Aging: not all DNA damage is equal.

Available online at www.sciencedirect.com

ScienceDirect Aging: not all DNA damage is equal Wilbert P Vermeij, Jan HJ Hoeijmakers and Joris Pothof Recent advances have identified accumulation of DNA damage as a major driver of aging. However, there are numerous kinds of DNA lesions each with their own characteristics and cellular outcome, which highly depends on cellular context: proliferation (cell cycle), differentiation, propensity for survival/ death, cell condition and systemic hormonal and immunological parameters. In addition, DNA damage is strongly influenced by cellular metabolism, anti-oxidant status and exogenous factors, consistent with the multi-factorial nature of aging. Notably, DNA lesions interfering with replication have very different outcomes compared to transcription. These considerations provide a conceptual framework in which different types of DNA damage and their setting contribute to the aging process in differential manners. Addresses Department of Genetics, Erasmus University Medical Center, Wytemaweg 80, 3015CN Rotterdam, The Netherlands Corresponding author: Pothof, Joris ([email protected])

Current Opinion in Genetics & Development 2014, 26:124–130 This review comes from a themed issue on Molecular and genetic bases of disease Edited by Cynthia T McMurray and Jan Vijg

http://dx.doi.org/10.1016/j.gde.2014.06.006 0959-437X/# 2014 Elsevier Ltd. All right reserved.

Introduction A wide variety of processes has been implicated in aging [1], however, recent evidence points to DNA damage accumulation as an important driver of the aging process [2,3]. DNA integrity is unceasingly challenged by endogenous reactive oxygen and nitrogen species (RONS), numerous other reactive metabolic (by)products and exogenous agents such as environmental chemicals and various forms of radiation. Each agent typically causes multiple types of DNA injuries, because of the physico-chemically similar reactivity of the nucleotides. Hence, the plethora of genotoxic agents induces altogether an enormous diversity of DNA lesions. For instance, RONS alone cause 70 characterized oxidized nucleosides [4]. Although difficult to accurately determine, damage to DNA is estimated to occur at a level of 104–105 lesions per mammalian cell per day [5–7]. Current Opinion in Genetics & Development 2014, 26:124–130

Obviously, besides DNA other bio-macromolecules, such as proteins, RNA and lipids are also subject to chemical degeneration by endogenous reactive compounds. Nevertheless, several considerations argue for DNA as key target in aging. DNA is the only cellular component that cannot be replaced upon damage and thus solely relies on repair, rendering DNA the oldest molecule in the cell especially in post-mitotic cells, which is relevant in view of the factor time in aging. Furthermore, when maternal and paternal alleles are considered distinct, genes are present in only one copy in the G0 and G1 stage of the cell cycle, in which most somatic cells reside. Furthermore, DNA is the largest biomolecule in the cell, thus able to acquire a high damage load. Importantly, DNA is at the top of the informational hierarchy. Hence, damage to our genes may have lasting and indirect effects, which can even affect progeny cells. The notion that most multi-system premature aging syndromes are caused by defects in genome maintenance or affect genome function otherwise highlights a prominent role of genome integrity in aging. Examples are Werner syndrome (WS), Cockayne syndrome (CS), trichothiodystrophy (TTD), Ataxia telangiectasia (AT), Fanconi’s anemia (FA), dyskeratosis congenita (DKC), and likely Hutchinson-Gilford progeria syndrome (HGPS) [7–9]. Transgenic mouse mutants carrying defects in specific DNA repair systems also display many progeroid phenotypes in a dose-dependent and type-dependent manner [10,11], further stressing a causal relationship. Moreover, long-term survivors of DNA-damaging chemotherapy are now recognized to exhibit multiple features of accelerated aging [12]. Nevertheless, direct unequivocal proof for accumulating DNA lesions in organs and tissues correlating with aging is technically extremely challenging to obtain [13]. Finally, it is important to realize that despite the presence of elaborate and highly sophisticated genome maintenance machineries, DNA damage can never be completely prevented from exerting deleterious effects, and investments in these systems are only necessary to the extent that they allow the organism to function properly until offspring has reached independence. When using the term ‘DNA damage theory of aging’ it should be noted that DNA damage implies all types of lesions and that each type has its own characteristics and cellular outcome. For instance, some DNA lesions, such as several oxidative lesions (e.g. 8-oxodG) are mainly mutagenic; others like double strand breaks (DSBs) and interstrand cross-links (ICLs) are predominantly cytotoxic or cytostatic; many lesions, including most bulky adducts, are both to a varying degree. The same www.sciencedirect.com

