Early diagnosis of renal cell carcinoma: use of a nanowire biosensor for detection of small nucleolar ribonucleic acid SNORA77 in patient’s blood

Yu. D. Ivanov; Иванов Ю. Д.; K. V. Goldaeva; Голдаева К. В.; E. D. Nevedrova; Неведрова Е. Д.; A. V. Vinogradova; Виноградова А. В.; A. N. Ableev; Аблеев А. Н.; I. D. Shumov; Шумов И. Д.; A. F. Kozlov; Козлов А. Ф.; S. I. Kapustina; Капустина С. И.; O. N. Afonin; Афонин О. Н.; V. P. Popov; Попов В. П.; A. V. Glukhov; Глухов А. В.; N. E. Kushlinskii; Кушлинский Н. Е.; I. S. Stilidi; Стилиди И. С.; Z. Z. Mamedli; Матвеев В. Б.; D. V. Enikeev; Еникеев Д. В.; N. N. Burundaeva; Бурундаева Н. В.; V. A. Konev; Конев В. А.; O. B. Kovalev; Ковалев О. Б.; V. Y. Tatur; Татур В. Ю.; V. S. Ziborov; Зиборов В. С.; L. I. Grishin; Гришин Л. И.; A. Y. Dolgoborodov; Долгобородов А. Ю.; O. F. Petrov; Петров О. Ф.; S. V. Novikov; Новиков С. В.; E. S. Yushkov; Юшков Е. С.; A. I. Archakov; Арчаков А. И.

Early diagnosis of renal cell carcinoma: use of a nanowire biosensor for detection of small nucleolar ribonucleic acid SNORA77 in patient’s blood

Authors: Ivanov Y.D.¹, Goldaeva K.V.², Nevedrova E.D.², Vinogradova A.V.¹, Ableev A.N.², Shumov I.D.², Kozlov A.F.², Kapustina S.I.², Afonin O.N.², Popov V.P.³, Glukhov A.V.⁴, Kushlinskii N.E.⁵, Stilidi I.S.⁵, Mamedli Z.Z.⁶, Enikeev D.V.⁷, Burundaeva N.N.⁷, Konev V.A.⁸, Kovalev O.B.⁸, Tatur V.Y.⁹, Ziborov V.S.², Grishin L.I.¹⁰, Dolgoborodov A.Y.¹⁰, Petrov O.F.¹⁰, Novikov S.V.¹¹, Yushkov E.S.¹², Archakov A.I.²
Affiliations:
1. Institute of Biomedical Chemistry (IBMC)
2. Institute of Biomedical Chemistry
3. Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences
4. Novosibirsk Plant of Semiconductor Devices Vostok
5. Federal State Budgetary Institution «N.N. Blokhin National Medical Research Center of Oncology» of the Russian Ministry of Health
6. N. N. Blokhin National Medical Research Center of Oncology оf the Ministry of Health of the Russian Federation
7. Sechenov University
8. Pirogov Russian National Research Medical University
9. Foundation of Perspective Technologies and Novations
10. Joint Institute for High Temperatures of the Russian Academy of Sciences
11. Associate Printing-and-Publication Centre Technosphera
12. National Research Nuclear University MEPhI
Issue: Vol 74, No 5 (2025)
Pages: 77-87
Section: MEDICAL AND BIOLOGICAL MEASUREMENTS
URL: https://journals.rcsi.science/0368-1025/article/view/380321
ID: 380321

Cite item

Full Text

Open Access
Restricted Access

Access granted
Restricted Access

Subscription Access

Abstract
About the authors
References
Supplementary files
Statistics

Abstract

Renal cell carcinoma is the most common form of kidney cancer (more than 90 % of all oncological pathologies of the kidney). At an early stage of development, renal cell carcinoma can be asymptomatic, and this significantly complicates its diagnosis. Commonly used methods for diagnosing renal cell carcinoma do not allow for timely detection of this disease at early stages, thus it is necessary to develop effective and non-invasive methods for its diagnosis using biological macromolecules detectable in blood – biomarkers of this type of cancer. Small nucleolar RNAs are of great interest as such biological macromolecules. In this study, a SiNW biosensor was designed and manufactured for the direct detection of small nucleolar RNA SNORA77 in the blood, associated with renal cell carcinoma. The key element of the SiNW biosensor developed is a nanowire chip based on “siliconon- insulator” structures. The chip is manufactured using a technology similar to Smart Cut, and contains an array of silicon nanowires with n-type conductivity, on whose surface DNA oligonucleotide probes are covalently immobilized. To ensure the specificity of the analysis, the nucleotide sequence of the immobilized DNA probes is complementary to the target sequence of the small nucleolar RNA SNORA77. Purified buffer solutions containing various concentrations of synthetic DNA oligonucleotides, whose sequence is similar to the target detectable sequence of SNORA77, have been analyzed. Using the SiNW biosensor developed, the detection limit of SNORA77 was determined to be approximately 10–17 M. The SiNW biosensor has allowed us to detect an elevated level of SNORA77 in a sample isolated from the blood plasma of a patient with confirmed diagnosis of renal cell carcinoma in comparison with that in a control sample isolated from the plasma of a patient with a non-oncologic disease. The results of the study will be useful for further development of early diagnostic systems for renal cell carcinoma.

