Special Projects: NIH Program Project 'DNA repair, mutations, and cellular aging'

The NIA Program Project ‘DNA Repair, Mutations, and Cellular Aging’ integrates research programs of six scientists with different, but complementary, expertise and one major common interest: understanding the molecular and cellular basis of aging. These scientists are: (1) Jan Hoeijmakers (Erasmus University Rotterdam), the leader of Project 1, with a long-standing focus on the mechanisms of DNA repair, now increasingly with the pathophysiology of aging as its clinical endpoint; (2) Jan Vijg (Albert Einstein College of Medicine, New York), the leader of Project 2 and PI of the program as a whole, long since focused on genome instability as a major cause of aging; (3) Judith Campisi (Buck Institute for Research on Aging, Novato), leader of Project 3, who aims to understand how the DNA damage response and cellular senescence contribute to aging; (4) Paul Hasty (University of Texas Health Science Center, San Antonio), leader of Project 4, who studies how defects in DNA double-strand breaks and the resulting engagement of tumor suppressor pathways cause premature aging; (5) Yousin Suh (Albert Einstein College of Medicine, New York), leader of Project 5, who will translate our findings that genome maintenance systems assure longevity in the mouse to the hypothesized pro-longevity effects of rare genetic variants present in human centenarians; and (6) Harry van Steeg (National Institute for Public Health and the Environment, Bilthoven, The Netherlands), leader of Core B ( Animal and Pathology Core), with his interest in the long-term pathological consequences of defects in DNA repair and possibilities for intervention.   

The PPG is driven by the hypothesis that genome maintenance systems are major determinants of aging and longevity. At the time this PPG was first funded (1998), this hypothesis lacked hard support.  We strongly believe our efforts and results have greatly contributed to the acceptance of genome maintenance as a major pro-longevity force. Our findings contributed to a new concept: that various molecular and cellular endpoints of aging are logically explained by spontaneous DNA damage (e.g., see Hasty P, Campisi J, Hoeijmakers J, van Steeg H, Vijg J., Science 2003;299:1355-1359. Aging and genome maintenance: lessons from the mouse?). Key findings of the group are listed below.    

Project 1 (Jan Hoeijmakers). Genetic and environmental manipulation of aging. Previously we disclosed a very strong link between DNA repair and many aspects of aging and found that DNA repair deficient progeroid mouse mutants (and presumably the corresponding DNA repair syndrome patients) in response to accumulating DNA damage suppress the GH/IGF1 somatotroph axis and upregulate anti-oxidant mechanisms. Redirection of resources from growth to maintenance has been found associated with longevity (e.g., in Ames dwarf mice and in dietary-restricted mice) and is interpreted as an attempt to counteract the accelerated aging and extend life span. Recently, in close collaboration with Core B we found that lifespan of progeroid, repair-deficient mice can be dramatically extended (upto 300%) by dietary restriction (DR) with a concomitant delay in onset of all aspects of aging investigated. Hence the prematurely aging mice can serve as a paradigm for understanding the mechanism underlying the longevity-promoting effect of DR, identification of biomarkers and search for DR mimetics which promote healthy aging. 

Key publications:  

Niedernhofer LJ, Garinis GA, Raams A, Lalai AS, Robinson AR, Appeldoorn E, Odijk H, Oostendorp R, Ahmad A, van Leeuwen W, Theil AF, Vermeulen W, van der Horst GT, Meinecke P, Kleijer WJ, Vijg J, Jaspers NG, Hoeijmakers JH. A new progeroid syndrome reveals that genotoxic stress suppresses the somatotroph axis. Nature 2006;444:1038-1043.  

Hoeijmakers JH. DNA Damage, aging, and cancer. NEJM 2009, 361: 1475-1485 

Nicolaije C, Diderich KE, Botter SM, Priemel M, Waarsing JH, Day JS, Brandt RM, Schilling AF, Weinans H, Van der Eerden BC, van der Horst GT, Hoeijmakers JH, van Leeuwen JP. Age-related skeletal dynamics and decrease in bone strength in DNA repair deficient male trichothiodystrophy mice. PLoS One. 2012;7(4):e35246. PMCID: PMC3323647 

Project 2 (Jan Vijg). Genome dynamics in aging. Workers in Project 2 defined, for the first time, the phenomenon of transcriptional noise in higher organisms through their demonstration that normal cardiomyocytes freshly isolated from the mouse heart show significant stochastic variation in transcript levels of both housekeeping and heart-specific genes. This cell-to-cell variation in the heart was found to increase with age and could also be elevated in cultured human and mouse fibroblasts after exposure to genotoxic agents.  