Aging: not all DNA damage is equal Vermeij, Hoeijmakers and Pothof 125

applies to the arsenal of DNA repair pathways. Some DNA repair systems, such as global genome nucleotide excision repair (GG-NER) that eliminates helix-distorting lesions, mainly protect from mutagenesis. Others including transcription-coupled repair (TCR), which ensures rapid recovery of transcription stalled by DNA damage, protect from cell death. Similarly, DSB and ICL repair, correcting very cytotoxic and cytostatic DSBs or ICLs primarily protect from cell death and cellular senescence [14]. Human hereditary syndromes with a defect in genome maintenance systems display a variety of phenotypes in which cancer predisposition and pathology reminiscent of accelerated aging are most prominent. Are progeria syndromes, aging and age-related diseases the result of specific types of DNA lesions? Therefore, we clustered these human genome instability syndromes based on their cancer and/or aging phenotype, underlying DNA repair defect and associated causal DNA lesion (Figure 1). This classification indicates that the three main DNA lesions in these genetic diseases, i.e. bulky lesions, DSBs and ICLs, are causally involved in both cancer and aging depending on the specific mutated genome maintenance pathway. Thus, the cellular outcome of DNA lesions also depends on cellular context such as stage in the cell cycle, proliferation and differentiation status of a cell or its overall condition [15]. Furthermore, systemic factors such as inflammatory, immunological and hormonal parameters influence the biological outcome of DNA injury [16,17]. Levels of DNA damage also depend on the activity of many cellular metabolic pathways (e.g.

mitochondrial oxidative phosphorylation, p450 (de)toxification) and anti-oxidant systems [18]. Consequently, each specific DNA lesion likely affects different aspects of aging to a varying degree. Currently, the types of DNA lesions targeted by the major DNA repair pathways have been well established. Moreover, the cellular consequences of specific DNA lesions have been extensively studied. Therefore, analysis of DNA repair deficient mouse models and human genome instability syndromes can tentatively assign aging phenotypes to specific DNA lesions, although redundancy between repair systems may mask the impact of specific lesions on aging. In this review, we will provide a framework on the impact of specific DNA lesions and their cellular context on aging. We will discuss why, in which context and how specific DNA lesions contribute to aging. This framework will not only lead to a better understanding of the role of DNA damage in aging, but could also be used to select proper experimental genotoxic agents to study aging-related processes in vitro.

DNA damage interfering with DNA replication and chromosome segregation DNA lesions interfere with the prime functions of DNA, i.e. safe storage, proper transmission and usage of genetic information. This implicates the vital processes of DNA replication and ensuing chromosome segregation as well as transcription, which critically depend on an intact DNA template. Concerning the effect of DNA damage on replication and chromosome segregation three

GGNHEJ NER

bulky lesion

BS

TS

WS

ICL

E

R ass ecq oci heli ate cas dr e ep air R

IC

L

FA

XF

DSB

AGING

DSB response & repair

HR

R

A RC

TT CS

AT

XP

SCID

R TC

NBS

B

ER NC

D

CA

Figure 1

DNA lesion & repair

Hereditary disease

ICL:

XP: TTD: CS: XFE: FA: WS: RTS:

Interstrand crosslink DSB: Double strand break GG-NER: Global genome nucleotide excision repair TCR: Transcriptioncoupled repair ICLR: Interstrand crosslink repair HR: Homologous recombination NHEJ: Non homologous end joining

