Glen M. Borchert, Ph.D.
Biography
Dr. Glen Borchert, Professor, received his Baccalaureate in biology from the University of Tennessee in Knoxville, his Ph.D. in genetics from the University of Iowa in Iowa City, and completed a postdoctoral fellowship in structural biology at the University of California in Berkeley as well as a postdoctoral fellowship in immunology at Illinois State University in Normal, IL.
Research
Research in the Borchert laboratory explores the regulation of gene expression by noncoding RNAs and G4s. Our main focuses are on microRNAs (miRNAs), microRNA-like sequences excised from other RNAs (e.g., tRNAs and snoRNAs), sRNAs (similarly functioning short noncoding RNAs in prokaryotes), and long noncoding RNAs. Our lab examines the roles noncoding RNAs and G4 structures play during growth and development, infectious disease, how their misregulations contribute to various diseases and oncogenesis, and also how they evolve and contribute to speciation.
Goal 1 鈥� Ascertain microRNA molecular origins to facilitate target prediction
Computationally predicting miRNA targets. Active transposable elements (TEs) regularly
integrate into inter- and intragenic regions. Since numerous miRNAs have now been
identified as being formed from TEs, and miRNAs target mRNAs through complementarity,
logic dictates that a miRNA regulates transcripts baring copies of its progenitor
TE. In our lab, student researchers are trained to actively search characterized and
novel genomes alike for functional miRNA targets using a unique computational strategy
which limits miRNA target searches to transcripts containing that miRNA鈥檚 progenitor
TE.
Goal 2 - Identify novel genomic repeat and microRNA compositions
Another focus of our lab is de novo genome sequencing as well as training students
in the retrieval of sequences from publicly available datasets. Following sequence
acquisition, students are trained how to annotate these and to identify genomic hairpins,
putative miRNAs, and novel repeats.
Goal 3 鈥� Characterize novel prokaryotic and eukaryotic small RNAs
Life and all cellular activity is coordinated by small, noncoding RNA biology. Unfortunately
due to their small size, the vast majority of small, noncoding RNAs remain undescribed.
Another focus of our laboratory is the sequencing and characterization of small RNA
populations from a variety of prokaryotic and eukaryotic species.
Goal 4 - Characterize noncoding RNA misregulations with casual roles in oncogenesis
Utilizing many of the tools described above, students computationally examine additional
putative (potentially causal) noncoding RNA interactions through exploring small RNA
libraries derived from specific oncologies.
Publications
Jeffrey D DeMeis, Justin T Roberts, Haley A Delcher, Noel L Godang, Alexander B Coley, Cana L Brown, Michael H Shaw, Sayema Naaz, Enas S Alsatari, Ayush Dahal, Shahem Y Alqudah, Kevin N Nguyen, Anita D Nguyen, Sunita S Paudel, Hong Dang, Wanda K O'Neal, Michael R Knowles, Dominika Houserova, Mark N Gillespie, Glen M Borchert. Long G4-rich enhancer physically interacts with EXOC3 promoter via a G4:G4 DNA-based mechanism. bioRxiv 2024.01.29.577212; doi: https://doi.org/10.1101/2024.01.29.577212.
Delcher HA, DeMeis JD, Ghobar N, Godang NL, Knight SL, Alqudah SY, Nguyen KN, Watters BC, Borchert GM. SARS-Cov-2 small viral RNA suppresses gene expression via complementary binding to mRNA 3' UTR. MicroPubl Biol. 2024 Jan 18;2024. doi: 10.17912/micropub.biology.000790. PMID: 38312351; PMCID: PMC10835431.
Olliff NS, Hunt MA, Paudel SS, Nguyen KN, Delcher HA, DeMeis JD, Roberts JT, Fouty BW, Audia JP, Kim JH, Borchert GM. Human YRNA 4 (HY4) plasma levels are a prognostic indicator of SARS-CoV-2 infection clinical severity. MicroPubl Biol. 2023 Aug 18;2023:10.17912/micropub.biology.000925. doi: 10.17912/micropub.biology.000925. PMID: 37662051; PMCID: PMC10474479.
Lee JY, Stevens RP, Pastukh VV, Pastukh VM, Kozhukhar N, Alexeyev MF, Reisz JA, Nerguizian D, D'Alessandro A, Koloteva A, Gwin MS, Roberts JT, Borchert GM, Wagener BM, Pittet JF, Graham BB, Stenmark KR, Stevens T. PFKFB3 Inhibits Fructose Metabolism in Pulmonary Microvascular Endothelial Cells. Am J Respir Cell Mol Biol. 2023 Sep;69(3):340-354. doi: 10.1165/rcmb.2022-0443OC. PMID: 37201952; PMCID: PMC10503305.