Keywords

biosensor, silicon nanowire, small nucleolar ribonucleic acid, biomarker, renal cell carcinoma

References

Tran J., Ornstein M. C. Clinical review on the management of metastatic renal cell carcinoma. JCO Oncology Practice, 18(3), 187–196 (2022). https://doi.org/10.1200/OP.21.00419
Hsieh J. J. et al. Renal cell carcinoma. Nature Reviews Disease Primers, 3(1), 1–19 (2017). https://doi.org/10.1038/nrdp.2017.9
Ljungberg B., Purdue M. P., Signoretti S. et al. European Association of Urology guidelines on renal cell carcinoma: the 2022 update. European Urology, 82(4), 399–410 (2022). https://doi.org/10.1016/j.eururo.2022.03.006
Sung H., Ferlay J., Siegel R. L. et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: a Cancer Journal for Clinicians, 71(3), 209–249 (2021). https://doi.org/10.3322/caac.21660
Bosma N. A., Warkentin M. T., Gan C. L et al. Effi cacy and safety of fi rst-line systemic therapy for metastatic renal cell carcinoma: a systematic review and network meta-analysis. European Urology Open Science, 37, 14–26 (2022). https://doi.org/10.1016/j.euros.2021.12.007
Tenold M., Ravi P., Kumar M. et al. Current approaches to the treatment of advanced or metastatic renal cell carcinoma. American Society of Clinical Oncology Educational Book, 40, 187–196 (2020). https://doi.org/10.1200/EDBK_279881
Motzer R. J., Bander N. H., Nanus D. M. Renal-cell carcinoma. New England Journal of Medicine, 335(12), 865–875 (1996). https://doi.org/10.1056/NEJM199609193351207
Gibbons R. P., Montie J. E., Correa Jr. R. J. et al. Manifestations of renal cell carcinoma. Urology, 8(3), 201–206 (1976). https://doi.org/10.1016/0090-4295(76)90366-6
McLaughlin J. K., Lipworth L., Tarone R. E. Epidemiologic aspects of renal cell carcinoma. Seminars in oncology. WB Saunders, 33(5), 527–533 (2006). https://doi.org/10.1053/j.seminoncol.2006.06.010
Padala S. A., Barsouk A., Thandra K. C. et al. Epidemiology of renal cell carcinoma. World Journal of Oncology, 11(3), 79 (2020). https://doi.org/10.14740/wjon1279
Wein A. J., Barsouk A., etc. Campbell-Walsh Urology, 11th ed. Elsevier Health Sciences, Philadelphia (2016).
Vasudev N. S., Wilson M., Stewart G. D. et al. Challenges of early renal cancer detection: symptom patterns and incidental diagnosis rate in a multicentre prospective UK cohort of patients presenting with suspected renal cancer. BMJ Open, 10(5), e035938 (2020). https://doi.org/10.1136/bmjopen-2019-035938
Wajahat M., Bracken C. P., Orang A. Emerging functions for snoRNAs and snoRNA-derived fragments. International Journal of Molecular Sciences, 22(19), 10193 (2021). https://doi.org/10.3390/ijms221910193
Huang Z., Du Y., Wen J, et al. SnoRNAs: functions and mechanisms in biological processes, and roles in tumor pathophysiology. Cell Death Discovery, 8(1), 259 (2022). https://doi.org/10.1038/s41420-022-01056-8
Lu B., Chen X., Liu X. et al. C/D box small nucleolar RNA SNORD104 promotes endometrial cancer by regulating the 2ʹ-O-methylation of PARP1. Journal of Translational Medicine, 20(1), 618 (2022). https://doi.org/10.1186/s12967-022-03802-z
Chow R. D., Chen S. Sno-derived RNAs are prevalent molecular markers of cancer immunity. Oncogene, 37(50), 6442–6462 (2018). https://doi.org/10.1038/s41388-018-0420-z
Mannoor K., Liao J., Jiang F. Small nucleolar RNAs in cancer. Biochimica et Biophysica Acta (BBA) – Reviews on Cancer, 1826(1), 121–128 (2012). https://doi.org/10.1016/j.bbcan.2012.03.005
Yang S., Rothman R. E. PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings. The Lancet Infectious Diseases, 4(6), 337–348 (2004). https://doi.org/10.1016/S1473-3099(04)01044-8
Ro S., Park C., Jin J. et al. A PCR-based method for detection and quantifi cation of small RNAs. Biochemical and Biophysical Research Communications, 351(3), 756–763 (2006). https://doi.org/10.1016/j.bbrc.2006.10.105
Yang T., Zhang M., Zhang N. Modifi ed Northern blot protocol for easy detection of mRNAs in total RNA using radiolabeled probes. BMC Genomics, 23(1), 66 (2022). https://doi.org/10.1186/s12864-021-08275-w
Ivanov Y. D., Romanova T.S., Malsagova K.A. et al. Use of silicon nanowire sensors for early cancer diagnosis. Molecules, 26(12), 3734 (2021). https://doi.org/10.3390/molecules26123734