Xeroderma pigmentosum Trichothiodystrophy Cockayne syndrome XFE progeroid syndrome Fanconi anemia Werner syndrome Rothmund-Thomson syndrome BS: Bloom syndrome AT: Ataxia telangiectasia NBS: Nijmegen breakage syndrome BRCA: Hereditary breast cancer SCID: Severe combined immunodeficiency Current Opinion in Genetics & Development

Classification of hereditary human genome instability syndromes according to their clinical consequences. Classification is based on cancer and/or aging phenotypes, underlying DNA repair defect and causally implicated type of DNA lesion. The inner circle depicts the causal DNA lesion, the second circle represents the involved DNA repair mechanisms, the third circle depicts the underlying human genome instability syndrome and the outer circle represents the associated cancer and/or aging phenotype. XFE patients with a defect in the DNA repair gene Ercc1 or Xpf are deficient in ICL repair, TCR, but also GG-NER that is not visualized in this classification scheme. Patients with GG-NER defects are cancer prone, but do not exhibit any significant accelerated aging phenotypes, while few XFE patients did not display cancer predisposition. Therefore, defective TCR and ICL repair seem to be the main drivers of pathology in XFE. www.sciencedirect.com

Current Opinion in Genetics & Development 2014, 26:124–130

126 Molecular and genetic bases of disease

(ii) The wide category of helix-distorting lesions, mostly eliminated by GG-NER, blocks normal DNA replication. A dedicated replication machinery has evolved comprised of at least five translesion synthesis (TLS) polymerases, each specialized in bypassing a specific subset of distortions. The proper TLS polymerase temporarily takes over from the regular replicative polymerase to synthesize over the critical damage in a relatively error-free manner [20]. Alternatively, bypass may occur by recombinational processes such as template switching, which is errorfree [21]. In both pathways, DNA lesions are not repaired, but tolerated and — when unrepaired — may again cause replication stress (and risk for mutations) in subsequent S-phases. Defects in TLS polymerases such as in the UV-sensitive human condition xeroderma pigmentosum (XP-V), deficient in TLS polymerase h, lead to enhanced mutagenesis

scenarios apply with very different biological and clinical consequences (see Figure 2), suggesting that damage is not equal. (i) Several subtle DNA lesions mostly repaired by the base excision repair (BER) pathway do not block the regular high fidelity replicative DNA polymerases. However, their altered base-pairing properties may enhance mutagenesis and thereby also tumorigenesis. An example is 8-oxodG, a main oxidative DNA product, equally base-pairing with C as with A eventually causing G!T transversions [19]. Such damages do not trigger the DNA damage response (DDR) and — like defects in the mismatch DNA repair system, which also cause increased base substitutions and small deletions or insertions — are carcinogenic, but have no significant aging consequences. Figure 2

Proliferating cells

Subtle

Bulky

lesion types: DSB SSB

non-dividing cells lesion types:* Bulky lesion

ICL

replication stress → DDR activation

TLS / error-prone repair

mutations, GCRs

transcriptional stress → DDR activation

arrested transcription

arrested replication

senescence, polyploidization

cellular functional decline

cell death

hypocellularity, loss of tissue homeostasis, tissue functional decline

cellular functional decline

AGING

CANCER

impact of DNA damage on cells, tissues and health Current Opinion in Genetics & Development

Flow chart describing the role of DNA damage in aging. Left side: DNA lesions interfering with cell proliferation and their consequences for cancer and aging. Right side: DNA lesions that stall transcription and their consequences for aging. *Note: currently only bulky DNA lesions have been characterized to block transcription, but it is conceivable that additional transcription-blocking lesions will be identified. Secondly, several additional types of DNA damage such as subtle lesions or very scarce DSBs also occur in non-dividing cells that can lead to mutations. It is currently not known whether mutation accumulation in non-dividing cells has any significant impact on health. Alternatively, persistent DSBs in non-dividing cells triggering large gH2AX foci, may locally interfere with gene expression contributing to time-dependent reduced transcriptional activity and aging-associated expression imbalance. Abbreviations: Subtle, subtle DNA lesions; Bulky, bulky DNA lesions; SSB, single-strand break; DSB, double-strand break; ICL, interstrand cross-link; DDR, DNA damage response; GCRs, gross chromosomal rearrangements; TLS, translesion synthesis. Current Opinion in Genetics & Development 2014, 26:124–130