Naaz S, Sakib N, Houserova D, Badve R, Crucello A, Borchert GM. Characterization of a novel sRNA contributing to biofilm formation in Salmonella enterica serovar Typhimurium. MicroPubl Biol. 2023 Apr 20;2023:10.17912/micropub.biology.000796. doi: 10.17912/micropub.biology.000796. PMID: 37151214; PMCID: PMC10160853.
Godang NL, DeMeis JD, Houserova D, Chaudhary NY, Salter CJ, Xi Y, McDonald OG, Borchert GM. Global Switch from DICER-dependent MicroRNA to DICER-independent SnoRNA-derived RNA Biogenesis in Malignancy. MicroPubl Biol. 2023 Feb 2;2023:10.17912/micropub.biology.000725. doi: 10.17912/micropub.biology.000725. PMID: 36818311; PMCID: PMC9936325.
Devadoss D, Acharya A, Manevski M, Houserova D, Cioffi MD, Pandey K, Nair M, Chapagain P, Mirsaeidi M, Borchert GM, Byrareddy SN, Chand HS. Immunomodulatory LncRNA on antisense strand of ICAM-1 augments SARS-CoV-2 infection-associated airway mucoinflammatory phenotype. iScience. 2022 Aug 19;25(8):104685. doi: 10.1016/j.isci.2022.104685. Epub 2022 Jun 30. PMID: 35789750; PMCID: PMC9242679.
Manevski M, Devadoss D, Long C, Singh SP, Nasser MW, Borchert GM, Nair MN, Rahman I, Sopori M, Chand HS. Increased Expression of LASI lncRNA Regulates the Cigarette Smoke and COPD Associated Airway Inflammation and Mucous Cell Hyperplasia. Front Immunol. 2022 Jun 14;13:803362. doi: 10.3389/fimmu.2022.803362. Erratum in: Front Immunol. 2022 Aug 08;13:988069. PMID: 35774797; PMCID: PMC9237255.
Coley AB, DeMeis JD, Chaudhary NY, Borchert GM. Small Nucleolar Derived RNAs as Regulators of Human Cancer. Biomedicines. 2022 Jul 28;10(8):1819. doi: 10.3390/biomedicines10081819. PMID: 36009366; PMCID: PMC9404758.
Coley AB, Stahly AN, Kasukurthi MV, Barchie AA, Hutcheson SB, Houserova D, Huang Y, Watters BC, King VM, Dean MA, Roberts JT, DeMeis JD, Amin KV, McInnis CH, Godang NL, Wright RM, Haider DF, Piracha NB, Brown CL, Ijaz ZM, Li S, Xi Y, McDonald OG, Huang J, Borchert GM. MicroRNA-like snoRNA-Derived RNAs (sdRNAs) Promote Castration-Resistant Prostate Cancer. Cells. 2022 Apr 12;11(8):1302. doi: 10.3390/cells11081302. PMID: 35455981; PMCID: PMC9032336.
Kasukurthi MV, Houserova D, Huang Y, Li S, Li D, Lin J, Yang G, Tan S, Bourrie D, Ma B, Borchert GM, Huang J. SURFR: A Real-Time Platform for Non-Coding RNA Fragmentation Analysis Using Wavelets. 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2021 Dec 9, pp. 2720-2727, doi: 10.1109/ BIBM52615.2021.9669696. Conference Paper. https://ieeexplore.ieee.org/document/9669696
Li S, Huang Y, Kasukurthi MV, Yang J, Li D, Yang G, Lin J, Tan S, Bourrie D, Ma B, Borchert GM, Huang J. A New Classification Algorithm and a New Oversampling Method of Mapping Common Data Elements to the BRIDG Model. 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2021 Dec 9, pp. 2788-2795, doi: 10.1109/BIBM52615.2021.9669697. Conference Paper. https://ieeexplore.ieee.org/document/9669697
Dominika Houserova, Yulong Huang, Mohan V. Kasukurthi, Brianna C. Watters, Fiza F. Khan, Raj V. Mehta, Neil Y. Chaudhary, Justin T. Roberts, Jeffrey D. DeMeis, Trevor K. Hobbs, Kanesha R. Ghee, Cameron H. McInnis, Nolan P. Johns, Abrianna J. Kegler, Alexander B. Coley, Cana L. Brown, Jenny L. Hewes, Marie M. McElyea, Monica N. Reeves, Tuan M. Tran, Natalie R. Bauer, Jingshan Huang, Jonathon P. Audia, John W. Foster, Glen M. Borchert. Salmonella Outer Membrane Vesicles contain tRNA Fragments (tRFs) that Inhibit Bacteriophage P22 infection. bioRxiv 2021 June 9: 467952; doi:
Devadoss D, Daly G, Manevski M, Houserova D, Hussain SS, Baumlin N, Salathe M, Borchert GM, Langley RJ, Chand HS. A long noncoding RNA antisense to ICAM-1 is involved in allergic asthma associated hyperreactive response of airway epithelial cells. Mucosal Immunol. 2021 May;14(3):630-639. doi: 10.1038/s41385-020-00352-9. Epub 2020 Oct 29. PMID: 33122732; PMCID: PMC8081750.