Ambhorkar P., Wang Z., Ko H. et al. Nanowire-based biosensors: from growth to applications. Micromachines, 9(12), 679 (2018). https://doi.org/10.3390/mi9120679
Kim K., Park C., Kwon D. et al. Silicon nanowire biosensors for detection of cardiac troponin I (cTnI) with high sensitivity. Biosensors and Bioelectronics, 77, 695–701 (2016). https://doi.org/10.1016/j.bios.2015.10.008
Ivanov Y. D., Malsagova K. A., Pleshakova T. O., et al. Aptamer-Sensitized nanoribbon biosensor for ovarian cancer marker detection in plasma. Chemosensors, 9(8), 222 (2021). https://doi.org/10.3390/chemosensors9080222
Ivanov Y., Pleshakova T., Malsagova K. et al. Detection of marker miRNAs, associated with prostate cancer, in plasma using SOI-NW biosensor in direct and inversion modes. Sensors, 19(23), 5248 (2019). https://doi.org/10.3390/s19235248
Ivanov Y. D., Malsagova K. A., Popov V. P. et al. Nanoribbon-based electronic detection of a glioma-associated circular miRNA. Biosensors, 11(7), 237 (2021). https://doi.org/10.3390/bios11070237
Иванов Ю. Д., Неведрова Е. Д., Виноградова А. В. и др. Детекция кольцевых РНК hsa_circ_0031263, hsa_circ_0072715 и hsa_circ_0136666, ассоциированных с колоректальным раком, в плазме крови с помощью нанопроводных чипов. Альманах клинической медицины, 52(3), 120–131 (2024)
Patolsky F., Zheng G., Hayden O. et al. Electrical detection of single viruses. Proceedings of the National Academy of Sciences of the United States of America, 101(39), 14017–14022 (2004). https://doi.org/10.1073/pnas.0406159101
Malsagova K. A., Pleshakova T. O., Kozlov A. F. et al. Detection of infl uenza virus using a SOI-nanoribbon chip, based on an N-type fi eld-effect transistor. Biosensors, 11(4), 119 (2021). https://doi.org/10.3390/bios11040119
Popov V. P., Antonova A. I., Frantsuzov P. A. et al. Properties of silicon-on-insulator structures and devices. Semiconductors, 35, 1030–1037 (2001). https://doi.org/10.1134/1.1403567
Ivanov Y., Pleshakova T., Malsagova K. et al. Detection of marker miRNAs, associated with prostate cancer, in plasma using SOI-NW biosensor in direct and inversion modes. Sensors, 19(23), 5248 (2019). https://doi.org/10.3390/s19235248
Mattson G., Conklin E., Desai S. et al. A practical approach to crosslinking. Molecular Biology Reports, 17, 167–183 (1993). https://doi.org/10.1007/BF00986726
Stern E., Wagner R., Sigworth F. J. et al. Importance of the Debye screening length on nanowire fi eld effect transistor sensors. Nano Letters, 7(11), pp. 3405–3409 (2007). https://doi.org/10.1021/nl071792z
Laborde C., Pittino F., Verhoeven H. A. et al. Real-time imaging of microparticles and living cells with CMOS nanocapacitor arrays. Nature Nanotechnology, 10(9), pp. 791–795 (2015). https://doi.org/10.1038/nnano.2015.163
Namdari P., Daraee H., Eatemadi A. Recent advances in silicon nanowire biosensors: synthesis methods, properties, and applications. Nanoscale Research Letters, 11, 1–16 (2016). https://doi.org/10.1186/s11671-016-1618-z
Zhang H., Kikuchi N., Ohshima N. et al. Design and fabrication of silicon nanowire-based biosensors with integration of critical factors: toward ultrasensitive specifi c detection of biomolecules. American Chemical Society Applied Materials and Interfaces, 12(46), 51808–51819 (2020). https://doi.org/10.1021/acsami.0c13984
Rissin D. M., Kan C. W., Campbell T. G. et al. Single-molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations. Nature Biotechnology, 28(6), 595–599 (2010). https://doi.org/10.1038/nbt.1641
Banerjee D., Tateishi-Karimata H., Ohyama T. et al. Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition. Nucleic Acids Research, 48(21), 12042–12054 (2020). https://doi.org/10.1093/nar/gkaa572
SantaLucia J., Hicks D. The thermodynamics of DNA structural motifs. Annual Review of Biophysics, 33, 415–440 (2004). https://doi.org/10.1146/annurev.biophys.32.110601.141800

Supplementary files

Supplementary Files

Action

1. JATS XML

Download

Username
Password
Remember me

Forgot password?	Register

Username
Password
Remember me

Forgot password?	Register

Early diagnosis of renal cell carcinoma: use of a nanowire biosensor for detection of small nucleolar ribonucleic acid SNORA77 in patient’s blood

Full Text

Abstract

Keywords

About the authors

References

Supplementary files