Publications

1. Pant D, , Kakani P, Joshi Rushikesh, Agarwal S, Samaiya A, Shukla S*. Interplay of YEATS2 and GCDH mediates histone crotonylation and drives EMT in head and neck cancer”. bioRxiv 2024 https://doi.org/10.1101/2024.09.24.614679 (Under review). 

2. Mutnuru SA, Yadav P, Kakani P, Dhamdhere SG, Kumari P, Agarwal S, Samaiya A, Shukla S*. “PRMT5-mediated histone methylation regulates alternative splicing via MECP2-PTBP1 to promote EMT in breast cancer hypoxia”. bioRxiv 2024 https://doi.org/10.1101/2024.10.16.618678 (Under review)

3. Parik Kakani, Shruti Ganesh Dhamdhere, Deepak Pant, Rushikesh Joshi, Jharna Mishra, Atul Samaiya, Sanjeev Shukla*, Hypoxia-induced CTCF promotes EMT in breast cancer, Cell Reports [Volume 43, Issue 7] (2024). see link 

4. Pandey A, Kakani P, Shukla S, CTCF and BORIS-mediated Autophagy regulation via alternative splicing of BNIP3L in Breast Cancer, Journal of Biological Chemistry [Volume 300, Issue 7](2024). see link 

5. 1 Palma FR, Gantner BN, Sakiyama MJ, Kayzuka C, Shukla S, Lacchini R, Cunniff B, Bonini MG*. ROS production by mitochondria: function or dysfunction. Oncogene, 2024. see link

6. Pandkar MR, Raveendran A, Biswas K, Mutnuru SA, Mishra J, Samaiya A, Malys T, Mitrophanov AY, Sharan SK, Shukla S*. PKM2 dictates the poised chromatin state of PFKFB3 promoter to enhance breast cancer progression. NAR Cancer ,2023. see link

7. Pandkar MR, Sinha S,Samaiya A Shukla S*. Oncometabolite lactate enhances breast cancer progression by orchestrating histone lactylation-dependent c-Myc expression. Translational Oncology,2023. see link

8. Yadav P, Pandey A, Kakani P, Mutnuru SA, Samaiya A, Mishra J, Shukla S*. Hypoxia-induced loss of SRSF2-dependent DNA methylation promotes CTCF-mediated alternative splicing of VEGFA in breast cancer. iScience ,2023. see link

9. Kakani P, Dhamdhere S, Pant D, Mishra J, Samaiya A Shukla S*. Hypoxia-induced CTCF mediates alternative splicing via coupling chromatin looping and RNA Pol II pause to promote EMT in breast cancer. bioRxiv ,2023. see link

10. Thakur K, Sajeev TK, Singh S, Ragendu V, Dattatraya R, Rao AS, Kalra N, Shukla S, Rai V*. Human behavior inspired linchpin directed catalysis for traceless precision labeling of lysine in native proteins. Bioconjugate Chemistry ,2022. see link

11. Reddy NC, Molla R, Joshi PN, Sajeev TK, Basu I, Kawadkar J, Kalra N, Mishra RK, Chakrabarty S, Shukla S, Rai V*. Traceless cysteine-linchpin enables precision engineering of lysine in native proteins. Nature Communications ,2022. see link

12. Mishra T, Dalavi R, Joshi G, Kumar A, Pandey P, Shukla S, Mishra RK, Chande A*. The role of SARS CoV-2 spike NTD mutations in determining neutralization susceptibility and virion infectivity. Life Science Alliance ,2022. see link

13. Mishra T, Bhardwaj V, Ahuja N, Gadgil P, Ramdas P, Shukla S, Chande A*. Improved loss-of-function CRISPR/Cas9 genome editing in human cells concomitant with inhibition of TGFβ signaling. Molecular Therapy-Nucleic Acids,2022;28:202-218. see link

14. Pandey A, Yadav P, Shukla S*. Unfolding the role of autophagy in the cancer metabolism. Biochem. & Biophy. Reports,2021;28:1-18. see link

15. Yadav S, Pant D, Samaiya A, Kalra N, Gupta S, Shukla S*. ERK1/2-EGR1-SRSF10 axis mediated alternative splicing plays a critical role in head and neck cancer. Front. Cell Dev. Biol.,2021;9:1-13. see link

16. Cheemala A, Ahuja N, Natua S, Mishra J, Samaiya A, Shukla S*. E2F1 and epigenetic modifiers orchestrate breast cancer progression by regulating oxygen-dependent ESRP1 expression. Oncogenesis,2021;10(58):1-10. see link

17. Natua S, Dhamdhere SG, Mutnuru AS, Shukla S*. Interplay within tumor microenvironment orchestrates neoplastic RNA metabolism and transcriptome diversity. WIREs RNA, 2021. see link

18. Pandkar MR, Dhamdhere SG, Shukla S*. Oxygen gradient and tumor heterogeneity: The chronicle of a toxic relationship. BBA Reviews on Cancer , 2021. see link

19. Choksi A, Parulekar A, Pant R, Shah VK, Nimma R, Firmal P, Singh S, Kundu GC, Shukla S, Chattopadhyay S*. Tumor suppressor SMAR1 regulates PKM alternative splicing by HDAC6-mediated deacetylation of PTBP1. BMC Cancer & Metabolism , 2021. see link

20. Natua S, Cheemala A, Shukla S*. Hypoxia-induced alternative splicing in human diseases: the pledge, the turn, and the prestige. Cellular and Molecular Life Sciences , 2021. see link

21. Ahuja N, Cheemala A, Natua S, Pant D, Cherian A, Pandkar M, Yadav P, Narayanan S.S. V, Mishra J, Samaiya A, Shukla S*. Hypoxia-induced TGFb-RBFOX2-ESRP1 axis regulates human MENA alternative splicing and promotes EMT in breast cancer. NAR Cancer , 2020. see link