www.sciencedirect.com


and (skin) cancer [22], but have not any significant impact on premature aging. It is important to note that even though the number of mutations and cancer increase with age, consistent with timedependent accumulation of DNA damage, mutagenesis is likely not a key factor underlying non-cancer aging symptoms. Besides XP-V, also XP-C and XP-E patients and mouse mutants, which harbor a defect in GG-NER, show elevated mutagenesis and carcinogenesis, without clear progeroid symptoms [23]. Moreover, as mentioned above mouse mutants carrying defects in mismatch repair, which exhibit very high mutation frequencies, display cancer predisposition [24,25], but hardly show features of accelerated aging. Conversely, as discussed below, human CS patients and mouse mutants defective in TCR have no elevated mutation frequency, yet display many manifestations of premature aging [26]. (iii) Finally, cytotoxic and cytostatic DSBs and ICLs represent complete blocks for DNA replication when not repaired by non-homologous end joining (NHEJ) or homologous recombination (HR), for DSBs, or by ICL repair. Also incomplete replication interferes with normal chromosome segregation in mitosis. Such DNA injuries cause replication stress, activating DDR signaling, which coordinates repair and temporarily halts cell proliferation until repair is completed or damage is bypassed. In case of damage beyond repair — for instance because the DNA ends of a DSB have drifted apart too far — cell death or senescence will be induced depending on cell type, condition and other factors [27,28]. In some organs such as liver and kidney incomplete replication due to persisting replication-blocking lesions may trigger polyploidization [29]. Cell death leads to loss of tissue homeostasis when the (aged) tissue is not able to replace these lost cells. This will cause hypocellularity, which exhausts functional reserves, thereby affecting tissue function and overall fitness

of the organism. Depletion of the somatic stem cell pool, likely due to accumulating DNA damage, contributes to the inability to compensate for cell loss. Cellular senescence constitutes a permanent cell cycle arrest in response to persistent DNA damage, such as irreparable DSBs or critically short telomeres [27]. These lesions are visible as nuclear foci comprised of large chromatin regions neighboring a DSB that contain phosphorylated gH2AX, 53BP1 and numerous other proteins involved in DSB repair, triggering a chronically activated DDR [30]. However, in principle this state is reversible when the damage is repaired. Reactivation of telomerase in cells of mutant mice, which are senescent due to telomere attrition, reverses the senescent state and persuades cells to re-enter in the cell cycle, indicating the dependence of senescence on constant damage signaling and its reversible nature [31]. Senescent cells secrete a repertoire of factors defining the senescence-associated secretory phenotype, including several pro-inflammatory cytokines that recruit infiltrating immune cells [32,33]. It can be envisaged that cellular senescence could lead to functional decline by deterioration of celltype specific functions thereby altering cell behavior and eventually tissue function. Recent evidence indicates that genetic ablation of senescent cells from a number of tissues in the mouse may partially rejuvenate those organs and tissues [34]. An example of a human syndrome relevant in this context is FA, an autosomal recessive multi-system disorder, due to defects in ICL repair, which illustrates all three effects of DNA damage in a very informative manner. FA is characterized by variable congenital abnormalities, which are best explained by stochastic cytotoxic damage eliminating key stem and progenitor cells during embryogenesis, leading to for example, abnormal digits. In addition, FA patients develop early bone marrow failure manifested as

Table 1 Selection of aging features displayed by mouse models mimicking Cockayne syndrome (CS), Fanconi anemia (FA) and XPF-ERCC1 progeria (XFE) Progeria syndrome Gene defect in mouse model (references) Repair pathway Sensitivity for: RBL-associated pathology

TBL-associated pathology

CS

FA

XFE

Csb [47 ,48,49]

Fancd2 [50,51,52 ,53]

Ercc1 [11,54–59]

TCR TBLs – – – Photoreceptor loss Hearing loss Neurological abnormalities

ICLR RBLs Germ cell loss, hypogonadism Hematopoietic defects Increased tumor incidence – – –

