End-to-end computational approach to the design of RNA biosensors for detecting miRNA biomarkers of cervical cancer

Synthetic and Systems Biotechnology - Tập 7 - Trang 802-814 - 2022
Priyannth Ramasami S. Baabu1, Shivaramakrishna Srinivasan2,3, Swetha Nagarajan1, Sangeetha Muthamilselvan2, Thamarai Selvi2, Raghavv R. Suresh1, Ashok Palaniappan2
1Department of Bioengineering, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, 613 401, India
2Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu 613401, India
3Life Sciences Division, TCS Research, Tata Consultancy Services, Chennai, Tamil Nadu, 600042, India

Tài liệu tham khảo

Schiffman, 2007, Human papillomavirus and cervical cancer, Lancet, 370, 890, 10.1016/S0140-6736(07)61416-0 Sung, 2021, Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries, CA Cancer J Clin, 71, 209, 10.3322/caac.21660 Stelzle, 2021, Estimates of the global burden of cervical cancer associated with HIV, Lancet Global Health, 9, e161, 10.1016/S2214-109X(20)30459-9 Chandigarh, 2019 Globocan. Cervix Uteri.https://gco.iarc.fr/today/data/factsheets/cancers/23-Cervix-uteri-fact-sheet.pdf; 2020[accessed January, 2021]. Silverberg, 2003, Pathology of cervical cancer, Cancer J, 9, 335, 10.1097/00130404-200309000-00003 Ogedegbe, 2005, Perceptions of barriers and facilitators of cancer early detection among low-income minority women in community health centers, J Natl Med Assoc, 97, 162 Jearanaikoon, 2016, The evaluation of loop-mediated isothermal amplification-quartz crystal microbalance (LAMP-QCM) biosensor as a real-time measurement of HPV16 DNA, J Virol Methods, 229, 8, 10.1016/j.jviromet.2015.12.005 Surriabre, 2019, Assessment of a new low-cost, PCR-based strategy for high-risk human papillomavirus DNA detection for cervical cancer prevention, BMC Infect Dis, 19, 842, 10.1186/s12879-019-4527-9 Wang, 2009, Rapid detection of human papilloma virus using a novel leaky surface acoustic wave peptide nucleic acid biosensor, Biosens Bioelectron, 24, 3455, 10.1016/j.bios.2009.04.034 Roy, 2016, A microarray platform for detecting disease-specific circulating miRNA in human serum, Biosens Bioelectron, 75, 238, 10.1016/j.bios.2015.08.039 Pardini, 2018, MicroRNAs as markers of progression in cervical cancer: a systematic review, BMC Cancer, 18, 696, 10.1186/s12885-018-4590-4 Filipów, 2019, Blood circulating miRNAs as cancer biomarkers for diagnosis and surgical treatment response, Front Genet, 10, 169, 10.3389/fgene.2019.00169 Cui, 2019, Circulating MicroRNAs in cancer: potential and challenge, Front Genet, 10, 10.3389/fgene.2019.00626 Dembélé, 2014, Fold change rank ordering statistics: a new method for detecting differentially expressed genes, BMC Bioinf, 15, 14, 10.1186/1471-2105-15-14 van ’t Veer, 2002, Gene expression profiling predicts clinical outcome of breast cancer, Nature, 415, 530, 10.1038/415530a Slomovic, 2015, Synthetic biology devices for in vitro and in vivo diagnostics, Proc Natl Acad Sci Unit States Am, 112, 14429, 10.1073/pnas.1508521112 Vernon, 2003, Bioelectronic DNA detection of human papillomaviruses using eSensorTM: a model system for detection of multiple pathogens, BMC Infect Dis, 12 Ho, 2018, Visual and modular detection of pathogen nucleic acids with enzyme–DNA molecular complexes, Nat Commun, 9, 3238, 10.1038/s41467-018-05733-0 Xu, 2014, Fluorescent probe-based lateral flow assay for multiplex nucleic acid detection, Anal Chem, 86, 5611, 10.1021/ac5010458 Green, 2014, Toehold switches: de-novo-designed regulators of gene expression, Cell, 159, 925, 10.1016/j.cell.2014.10.002 Pardee, 2014, Paper-based synthetic gene networks, Cell, 159, 940, 10.1016/j.cell.2014.10.004 Pardee, 2016, Rapid, low-cost detection of Zika virus using programmable biomolecular components, Cell, 165, 1255, 10.1016/j.cell.2016.04.059 Hall, 2016, Synthetic biology provides a toehold in the fight against Zika, Cell Host Microbe, 19, 752, 10.1016/j.chom.2016.05.020 Takahashi, 2018, A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers, Nat Commun, 9, 3347, 10.1038/s41467-018-05864-4 Weinstein, 2013, The cancer Genome Atlas pan-cancer analysis project, Nat Genet, 45, 1113, 10.1038/ng.2764 Ritchie, 2015, Limma powers differential expression analyses for RNA-sequencing and microarray studies, Nucleic Acids Res, 43, e47, 10.1093/nar/gkv007 Benjamini, 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J R Stat Soc Ser B, 57, 289 Sarathi, 2019, Novel significant stage-specific differentially expressed genes in hepatocellular carcinoma, BMC Cancer, 663 Therneau, 2012 Lorenz, 2011, ViennaRNA package 2.0, Algorithm Mol Biol, 6, 26, 10.1186/1748-7188-6-26 Green, 2017, Complex cellular logic computation using ribocomputing