Devadoss D, Acharya A, Manevski M, Pandey K, Borchert GM, Nair M, Mirsaeidi M, Byrareddy SN, Chand HS. Distinct Mucoinflammatory Phenotype and the Immunomodulatory Long Noncoding Transcripts Associated with SARS-CoV-2 Airway Infection. medRxiv [Preprint]. 2021 May 18:2021.05.13.21257152. doi: 10.1101/2021.05.13.21257152. Update in: iScience. 2022 Aug 19;25(8):104685. PMID: 34031668; PMCID: PMC8142670.
Alexander B Coley, Ashlyn N Stahly, Mohan V Kasukurthi, Addison A Barchie, Sam B Hutcheson, Dominika Houserova, Yulong Huang, Brianna C Watters, Valeria M King, Meghan A Dean, Justin T Roberts, Jeffrey D DeMeis, Cameron H McInnis, Noel L Godang, Ryan M Wright, David F Haider, Neha B Piracha, Cana L Brown, Zohaib M Ijaz, Shengyu Li, Yaguang Xi, Oliver G McDonald, Jingshan Huang, Glen M Borchert. MicroRNA-like snoRNA-derived RNAs (sdRNAs) promote castration resistant prostate cancer. bioRxiv 2021.12.17.473174; doi:
Huang F, Leng X, Kasukurthi MV, Huang Y, Li D, Tan S, Lu G, Lu J, Benton RG, Borchert GM, Huang J. Utilizing Machine Learning Techniques to Predict the Efficacy of Aerobic Exercise Intervention on Young Hypertensive Patients Based on Cardiopulmonary Exercise Testing. J Healthc Eng. 2021 Apr 21;2021:6633832. doi: 10.1155/2021/6633832. PMID: 33968353; PMCID: PMC8084649.
Houserova D, Dahmer DJ, Amin SV, King VM, Barnhill EC, Zambrano ME, Dean MA, Crucello A, Aria KM, Spector MP, Borchert GM. Characterization of 475 Novel, Putative Small RNAs (sRNAs) in Carbon-Starved Salmonella enterica Serovar Typhimurium. Antibiotics (Basel). 2021 Mar 16;10(3):305. doi: 10.3390/antibiotics10030305. PMID: 33809610; PMCID: PMC8000849.
Mohan V Kasukurthi, Dominika Houserova, Yulong M Huang, Addison A Barchie, Justin T Roberts, Dongqi Li, Bin Wu, Jingshan Huang, Glen M. Borchert. SALTS: SURFR (small noncoding RNA) And LAGOOn (long noncoding RNA) Transcriptomics Suite. bioRxiv, 2021.Feb 8, 02.08.430280; doi:
Williams JD, Houserova D, Johnson BR, Dyniewski B, Berroyer A, French H, Barchie AA, Bilbrey DD, Demeis JD, Ghee KR, Hughes AG, Kreitz NW, McInnis CH, Pudner SC, Reeves MN, Stahly AN, Turcu A, Watters BC, Daly GT, Langley RJ, Gillespie MN, Prakash A, Larson ED, Kasukurthi MV, Huang J, Jinks-Robertson S, Borchert GM. Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction. Nucleic Acids Res. 2020 Jun 19;48(11):5907-5925. doi: 10.1093/nar/gkaa357. PMID: 32383760; PMCID: PMC7293029.
Ma B, Wu Z, Li S, Benton R, Li D, Huang Y, Kasukurthi MV, Lin J, Borchert GM, Tan S, Li G, Yang M, Huang J. Development of a support vector machine learning and smart phone Internet of Things-based architecture for real-time sleep apnea diagnosis. BMC Med Inform Decis Mak. 2020 Dec 15;20(Suppl 14):298. doi: 10.1186/s12911-020-01329-1. PMID: 33323112; PMCID: PMC7739462.
Li J, Zhang Z, Li S, Benton R, Huang Y, Kasukurthi MV, Li D, Lin J, Borchert GM, Tan S, Li G, Ma B, Yang M, Huang J. A partial encryption algorithm for medical images based on quick response code and reversible data hiding technology. BMC Med Inform Decis Mak. 2020 Dec 15;20(Suppl 14):297. doi: 10.1186/s12911-020-01328-2. PMID: 33323108; PMCID: PMC7739464.
Glen M. Borchert, Dominika Houserova, Raymond J. Langley, Mark N. Gillespie, Jonathan D. Williams. Long G4鈥恟ich Regions in the Human Genome Primarily Function as Enhancers and Form Higher Order, Composite G4 Structures via a Novel Loop:Loop Kissing Interaction. The FASEB Journal. 2020. 34. 1-1. 10.1096/fasebj.2020.34.s1.04316