TCR, GG-NER, ICLR TBLs, RBLs Infertile at early age Anemia, bone marrow aging No observed tumors Retinal degeneration Hearing loss Neurodegenerative and cognitive defects

A DNA repair mutant mouse model is given as example for each category. Repair pathways: transcription-coupled repair (TCR), interstrand cross-link repair (ICLR), global genome nucleotide excision repair (GG-NER). DNA lesion types: TBLs transcription-blocking lesions, RBLs: replication-blocking lesions. Tumor formation in Ercc1 mutant was never observed during extensive necropsy (unpublished results). www.sciencedirect.com



aplastic anemia due to aging-like exhaustion of hematopoietic stem and progenitor cells, because of massive damage-induced cell death. Occasional cells escaping cell death may develop into tumors due to the enhanced genome instability, explaining the high incidence of AML and other cancers (Table 1). In summary, DNA damage that induces replicational stress translates into cancer and/or segmental aging features — depending on the type of DNA lesion and repair/ response pathway — and specifically involves proliferative tissues and cell compartments, such as the hematopoietic and gonadal systems. Remarkably, one of the most proliferative tissues, the colon, appears to escape the fate of premature aging in DNA repair deficient syndromes and mouse models. Since the resident time of cells in colon epithelium is only 5 days, a possible explanation is that the proliferation rate in the colon stem and progenitor compartment is so high that the time for DNA damage to accumulate under normal conditions is too short to cause a significant fraction of cells to die. In addition, stem cell dynamics in the bottom of crypt takes care of frequent replacement of individual (damaged) stem cells in the pool [35].

DNA damage interfering with transcription Major differences adhere to DNA damage-blocking replication when compared with transcription, although much less is known in the latter case, for instance about the spectrum of lesions stalling transcription and the mechanisms of repair and response. For transcription only lesions affecting the transcribed strand are relevant. DNA lesion bypass options as discovered for DNA polymerases are not available for RNA polymerases, rendering the wide class of distorting DNA damage and probably also more subtle DNA lesions, which block RNA polymerase elongation, more challenging for transcription. An example of such helix-disruptive lesions are the two main UV damages, cyclobutane pyrimidine dimers and 6/4 photoproducts of which the former is most problematic, since it is very poorly recognized by GG-NER, and thus needs to be removed by TCR [36]. Additional examples are the endogenous lipid peroxidation product 4-hydroxy-2-nonenal and cyclopurines [37,38]. Although lesions like ICLs evidently also block transcription, their extreme cytotoxicity presumably prevents them from accumulating to levels that would affect transcription inhibition significantly. When a DNA lesion stalls an elongating RNA polymerase, repair is initiated by TCR that makes the lesion accessible for a multi-step ‘cut-and-patch’-type excision reaction, which utilizes many core NER factors. This permits resumption of the vital transcription process [14]. It is possible that persistent stalling of transcription at sufficient genomic important sites mainly translates into cell death in p53-dependent Current Opinion in Genetics & Development 2014, 26:124–130

