the biofunctionalization protocol of the 3D printed sensing gate with biorecognition elements for selective detection of pancreatic cancer biomarkers. The activities of WP2 have been focused on the study and optimization of the bio-functionalization protocol of the gate surface based on a systematic molecular characterization. Moreover, the validation and the assessment of the analytical figures of merit of the 4x4 and 8x12 SiMBiT prototypes is reported in D2.7 (M48). The complete validation of the final SiMBiT prototype has been accomplished and a fully functional multiparametric data processing has been developed to discriminate patients’ samples collected within WP6 the non-mucinous cyst, namely control samples, from high-grade and low-grade mucinous cysts. Moreover, the benchmarking of the SiMBiT technology has been performed by means of the user-customizable Simoa SP-X Homebrew assay for MUC1 and CD55 biomarkers.
W3: In M31 – M48 WP3 focused on the characterization, simulation, modelling and design optimization of EG-TFTs with bare and biofunctionalized gate. Both 4x4 and 8x12 biosensor matrixes were addressed. More in detail, Task 3.1 was devoted to the electrical and spectroscopic characterization. Task 3.2 developed a numerical framework for the two-dimensional (2D) physical-based simulation of electrolyte-gated transistors with bare and biofunctionalized gate. The framework accounted for the relevant physics, the meaningful geometries and the key device parameters. The combination of the electrical characterizations (Task 3.1) and 2D numerical simulations (Task 3.2) provided insight on the biosensor operation, and supported the development of physically based numerical and analytical models (Task 3.3). The analytical model is currently used for (i) the quantitative assessment of the SiMBiT technology, (ii) technology and system optimizations, and (iii) for the automated analysis of the SiMBiT bioelectronic cartridge.
W4: The process flow for the fabrication of single EG-TFTs, 4x4 and 8x12 arrays has been optimized and validated, by producing these devices and characterizing them in terms of performance, reproducibility and stability. Tridimensional gate arrays have also been realized according to an optimized 3D printing process, matching the same geometry of the commercial ELISA plates used as fluidics for the EGTFTs.
W5: During the third reporting period the module design of the final SiMBiT prototype was completed and reported in D5.5 based on learnings from the first prototype design. The components of the final prototype were fabricated and then the electrical verification of the OTFT addressing electronics, Si-IC and PCB were presented in D5.6.
W6: WP6 is dedicated to sample collection and analysis. Results of Next generation sequencing (NGS) for genomic markers and of ELISA and Simoa for protein markers are then compared to results obtained by the SiMBiT prototype. A further objective is the screening for possible additional biomarkers in pancreatic cyst fluids, which could be analyzed by SiMBiT in the future. In this third period, sample collection has proceeded according to the logistic established during the first and second period, facing the difficulties and delays in patients’ recruitment due to the COVID-19 pandemics. Additionally, a cyber-attack to the University Hospital of Dusseldorf, with following shutdown of all clinical activities as well as of clinical and research servers in September/October 2020 has further dramatically impaired sample collection and analysis. Nevertheless, sample collection has been successfully accomplished; all NGS and ELISA analyses have been performed and the screening for additional markers has delivered important results.
W7: WP7 is dedicated to communication, dissemination and outreach activities. One of SiMBiT communication and dissemination objective is creating awareness, raising interest, fostering engagement and accelerating the market uptake.
W2: WP2 is dedicated to the fabrication, characterization and optimization of the sensing device. During the third reporting period of the project, the efforts were focused on the optimization of the biofunctionalization protocol of the 3D printed sensing gate with biorecognition elements for selective detection of pancreatic cancer biomarkers. The activities of WP2 have been focused on the study and optimization of the bio-functionalization protocol of the gate surface based on a systematic molecular characterization. Moreover, the validation and the assessment of the analytical figures of merit of the 4x4 and 8x12 SiMBiT prototypes is reported in D2.7 (M48). The complete validation of the final SiMBiT prototype has been accomplished and a fully functional multiparametric data processing has been developed to discriminate patients’ samples collected within WP6 the non-mucinous cyst, namely control samples, from high-grade and low-grade mucinous cysts. Moreover, the benchmarking of the SiMBiT technology has been performed by means of the user-customizable Simoa SP-X Homebrew assay for MUC1 and CD55 biomarkers.
W3: In M31 – M48 WP3 focused on the characterization, simulation, modelling and design optimization of EG-TFTs with bare and biofunctionalized gate. Both 4x4 and 8x12 biosensor matrixes were addressed. More in detail, Task 3.1 was devoted to the electrical and spectroscopic characterization. Task 3.2 developed a numerical framework for the two-dimensional (2D) physical-based simulation of electrolyte-gated transistors with bare and biofunctionalized gate. The framework accounted for the relevant physics, the meaningful geometries and the key device parameters. The combination of the electrical characterizations (Task 3.1) and 2D numerical simulations (Task 3.2) provided insight on the biosensor operation, and supported the development of physically based numerical and analytical models (Task 3.3). The analytical model is currently used for (i) the quantitative assessment of the SiMBiT technology, (ii) technology and system optimizations, and (iii) for the automated analysis of the SiMBiT bioelectronic cartridge.
W4: The process flow for the fabrication of single EG-TFTs, 4x4 and 8x12 arrays has been optimized and validated, by producing these devices and characterizing them in terms of performance, reproducibility and stability. Tridimensional gate arrays have also been realized according to an optimized 3D printing process, matching the same geometry of the commercial ELISA plates used as fluidics for the EGTFTs.
W5: During the third reporting period the module design of the final SiMBiT prototype was completed and reported in D5.5 based on learnings from the first prototype design. The components of the final prototype were fabricated and then the electrical verification of the OTFT addressing electronics, Si-IC and PCB were presented in D5.6.
W6: WP6 is dedicated to sample collection and analysis. Results of Next generation sequencing (NGS) for genomic markers and of ELISA and Simoa for protein markers are then compared to results obtained by the SiMBiT prototype. A further objective is the screening for possible additional biomarkers in pancreatic cyst fluids, which could be analyzed by SiMBiT in the future. In this third period, sample collection has proceeded according to the logistic established during the first and second period, facing the difficulties and delays in patients’ recruitment due to the COVID-19 pandemics. Additionally, a cyber-attack to the University Hospital of Dusseldorf, with following shutdown of all clinical activities as well as of clinical and research servers in September/October 2020 has further dramatically impaired sample collection and analysis. Nevertheless, sample collection has been successfully accomplished; all NGS and ELISA analyses have been performed and the screening for additional markers has delivered important results.
W7: WP7 is dedicated to communication, dissemination and outreach activities. One of SiMBiT communication and dissemination objective is creating awareness, raising interest, fostering engagement and accelerating the market uptake.
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.