Key publications:  

Bahar R, Hartmann CH, Rodriguez KA, Denny AD, Busuttil RA, Dolle ME, Calder RB, Chisholm GB, Pollock BH, Klein CA, Vijg J. Increased cell-to-cell variation in gene expression in ageing mouse heart. Nature 2006;441:1011-1014.  

Vijg J, Campisi J. Puzzles, promises and a cure for ageing. Nature. 2008;454:1065-1071. PMC2774752 

Gundry M, Vijg J. Direct mutation analysis by high-throughput sequencing: From germline to low-abundant, somatic variants. Mutat Res. 2012;729:1-15. PMC3237897 

Vijg, J., and Suh, Y. Genome Instability and Aging. Annual Review of Physiology. 2013;75:645-668. PMID:23398157 

Maslov AY, Ganapathi S, Westerhof M, Quispe W, White RR, Van Houten B, Reiling E, Dollé ME, van Steeg H, Hasty P, Hoeijmakers JH, Vijg J. DNA damage in normally and prematurely aged mice. Aging Cell. 2013 12:467-477. PMID:23496256. 

Project 3 (Judith Campisi). Genome maintenance, cellular phenotypes and aging. Project 3 established a key role for oxidative DNA damage responses in causing cellular senescence, and identified DNA damage-induced lesions that are responsible for the senescence-associated secretory phenotype – the secretion of inflammatory and pro-tumorigenic molecules by senescent cells.  Together with Project 1 and Core B, they developed a new mouse model to identify senescent cells in vivo, and inducibly eliminate them after genotoxic stress or during aging.    

Key publications:   

Rodier F, Coppe JP, Patil CK, Hoeijmakers WAM, Munoz DP, Raza SR, Freund A, Campeau E, Davalos AR, Campisi J. 2009. Persistent DNA damage signaling triggers senescence-associated inflammatory cytokine secretion. Nature Cell Biol 11:973-979. PMC2743561 

Laberge RM, Zhou L, Sarantos MR, Rodier F, Freund A, deKeizer PLJ, Liu S, Demaria M, Cong YS, Kapahi P, Desprez PY, Hughes RE, Campisi J.  (2012)  Glucocorticoids suppress selected components of the senescence-associated secretory phenotype.  Aging Cell 11: 569-578.  PMC3387333 

Davalos AR, Kawahara M, Malhotra GK, Schaum N, Huang J, Ved U, Beausejour C, Coppe JP, Rodier F, Campisi J.  (2013)  p53-dependent release of Alarmin HMGB1is a central mediator of senescent phenotypes.  J Cell Biol 2013;201:613-629  PMID:23649808.   

Project 4 (Paul Hasty). The impact of cellular defense on the role of Ku80 in genome maintenance and longevity assurance. Workers in Project 4 better defined premature aging in their Ku80-deficient mice. They demonstrated that none of the premature aging phenotypes is due to severe combined immunodeficiency or chronic inflammation, which is also a consequence of the inactivation of the non-homologous endjoining DNA repair process due to ablation of V(D)J recombination. In addition, they showed that mice deleted for Ku70 have the same aging phenotype as mice deleted for Ku80 and that these mutant mice do not show increase levels of cancer. This firmly establishes the general role of the NHEJ DNA repair process as a pro-longevity system.  

Key publications:  

Li H, Vogel H, Holcomb VB, Gu Y, Hasty P. 2007 Deletion of Ku70, Ku80, or both causes early aging without substantially increased cancer. Mol Cell Biol. 23:8205-14.    

Kim TM, Ko JH, Hu L, Kim SA, Bishop AJ, Vijg J, Montagna C, Hasty P. RAD51 mutants cause replication defects and chromosomal instability. Mol Cell Biol 32, 3663-3680, doi:10.1128/MCB.00406-12 (2012). 

