¹ Institute of Biomedical Chemistry, Moscow, Russia

² Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow, Russia

³ Sechenov First Moscow State Medical University (Sechenov University) Moscow, Russia

⁴ Department of Urology, Rabin Medical Center, Petah Tikva, Israel

⁵ Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel

⁶ Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria

⁷ Faculty of Infectious Diseases in Children, N.I. Pirogov Russian National Research Medical University, Moscow, Russia

⁸ Moscow State Academy of Veterinary Medicine and Biotechnology Named after Skryabin, Moscow, Russia

⁹ Foundation of Perspective Technologies and Novations (FPTN), Moscow, Russia

¹⁰ Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Moscow, Russia

¹¹ Federal State Autonomous Educational Institution of Higher Education «Bauman Moscow State Technical University», Moscow, Russia

¹² N.N. Blokhin National Medical Research Center of Oncology, Moscow, Russia

Urogenital cancers represent one of leading causes of death, and thus novel simple, highly sensitive and reliable methods are required for their revelation at early stages in order to provide effective therapy and improve patients’ survival rate. Here we demonstrate parallel rapid label-free detection of a pool of (urogenital cancer)-associated non-coding RNA molecules of three different types — microRNAs, circular RNAs (circRNAs) and small nucleolar RNAs (snoRNAs) — in human blood with sub-femtomolar concentration sensitivity. This is achieved by employing a biosensor, whose nanotechnology-based sensor chip bears an array of oligonucleotide-sensitised silicon-on-insulator (SOI) nanoribbons fabricated using a ‘top-down’ technology. The simultaneous detection of different types of cancer-associated ncRNAs in one sample will increase the reliability of the diagnostic results, helping to avoid both false-positives and false-negatives. Owing to the high detection sensitivity, which reaches several thousands of target ncRNA molecules in 1 mL of the analysed sample, the nanoribbon biosensor proposed herein represents a promising tool for early revelation of urogenital cancers in humans.

Keywords: urogenital cancer; nanoribbon; biosensor; non-coding RNA; biomarker detection; silicon nanowire

Urogenital cancers are widely spread across the globe, being responsible for every fifth cause of cancer [1] and every seventh death of cancer [2]. Namely, the prostate cancer (PrC) is the fifth leading cause of death worldwide [3]. Furthermore, ovarian cancer (OvC) is the fifth leading cause of death of cancer among women [4]. Kidney (KiC) and bladder (BlC) cancers also occur quite often, amounting to 2 and 3% of all cancers registered worldwide, respectively [5] — while urethral cancer is relatively rare [6]. Urogenital cancers can be quite effectively cured at early stages, and their early diagnosis improves treatment outcomes and survival rate [7]. Unfortunately, the existing methods, which are employed in clinical practice for the diagnosis of urogenital cancers, do not allow their early revelation due to either poor sensitivity [8] or use of insufficiently specific markers (such as prostate specific antigen (PSA) in case with PrC [9,10] or carbohydrate antigen 125 (CA 125) in case with OvC [11]). Namely, cystoscopy [12,13] and biopsy are invasive and painful procedures, which potentially can cause complications [14]. Furthermore, in case of using tumour visualisation using ultrasound, magnetic resonance imaging and/or computer tomography one may lose sight of very small tumours and have troubles with correct interpretation of the results [15]. In this respect, non-invasive methods based on the so-called “liquid biopsy” are quite convenient [16], and so the task consists in the development of methods, which provide the detection of sufficiently specific biomarkers of urogenital cancers with high sensitivity.

The problem consists in proper selection of sufficiently specific biomarkers in order to reliably reveal urogenital cancers in humans at the early stages [9,10]. In this respect, various types of non-coding ribonucleic acids (ncRNAs) such as microRNAs [17,18], circular RNAs (circRNAs) [19] and small nucleolar RNAs (snoRNAs) [20,21,22] were reported to be promising cancer-specific biomarkers. At that, it should be emphasized that polymerase chain reaction (PCR)-based methods of RNA detection (such as northern blotting, next generation sequencing and in situ hybridisation) are very sensitive to contamination [23,24,25], which can cause RNA degradation [26] — in contrast to amplification-free nanoribbon-based detection. In contrast, nanotechnology-based approaches imply direct amplification-free and label-free detection of the target ncRNAs. These approaches to studying biological macromolecular compounds such as proteins and nucleic acids have allowed the scientists to detect and visualise single biomarker macromolecules, performing their in-deep studies [27,28]. The great potential of diagnostic use of nanotechnology-based biosensors with nanowires and nanoribbons as sensing elements was shown in 2000s [29], and one of the first reports on the use of nanowire-based biosensor, for direct label-free biomarker detection in blood samples was in 2009 [30]. The very high surface-to-volume ratio of nanowires and nanoribbons, achieved owing to their low thickness, provides their extremely high charge sensitivity, which can reach the value of several charged molecules per one nanoribbon [31]. This is why nanoribbon and nanowire biosensors allow one to directly detect proteins [32] and nucleic acids [33,34] at subfemtomolar concentrations, and single viral particles [35].

Herein, we propose the use of nanoribbon biosensor with the sensor chip bearing an array of twelve oligonucleotide-sensitised silicon nanoribbons for non-invasive, highly sensitive and amplification-free parallel detection of three different types of (urogenital cancer)-associated ncRNAs in human blood. Such an approach provides early diagnosis of urogenital cancer with increased (as compared to the analysis of only one ncRNA type) diagnosis reliability. The use of sensor chips bearing a large array of multiple nanoribbons/nanowires on a single chip provides parallel detection of multiple biomarkers [35], and this is what we have realised in our work reported. For fabrication of SOI nanoribbons, we have employed a complementary metal oxide semiconductor (CMOS)-compatible ‘top-down’ technology, whose advantages were justified by M. Reed et al. [29]. The application of CMOS-compatible “top-down” technology for fabrication of nanoribbon sensor chips allows to avoid typical problems of “bottom-up” approach [36].

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Ivanov, Y.; Shumov, I.; Enikeev, D.; Goldaeva, K.; Kozlov, A.; Ableev, A.; Popov, V.; Glukhov, A.; Nevedrova, E.; Vinogradova, A.; Kapustina, S.; Agletdinova, M.; Orlova, D.; Potoldykova, N.; Ziborov, V.; Dolgoborodov, A.; Petrov, O.; Kovalev, O.; Ivanova, N.; Tatur, V.; Lukyanitsa, A.; Morozov, A.; Kushlinskii, N.; Archakov, A. Nanoribbon Biosensor-Based Detection of Three Different Types of Non-Coding RNAs in Plasma for Early Revelation of Urogenital Cancers in Humans. Preprints 2025, 2025091315. https://doi.org/10.20944/preprints202509.1315.v1