The primary focus of our lab is to study the preferential repair
of oxidative DNA damage and DNA strand breaks (SBs) in transcribed
genes. Various environmental factors such as ultraviolet lights, other
radiations and chemical toxins can induce various types of genomic
damage in human cells. However, the cells are also equipped with
elaborate repair machinery for maintaining genomic integrity. Oxidative
genome damage is repaired via the DNA base excision repair (BER)
pathway, initiated with the excision of the damaged base by DNA
glycosylases. We have identified and characterized a family of DNA
glycosylases (NEIL1-3) and a new BER subpathway involving the NEILs,
and showed that the NEIL1- and 2-initiated pathways are AP endonuclease
(APE1)-independent, but dependent on polynucleotide kinase
3'-phosphatase (PNKP). Furthermore, we established that
NEIL2 initiates a new transcription-coupled BER pathway for the
preferential repair of oxidized bases from the transcribing genes. We
postulate that this particular repair pathway will have far-reaching
consequences in understanding the mechanism of various pathologies,
particularly cancers. We recently observed a unique property of a NEIL2
variant that was found to be predominantly present in lung cancer
patients. When characterized biochemically, the variant showed a modest
decrease in DNA glycosylase activity; however, total BER was markedly
reduced. Surprisingly, the variant gained its repair function under
oxidative stress. How this differential repair activity of the variant
is linked to lung pathogenesis is currently under investigation.
Polynucleotide kinase 3'-phosphatase (PNKP) is one of the major DNA
end-processing enzymes for blocked DNA ends (3'-phosphate and
5'-hydroxyl) in mammalian cells, and has dual activities:
3'-phosphatase and 5'-kinase. We and others have recently reported that
perturbation in PNKP's activity is linked to various
neurological/developmental disorders. PNKP is involved in a multitude of
repair processes; its role in DNA base excision (BER) and
single-strand break (SSBR) repair is well characterized, but not in
double-strand break repair (DSBR). DNA strand breaks have been linked
to various age-associated pathologies, particularly neurodegenerative
diseases and cancers. We are examining the role of PNKP in DNA strand
break repair in maintaining genomic integrity via error-free repair.
1. Hazra TK, Izumi T, Boldogh I, Imhoff B, Kow
YW, Jaruga P, Dizdaroglu M, Mitra S. 2002. Identification and
characterization of a human DNA glycosylase for repair in modified
bases in oxidatively damaged DNA. Proc. Natl. Acad. Sci. 99:3523-3528 (Cover page article and special press release).
2. Hazra, TK, Kow, Y. W.,
Hatahet, Z., Imhoff, B., Boldogh, I., Mokkapati, S. K., Mitra, S., and
Izumi, T. 2002. Identification and characterization of a novel human
DNA glycosylase for repair of cytosine-derived bases.Â J. Biol. Chem. 277:30417-30420 (Accelerated publication).).
3. Dou, H., Mitra, S., and Hazra,TK. 2003. Repair of oxidized bases from DNA bubble structures by human DNA glycosylases NEIL1 and NEIL2. J. Biol. Chem. 278:49679-49684,).
4. Wiederhold, L., Leppard JB., Kedar P.,Karimi-Busheri F.,
Rasouli-Nia, A., Weinfeld, M., Tomkinson, AE., Izumi, T., Prasad R.,
Wilson, SH., Mitra S., Hazra TK. 2004. AP Endonuclease-independent DNA base excision repair in human cells. Mol Cell, 15:209-220, ).
5. Das S, Chattopadhyay R, Bhakat KK, Boldogh I, Kohno K, Prasad R, Wilson SH, Hazra TK. 2007. Stimulation of NEIL2-mediated oxidized base excision repair via YB-1 interaction during oxidative stress. J. Biol. Chem. 282:28474-84. ).
6. Banerjee D, Mandal SM, Das A, Hegde ML, Das S, Bhakat KK, Boldogh I, Sarkar PS, Mitra S, Hazra TK. 2011. Preferential repair of oxidized base damage in the transcribed genes of mammalian cells. J Biol Chem. 286: 6006-16. ).
7. Mandal SM, Hegde ML, Chatterjee A, Hegde PM, Szczesny B,
Banerjee D, Boldogh I, Gao R, Falkenberg M, Gustafsson M, Sarkar PS, Hazra TK. 2012. The
role of human DNA glycosylase NEIL2 and the single-strand break repair
protein polynucleotide kinase 3'-phosphatase in maintenance of the
mitochondrial genome. J Biol Chem. 287:2819-29. ).
8. Dey S, Maiti AK, Hegde ML, Hegde PM, Boldogh I, Sarkar PS,
Abdel-Rahman SZ, Sarker AH, Hang B, Xie J, Tomkinson AE, Zhou M, Shen B,
Wang G, Wu C, Yu D, Lin D, Cardenas V, Hazra TK. 2012. Increased Risk of Lung Cancer Associated with a Functionally Impaired Polymorphic Variant of the Human DNA Glycosylase NEIL2. DNA Repair 11(6):570-8. ).
9. Chatterjee A, Saha S, Chakraborty A, Silva-Fernandes A,
Mandal SM, Neves-Carvalho A, Liu Y, Pandita RK, Hegde ML, Hegde PM,
Boldogh I, Ashizawa T, Koeppen AH, Pandita TK, Maciel P, Sarkar PS, Hazra TK. 2014.
The role of the mammalian DNA end-processing enzyme polynucleotide
kinase 3'-phosphatase in spinocerebellar ataxia type 3 pathogenesis. PLoS Genetics (Perspective article, in press).).
10. Gao R, Liu Y, Silva-Fernandes A, Fang X,
Paulucci-Holthauzen A, Chatterjee A, Zhang H, Matsuura T, Choudhary S,
Ashizawa T, Koeppen AH, Maciel P, Hazra TK,
2014. Inactivation of PNKP by mutant ATXN3 triggers apoptosis by
activating the DNA damage-response pathway in SCA3, PLoS Genetics
(Perspective article, in press