devices, Nature, 548, 117, 10.1038/nature23271 To, 2018, A comprehensive web tool for toehold switch design, Bioinformatics, 34, 2862, 10.1093/bioinformatics/bty216 Chollet, 2021 CLSB-UK, 2017 Stögbauer, 2012, Experiment and mathematical modeling of gene expression dynamics in a cell-free system, Integr Biol, 4, 494, 10.1039/c2ib00102k Zadeh, 2011, Software news and updates NUPACK: analysis and design of nucleic acid systems, J Comput Chem, 32, 170, 10.1002/jcc.21596 Balacescu, 2017, The role of miRNAs in diagnosis, prognosis and treatment prediction in cervical cancer, Colposc. Cerv. Pathol., 10.5772/68011 Kang, 2012, miR-20a promotes migration and invasion by regulating TNKS2 in human cervical cancer cells, FEBS Lett, 586, 897, 10.1016/j.febslet.2012.02.020 Zhao, 2015, MiR-20a promotes cervical cancer proliferation and metastasis in vitro and in vivo, PLoS One, 10 Zamani, 2019, Deregulation of miR-21 and miR-29a in cervical cancer related to HPV infection, MicroRNA, 8, 110, 10.2174/2211536607666181017124349 Zhang, 2018, MicroRNA-21 promotes proliferation, migration, and invasion of cervical cancer through targeting TIMP3, Arch Gynecol Obstet, 297, 433, 10.1007/s00404-017-4598-z Wei, 2017, Orthotopic xenograft mouse model of cervical cancer for studying the role of MicroRNA-21 in promoting lymph node metastasis, Int J Gynecol Cancer, 27, 1587, 10.1097/IGC.0000000000001059 Cao, 2021, Identification of a serum three-microRNA signature for cervical cancer diagnosis, Chin Med J (Engl), 134, 1756, 10.1097/CM9.0000000000001327 Rao, 2012, Aberrant microRNA expression in human cervical carcinomas, Med Oncol, 29, 1242, 10.1007/s12032-011-9830-2 Xin, 2016, A circulating serum miRNA panel as early detection biomarkers of cervical intraepithelial neoplasia, Eur Rev Med Pharmacol Sci, 20, 4846 Zhao, 2013, Circulating miRNA-20a and miRNA-203 for screening lymph node metastasis in early stage cervical cancer, Genet Test Mol Biomarkers, 17, 631, 10.1089/gtmb.2013.0085 Chen, 2013, Serum microRNA expression levels can predict lymph node metastasis in patients with early-stage cervical squamous cell carcinoma, Int J Mol Med, 32, 557, 10.3892/ijmm.2013.1424 Liu, 2018, Oncogenic microRNA signature for early diagnosis of cervical intraepithelial neoplasia and cancer, Mol Oncol, 12, 2009, 10.1002/1878-0261.12383 Wang, 2019, The role of miRNAs in the invasion and metastasis of cervical cancer, Biosci Rep, 39, 10.1042/BSR20181377 Quillet, 2020, Improving bioinformatics prediction of microRNA targets by ranks aggregation, Front Genet, 10, 10.3389/fgene.2019.01330 Huang, 2009, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat Protoc, 4, 44, 10.1038/nprot.2008.211 2018 Lee, 2019, In Vitro use of cellular synthetic machinery for biosensing applications, Front Pharmacol, 10, 10.3389/fphar.2019.01166 Chan, 2019, DNA switch: toehold-mediated DNA isothermal amplification for dengue serotyping, SLAS Discov Adv Sci Drug Discov, 24, 68, 10.1177/2472555218791743 Hwang, 2021, Signal amplification and optimization of riboswitch-based hybrid inputs by modular and titratable toehold switches, J Biol Eng, 15, 11, 10.1186/s13036-021-00261-w Pieters, 2021, Cell-free characterization of coherent feed-forward loop-based synthetic genetic circuits, ACS Synth Biol, 10, 1406, 10.1021/acssynbio.1c00024 Ma, 2018, Low-cost detection of norovirus using paper-based cell-free systems and synbody-based viral enrichment, Synth Biol, 3, 10.1093/synbio/ysy018 Li, 2020, Homogeneous and universal detection of various targets with a dual-step transduced toehold switch sensor, Chembiochem, 21, 1418, 10.1002/cbic.201900749 Premkumar, 2020, Riboflow: using deep learning to classify riboswitches with ∼99% accuracy, Front Bioeng Biotechnol, 8, 10.3389/fbioe.2020.00808 Angenent-Mari, 2020, A deep learning approach to programmable RNA switches, Nat Commun, 11, 5057, 10.1038/s41467-020-18677-1 Valeri, 2020, Sequence-to-function deep learning frameworks for engineered riboregulators, Nat Commun, 11, 5058, 10.1038/s41467-020-18676-2 Minuesa, 2021, MoiRNAiFold: a novel tool for complex in silico RNA design, Nucleic Acids Res, 49, 4934, 10.1093/nar/gkab331 Geraldi, 2018, Synthetic biology-based portable in vitro diagnostic platforms, Alexandria J Med, 54, 423, 10.1016/j.ajme.2018.11.003 Pardee, 2018, Perspective: solidifying the impact of cell-free synthetic biology through lyophilization, Biochem Eng J, 138, 91, 10.1016/j.bej.2018.07.008 Tinafar, 2019, Synthetic biology goes cell-free, BMC Biol, 17, 64, 10.1186/s12915-019-0685-x Chen, 2018, DCEO biotechnology: tools to design, construct, evaluate, and optimize the metabolic pathway for biosynthesis of chemicals, Chem Rev, 118, 4, 10.1021/acs.chemrev.6b00804