Position title: Professor
Genetic control of DNA replication and repair in mammals. Mechanisms of neurodegeneration in amyotrophic lateral sclerosis (ALS)
- WIMR 3059
- Human Oncology
- Research Interests
- Genome surveillance; DNA repair; proteostasis; neurodegeneration; signal transduction
- Research Fields
- Cell Biology, Disease, Genomics, Neuro
Research projects in our lab broadly pertain to genomic surveillance/tumor suppression and molecular mechanisms of neurodegeneration in amyotrophic lateral sclerosis (ALS). (i) Genome surveillance and cell growth regulation. There are currently two active projects that broadly pertain to mechanisms of genome surveillance growth regulation, and tumor suppression. a. Interface between DNA damage signaling and CREB-mediated transcription: implications for tumor suppression and metabolic control. The ataxia-telangiectasia-mutated (ATM) protein kinase, and related proteins ATR, and DNA-PK, function as master regulators of the cellular DNA damage response, phosphorylating hundreds of proteins in response to various types of genotoxic stress.
Mutations in ATM cause ataxiatelangiectasia (A-T), a syndrome of cancer susceptibility and neurodegeneration characterized at the cellular level by radiation sensitivity and dramatically impaired ability to signal and repair DNA double-strand breaks. A-T patients and ATM-deficient mice also manifest metabolic abnormalities suggesting that ATM senses and responds to metabolic cues. We are investigating how ATM signaling through the CREB (cAMP-response element-binding protein) contributes to cell growth and metabolic control. CREB fulfills key roles in metabolism (gluconeogenesis) and long-term memory formation, and has been strongly implicated as a protooncogene in a host of cancers. We have defined a new mechanism of CREB regulation whereby ATM-dependent phosphorylation of a conserved cluster of Ser/Thr residues diminishes CREB DNA binding activity through an autoinhibitory mechanism.
In addition, ATM-independent pathways mediate CREB autoinhibition in response to a variety of growth-inhibitory stimuli, whereas signaling through the pro-growth mTOR pathway promotes CREB dephosphorylation (Fig. 1). In addition to defining these pathways and elucidating biochemical mechanisms of autoinhibition, we are currently investigating functional impacts of cancer associated mutations that may diminish CREB autoinhibition. The importance of these pathways in tumor suppression and other CREB-mediated processes is being tested using CREB gene-edited mice. b. Novel roles of RNA-binding proteins in DNA damage repair and tumor suppression. A second project is focusing on emergent roles for RNA-bindings proteins (RBPs) in DNA damage-dependent alternative splicing, DNA repair, and tumor suppression. We are elucidating pathways controlling DNA damage-dependent changes in alternative splicing and modeling the implications of these changes in mice using CRISPR/CAS9-mediated genome editing in mice.
The long-term goal of these studies is to understand fundamental aspects of DNA damage repair and response that can be used to guide radio- and chemotherapeutic strategies for cancer patients. (ii) Molecular pathogenesis of ALS. ALS is a fatal neurodegenerative disease that affects motor neurons. Recent genetic advances have identified genes that are critically involved in the ALS disease process, including the RNA-binding proteins TDP-43 and FUS/TLS, the uncharacterized open reading frame, C9ORF72, and UBQLN2. We are using cell culture, Drosophila melanogaster (fruit fly), and mouse models to understand how ALS-associated mutations in these genes instigate neurodegeneration. We are particularly interested in how ALS mutations in the ubiquitin chaperone UBQLN2 promote its misfolding and aggregation, leading to disruption of protein clearance mechanisms and neuron death. The long-term goal of this work is to identify key pathways that may be amenable to therapeutic intervention in ALS and related dementias.
1. Sakasai, R. and Teraoka, H., and Tibbetts, R.S. (2009). Proteasome inhibition suppresses DNA-dependent protein kinase activation caused by camptothecin. DNA Repair 9, 76-82 [PMCID: 281842].
2. Sakasai, R., Teraoka, H., Takagi, M., and Tibbetts, R.S. (2010) Transcription-dependent activation of ataxia telangiectasia mutated prevents DNA-dependent protein kinase-mediated cell death in response to topoisomerase I poison. J. Biol. Chem. 285, 15201-8 [PMCID: PMC2865312].