Hu, L., Kim TM., Son MY., Kim SA., Holland CL., Tateishi S., Kim DH., Yew PR., Montagna C., Dmitrache LC., Hasty P. Two replication fork maintenance pathways fuse inverted repeats to rearrange chromosomes. Nature (in press) 

Project 5 (Yousin Suh). Genome Maintenance and Human Longevity. The long-term objective of Project 5 is to test the hypothesis that genetic variation at genome maintenance loci is associated with extreme longevity. For this purpose they are performing targeted resequencing to determine rare variants in ~ 300 candidate genes in Ashkenazi Jewish Centenarians and controls. The results indicate that variants in genome maintenance pathways, most notably DNA double-strand break repair, are indeed associated with extreme longevity. Using TALEN technology they are currently studying these extreme longevity genotypes in short-term cell culture assays to determine the impact of these rare variants on cell survival and mutation frequency.  

Key publications: 

Han, J., Hubbard, B.P., Lee, J., Montagna, C., Lee, H.-W., Sinclair, D.A., and Suh, Y. Analysis of 41 cancer cell lines reveals excessive allelic loss and novel mutations in the SIRT1 gene. Cell Cycle. Jan 15;12(2). [Epub ahead of print] 2013. PMID:23255128. PMC in process 

Han, J., Ryu, S., Moskowitz, D.M.,  Rothenberg, D., Atzmon, G., Barzilai, N., and Suh, Y. Discovery of novel non-synonymous SNP variants in 988 candidate genes from 6 centenarians by target capture and next-generation sequencing. Mechanisms of Ageing and Development. 2013. (In Press) 

Gombar S, Jung HJ, Dong F, Calder B, Atzmon G, Barzilai N, Tian XL, Pothof J, Hoeijmakers JH, Campisi J, Vijg J, Suh Y. Comprehensive microRNA profiling in B-cells of human centenarians by massively parallel sequencing. BMC Genomics. 2012 Jul 31;13(1):353. Free article 

Core B (Harry van Steeg). Animal and Pathology Core. There are few if any comprehensive descriptions of age-related patterns of multiple pathology in the mouse. One unfortunate result of this lack in our knowledge base regarding aging of the mouse is the persistent myth that premature aging, as observed in mouse models harboring defects in DNA repair genes, does not resemble the normal age-related phenotype. Based on generous institutional support above and beyond the PPG budget, the Animal and Pathology Core of this PPG has been able to meticulously define premature aging in multiple DNA repair defective mouse models: examples are the XpdTTD (project 1), the Ercc1 (project 1), the Ku80 (project 4) and the DNAPKcs (project 4) mutant mice. As a service for projects 2 and 3, the lacZ mutation and the p16-3MR senescence marker-transgenes are introduced in all cohorts. Recently Core B found that diet restriction (DR), an intervention that increases life span by slowing down aging in many if not all organisms across the animal world, extended the life span of Ercc1 mice more than two-fold and delayed their symptoms of aging (unpublished results). Importantly, Ercc1 mice responded very similar to DR compared to wild type mice based on gene expression levels. Collectively, these results establish the Ercc1 mouse as a short-term model uniquely suited for testing anti-aging interventions. 

Key publications:  

Wijnhoven SW, Beems RB, Roodbergen M, van den Berg J, Lohman PH, Diderich K, van der Horst GT, Vijg J, Hoeijmakers JH, van Steeg H. Accelerated aging pathology in ad libitum fed Xpd(TTD) mice is accompanied by features suggestive of caloric restriction. DNA Repair 2005;4:1314-1324. PMID:16472827 

Calder RB, Beems RB, van Steeg H, Mian IS, Lohman PH, Vijg J. MPHASYS: a mouse phenotype analysis system. BMC Bioinformatics 2007;8:183. PMC1899519 

Dollé ME, Kuiper RV, Roodbergen M, Robinson J, de Vlugt S, Wijnhoven SW, Beems RB, de la Fonteyne L, de With P, van der Pluijm I, Niedernhofer LJ, Hasty P, Vijg J, Hoeijmakers JH, van Steeg H. Broad segmental progeroid changes in short-lived Ercc1(-/Δ7) mice. Pathobiol Aging Age Relat Dis. 2011;1. doi: 10.3402/pba.v1i0.7219. PMC3417667 

Jonker MJ, Melis JP, Kuiper RV, van der Hoeven TV, Wackers PF, Robinson J, van der Horst GT, Dollé ME, Vijg J, Breit TM, Hoeijmakers JH, van Steeg H. Life spanning murine gene expression profiles in relation to chronological and pathological aging in multiple organs. Aging Cell. 2013 Jun 25. doi: 10.1111/acel.12118. PMID:23795901 

PPG News:

Other Special Projects in the Department of Genetics:

• The C. elegans Connectome Project 
• The ENCODE Project