The Kharel Lab era

(The University of Kansas Medical Center, Kansas City, KS)

1. G Li, L Sun, C Xin, T Hao, P Kharel, AC Manning, CL O’Connor, H Moore, S Lei, P Gokulnath, X Yang, R Sharma, K Garcia-Mansfield, P Pantham, C Xiao, HY Wang, E Chatterjee, S Yim, LB Ren, M Spanos, H Zhu, H Li, J Lei, JF Markmann, LC Laurent, JJ Rossi, O Akeju, Q Sheng, RV Shah, WA Goddard, TM Lowe, P Pirrotte, M Bitzer, P Ivanov, JV Bonventre, S Das, A hypoxia-responsive tRNA-derived small RNA confers renal protection through RNA autophagy, Science 2025, 389: eadp5384. 
2. P Kharel*, N Bhatter, S Zubair, S Lyons, P Anderson, P Ivanov, G-quadruplex topologies determine the functional outcome of guanine rich bioactive oligonucleotides. Nucleic Acids Res 2025, 53(12): gkaf590. *Corresponding author.

Post-doctoral era: Paul Anderson and Pavel Ivanov Labs

(Harvard Medical School and Brigham and Women’s Hospital, Boston, MA)

3. P Kharel*, Transfer RNA derived RNAs that form tetramolecular assemblies, Methods Enzymol 2025, 711: 47-63. *Corresponding author.
4. E Deforzh, P Kharel, A Karelin, P Ivanov, A Krichevsky, HOXDeRNA activates a cancerous transcription program and super-enhancers genome-wide, Mol Cell 2024, 84(20): 3950-3966.
5. P Kharel, P Ivanov, PKM2-G-quadruplex interactions conspire to regulate the cancer transcriptome. Invited overview, Mol Cell 2024, 84(19): 3574-3575.
6. P Kharel*, P Ivanov, RNA G-quadruplexes and stress: Emerging mechanisms and functions, Invited review, Trends Cell Biol 2024, 34(9): 771-784. *Corresponding author.
7. P Kharel*, P Ivanov, Identification of bona fide RNA G-quadruplex binding proteins, Methods Enzymol 2024, 695: 255-274. *Corresponding author.
8. P Kharel, P Ivanov, Structure and functions of RNA G-quadruplexes, RNA Technologies 2023, 14 Springer Books (Ed. Jan Barciszewski).
9. P Kharel, M Fay, EV Manasova, PJ Anderson, AV Kurkin, JU Guo, P Ivanov, Stress promotes RNA G-quadruplex folding in human cells, Nature Commun 2023, 14(205).
10. SM Lyons, P Kharel, Y Akiyama, D Dave, V Tsvetkov, W Merrick, P Ivanov, PJ Anderson, eIF4G has intrinsic G-quadruplex binding activity that is required for tiRNA function, Nucleic Acids Res 2020, 48(11): 6223–6233.
11. P Kharel, G Becker, V Tsvetkov, P Ivanov, Properties and biological impacts of RNA G quadruplexes: from order to turmoil and back, Invited review, Nucleic Acids Res 2020, 48(22): 12534-12555.
12. M Mineo, SM Lyons, M Zdioruk, N von Spreckelsen, R Ferrer-Luna, H Ito, QA Alayo, P Kharel, A Giantini Larsen, WY Fan, S Auduong, K Grauwet, C Passaro, JK Khalsa, K Shah, DA Reardon, KL Ligon, R Beroukhim, H Nakashima, P Ivanov, PJ Anderson, SE Lawler, EA Chiocca, Tumor interferon signaling is regulated by a lncRNA INCR1 transcribed from the PD-L1 locus, Mol Cell 2020, 78 (6): 1207-1223.
13. Y Akiyama, P Kharel, T Abe, P Anderson, P Ivanov, Isolation and initial structure-functional characterization of endogenous tRNA-derived stress-induced RNAs, RNA Biol 2020, 17(8): 1116-1124.

Graduate era: Soumitra Basu Lab

(Kent State University, Kent, OH)

14. P Kharel, N Singhal, T Mahendran, B Croos, N West, J Rana, L Smith, E Freeman, A Chattopadhyay, J McDonough, S Basu, NAT8L mRNA oxidation is linked to neurodegeneration in multiple sclerosis, Cell Chem Biol 2023, 30(3): 308-20.e5.
15. P Gyawali, R Saha, GP Smith, M Salamonczyk, P Kharel, S Basu, R Li, M Fukuto, JT Gleeson, NA Clark, A Jákli, H Balci, S Sprunt, Mono- and bilayer smectic liquid crystal ordering in dense solutions of “gapped” DNA duplexes. Proc Nat Acad Sci USA 2021, 118(12): e2019996118.Read more: https://www.pnas.org/doi/10.1073/pnas.2019996118
16. N Beals^‡, MM Farhath^‡, P Kharel^‡, T Mahendran, B Croos, J Johnson, S Basu, Rationally designed DNA therapeutics can modulate human TH expression by controlling specific GQ formation in its promoter. Mol Therapy 2022, 30(2): 831-844. ^‡Equal contribution.
17. P Kharel, S Balaratnam, N Beals, S Basu, RNA G-quadruplexes in human diseases and in therapeutics, Invited review, WIREs RNA 2020, 11(1): e1568.
18. GM Arachchilage, P Kharel_, J Reid, S Basu, Targeting of G-quadruplex harboring pre-miRNA 92b by LNA rescues PTEN expression in NSCL cancer cells, ACS Chem Bio 2018, 13(4): 909-914.
19. D Bhattacharyya, MJ Morris, P Kharel, GM Arachchilage, KM Fedeli, S Basu, Engineered domain swapping indicates context dependent functional role of RNA G-quadruplexes, Biochimie 2017, 137: 147-150.
20. P Kharel, J McDonough, S Basu, Evidence of extensive RNA oxidation in normal appearing cortex of multiple sclerosis brain, Neurochem Int 2016, 92: 43-48.
21. BA Gibbons, P Kharel, LC Robinson, RA Synowicki, MA Model, Volume measurements and fluorescent staining indicate an increase in permeability for organic cation transporter substrates during apoptosis, Exp Cell Res 2016, 344 (1): 112-119.