3. Hutchinson, J.A., Shanware, N.P., Bowler, M.B., and Tibbetts, R.S. (2011) Casein kinase 1 regulates protein translation through phosphorylation of ribosomal protein S6. J. Biol. Chem. 286, 8688-96 [PMCID: 3048750]
4. Shanware, N.P., Hutchinson, J.A., Kim, S.H., Bowler, M.J., Zhan, L., Bowler, M.B., and Tibbetts, R.S. (2011) Casein kinase 1-dependent phosphorylation of familial advanced sleep phase syndrome-associated residues controls period 2 stability. J. Biol. Chem. 286, 12766-74 [PMCID: 3069476]
5. Mastrocola, A.S., Kim, S.H., Trinh, A.T., Rodenkirch, L., and Tibbetts, R.S. (2013) The RNA Binding Protein Fused In Sarcoma (FUS) Functions Downstream of PARP in Response to DNA Damage J. Biol. Chem. 288, 24731-24741 [PMCID: 3750169]
6. Shi, Y., Venkataraman, S., Dodson, G.E., Mabb, A.M., LeBlanc, S., and Tibbetts, R.S. (2004) Direct regulation of CREB transcriptional activity by ATM in response to DNA damage. Proc.Natl.Acad.Sci. 101, 5898-5903 [PMCID: 395895].
7. Shanware, N.P., Trinh, A.T., Williams, L.M., and Tibbetts, R.S. (2007) Coregulated ATM and casein kinase sites modulate CREB coactivator interactions in response to DNA damage. J. Biol. Chem. 282, 6283-6291 [PMID: 17209043].
8. Shanware, N.P, Zhan, L., Hutchinson, J.A., Kim, S.H., Williams, L.M., and Tibbetts, R.S. (2010) Conserved and distinct modes of CREB/ATF transcription factor regulation by PP2A/B56 and genotoxic stress. PLoS One 5, e12173 [PMCID: 2921338].
9. Kim, S.H., Trinh, A.T., Larsen, M.C., Mastrocola, A.S., Bushel, P.R., Jefcoate, C., and Tibbetts, R.S. (2016) Tunable regulation of CREB DNA binding activity couples genotoxic stress response and metabolism. Nucleic Acids Res 44, 9667-9680
10. Kim, S.H. Shi, Y., Hanson, K., Williams, L.M., Sakasai, R., Bowler, M.J. and Tibbetts, R.S. Potentiation of ALS-associated TDP-43 aggregation by the proteasome-targeting factor, Ubiquilin 1 (2009) J. Biol. Chem. 84, 8083-92. [PMCID: 2658102]
11. Hanson, K.A., Kim, S.H., Wassarman, D.A. and Tibbetts, R.S. (2010) Ubiquilin modifies toxicity of the 43 kilodalton TARDNA binding protein (TDP-43) in a Drosophila model of amyotrophic lateral sclerosis (ALS). J. Biol. Chem. 285, 11068-72 [PMCID: 2856981].
12. Kim, S.H., Shanware, N.P., Bowler, M.B., Tibbetts, R.S. (2010) ALS-associated proteins TDP-43 and FUS/TLS function in a common biochemical complex to coregulate
HDAC6 mRNA. J. Biol. Chem. 285, 34097-105 [PMCID: 2962508]
13. Kim, S.H., Zhan, L., Hanson, K.A., and Tibbetts, R.S. (2012) High-content RNAi screening identifies the Type 1 inositol triphosphate receptor as a modifier of TDP-43 localization and neurotoxicity Hum. Mol. Gen. 21, 4845-56 [PMCID: 3529575]
14. Zhan, L., Xie, Q., and Tibbetts, R.S. (2015) Opposing roles of SAPKs p38 and JNK in a Drosophila model of TDP-43 proteinopathy reveal oxidative stress and innate immunity as pathogenic components of neurodegeneration Hum. Mol. Gen. 24, 757-72. [PMID: 25281658].
15. 4. Kim, S.H., Stiles, S.G., Feichtmeier, J.M., Ramesh, N., Zhan, L., Scalf, M.A., Smith, L.M., Pandey, U.B., and Tibbetts, R.S. (2017) Mutation-dependent aggregation and toxicity in a Drosophila model for UBQLN2-associated ALS. Hum. Mol. Gen. 24, 757-72. [Epub ahead of print]