22. Gupta A, Yadav S, Archana PT, Mishra J, Samaiya A, Panday RK, Shukla S*. HNRNP2B1-MST1R-AKT axis contributes to the EMT in head and neck cancer. Nature Laboratory Investigation , 2020. see link

23. Adusumalli SR, Rawale DG, Thakur K, Purushottam L, Reddy NC, Kalra N, Shukla S, Rai V. Chemoselective and Site‐Selective Lysine‐Directed Lysine Modification Enables Single‐Site Labeling of Native Proteins. Angewandte Chemie IE , 2020, 59, 10332-36 . see link

24. Pant D, Narayanan SP, Vijay N*, Shukla S*. Hypoxia-induced changes in intragenic DNA methylation correlate with alternative splicing in breast cancer. J of BioSci , 2020, 45(3). see link

25. Yadav S, Bhagat SD, Gupta A, Samaiya A, Srivastava A, Shukla S*. Dietary-phytochemical mediated reversion of cancer-specific splicing inhibits Warburg effect in head and neck cancer. BMC Cancer , 2019, 19, pp 1031-. see link

26. Adusumalli SR, Rawale DG, Singh U, Tripathi P, Paul R, Kalra N, Mishra RK, Shukla S, Rai V*. Single-Site Labeling of Native Proteins Enabled by a Chemoselective and Site-Selective Chemical Technology. J. Am. Chem. Soc. , 2018, 140 (44), pp 15114- 15123. see link

27. Gupta A, Athira A, Panday RK, Samaiya A, Shukla S*. PAK2-c-MYC-PKM2 axis plays an essential role in head and neck oncogenesis via regulating Warburg effect. Cell Death & Disease 9;825 (2018) see link

28. Chilamari M, Kalra N, Shukla S, Rai V*. Single-site labeling of lysine in proteins through a metal-free multicomponent approach. Chem. Commun., (2018); DOI:10.1039/C8CC03311K See link

29. Singh S, Narayanan SP, Biswas S, Gupta A, Ahuja A, Yadav S, Panday RK, Samaiya A, Sharan SK, Shukla S*. Intragenic DNA methylation and BORIS mediated cancer-specific splicing contributes to Warburg effect. Proc Natl Acad Sci U S A (2017) 114 (43): 11440-45. See link

30. Narayanan SP, Singh S, Shukla S*. A saga of cancer epigenetics: linking epigenetics to alternative splicing. Biochemical J. (2017) 474(6): 885-896. see link

31. Marina RJ, Sturgill D, Bailly MA, Thenoz M, Varma G, Prigge MF, Nanan KK, Shukla S, Haque N, Oberdoerffer S. TET-catalyzed oxidation of intragenic 5-methylcytosine regulates CTCF-dependent alternative splicing. EMBO J. (2016) 35(3):335-55 see link

32. Narayanan SP, Singh S, Gupta A, Yadav S, Singh SR*, Shukla S*. Integrated genomic analyses identify KDM1A's role in cell proliferation via modulating E2F signaling activity and associate with poor clinical outcome in oral cancer. Cancer Letters (2015) 367: 162-172. see link

33. Pranay A, Shukla S, Kannan S, Malgundkar SA, Govekar RB, Patil A, Kane SV, Chaturvedi P, D'Cruz AK, Zingde SM. Prognostic utility of autoantibodies to alpha-enolase and Hsp70 for cancer of the gingivobuccal complex using immunoproteomics. Proteomics Clinical Applications (2013) 7(5-6): 392-402. see link

34. Shukla S, Oberdoerffer S. Co-transcriptional regulation of alternative pre-mRNA splicing. BBA-Gene Regulatory Mechanism (2012) 1819 (7): 673-683. see link

35. Shukla S, Kavak E, Gregory M, Imashimizu M, Shutinoski B, Kashlev M, Oberdoerffer P, Sandberg R, Oberdoerffer S. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature (2011) 479: 74-79. see lin

    • 1. 1. • This article was highlighted in Cell Research - Kornblihtt A. "CTCF: from insulators to alternative splicing regulation", Cell Research advance online publication 7 February 2012; doi:10.1038/cr.2012.22 see link

            • This article was also highlighted in CCR Connections Vol 6 (1), 2012 "CTCF, a Novel Regulator of Alternative Splicing" see link

            • Received F1000 article factor (FFa) -17 (exceptional rating) from Faculty of 1000 based on the following 4 evaluations. see link

36. Shukla S, Pranay A, D'Cruz AK, Chaturvedi P, Kane SV, Zingde SM. Immunoproteomics reveals that cancer of the tongue and the gingivo buccal complex exhibit differential autoantibody response. Cancer Biomarkers (2009) 5(3): 127-35. see link

37. Shukla S, Govekar RB, Sirdeshmukh R, Sundaram CS, D'Cruz A, Pathak KA, Kane SV, Zingde SM. Tumor antigens eliciting autoantibody response in cancer of gingivo-buccal complex. Proteomics Clinical Applications (2007) 1(12): 1592-1604. see link

*Corresponding author

Patent

1. Zingde, Shukla*, Sirdeshmukh, Sundaram D'Cruz, Pathak, Kane [Inventors] Autoantibodies for protein antigens as markers for cancer of the ginigivo-buccal complex:

   • 1. 1. • US Patent granted: US 8492100 B2

           • European Patent granted: EP2126578 (Published: Feb 12, 2009)

           • CSIR: Ref No: 0187NF 2006/1N, filed on Feb 14, 2007; 290DEL 2007