and p53-independent manners [39,40], while a senescence-like response linked with transcriptional arrest has not been documented up to now. In addition, stochastic accumulation of transcriptionblocking lesions may contribute to increased cell-to-cell variation in gene expression with age [41]. This transcriptional noise might negatively affect cell and tissue function. Interestingly, gene expression profiles of normal aged mouse organs resemble profiles triggered by persistent transcription-blocking lesions, and differ from profiles elicited by other genotoxic stresses [42]. Most importantly, in contrast to replication the problem of DNA damage interfering with transcription will affect all cells, proliferating as well as post-mitotic. In fact, proliferating cells may be better off as they are expected to carry less damage, due to first, the damage dilution effect of DNA replication and cell division; second, the contribution of replication-associated repair systems; and third, the fact that lesion-stalled RNA polymerases may get resolved when the replication machinery passes by. Post-mitotic cells do not have these advantages and likely accumulate more time-dependent damage. Thus, inefficient TCR will cause more accelerated cell loss and functional decline in post-mitotic tissues, such as the neuronal system, than in proliferative tissues (Figure 2). This explains the hallmark of progressive neurological dysfunction of the TCR-disorder CS (Table 1). The other main CS symptom, early cessation of growth, conveniently matches the finding that damage induced transcriptional arrest triggers a growth-suppressive ‘survival’ response, which redirects energy resources from growth to maintenance by attenuating the somatotrophic (growth hormone and IGF1), lactotrophic and thyrotrophic hormonal axes and up-regulating for example, the anti-oxidant defense. This response resembles the longevity-promoting response triggered by dietary restriction, which is constitutive in long-lived dwarf mutants [10,43]. Hence, the damage-induced survival response triggered by transcriptional stress likely constitutes an attempt to counteract the accelerated aging and extend lifespan. Interestingly, when TCR-deficient CS mice are crossed with GG-NER-deficient mutants, the CS/XP double mutants show a dramatic synergistic shortening of lifespan, growth retardation and acceleration of premature aging features [44]. This is consistent with the notion that transcriptional stress in the TCR mutant is amplified due to excess of accumulating lesions, which otherwise would have been removed by GG-NER. This is also reflected in the human progeroid disorder TTD, which is due to partial defects in both TCR and GG-NER and the very severe condition Cerebro-Oculo-FacioSkeletal syndrome (COFS, life expectancy less than 2 years), carrying even more severe defects in both repair pathways [45]. www.sciencedirect.com


Neveling K, Bechtold A, Hoehn H: Genetic instability syndromes with progeroid features. Z Gerontol Geriatr 2007, 40:339-348.

Finally, the most extreme and widespread premature aging phenotype due to DNA damage is presented by Ercc1 mutant mice (and the human XFE syndrome [10], Table 1), which is deficient in at least three repair processes: TCR, GG-NER as well as ICL repair [14] (and likely sub-pathways of DSB repair [46]) combining transcription-related and replication-related DNA damage consequences. As a result Ercc1 mutant mice exhibit in a progressive manner premature and even in some cases excessive aging features in almost all organs and tissues including brain, bone marrow, liver, kidney, gonads, skeleton, cardiovascular tissue, thymus, retina, etc. [11] (Table 1 and unpublished results). The striking correlation between dose and type of DNA damage and repair and response processes on the one hand and the onset and severity of multiple features of accelerated aging on the other hand provide a strong experimental basis for the concept that DNA damage is a main contributor of the aging process in mammals, but that not all damage is equal.

9.

Acknowledgements

16. Polkinghorn WR, Parker JS, Lee MX, Kass EM, Spratt DE, Iaquinta PJ, Arora VK, Yen WF, Cai L, Zheng D et al.: Androgen receptor signaling regulates DNA repair in prostate cancers. Cancer Discov 2013, 3:1245-1253.

We acknowledge support of the European commission FP7 Markage (FP7-Health-2008-200880), DNA Repair (LSHG-CT-2005-512113) and National Institute of Health (NIH)/National Institute of Ageing (NIA) (1PO1 AG-17242-02), NIEHS (1UO1 ES011044), and the Royal Academy of Arts and Sciences of the Netherlands (academia professorship to JHJH) and a European Research Council (DamAge (ERC-2008-AdG-233424)) Advanced Grant to JHJH. The research leading to these results has received funding from the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement No. HEALTH-F2-2010-259893.

References and recommended reading Papers of particular interest, published within the period of review, have been highlighted as: of special interest of outstanding interest

1. Lopez-Otin C, Blasco MA, Partridge L, Serrano M, Kroemer G: The hallmarks of aging. Cell 2013, 153:1194-1217. This paper describes the molecular and cellular hallmarks that control the rate of aging. 2.

Hoeijmakers JH: DNA damage, aging, and cancer. N Engl J Med 2009, 361:1475-1485.

3.

Garinis GA, van der Horst GT, Vijg J, Hoeijmakers JH: DNA damage and ageing: new-age ideas for an age-old problem. Nat Cell Biol 2008, 10:1241-1247.

4.

Cadet J, Douki T, Frelon S, Sauvaigo S, Pouget JP, Ravanat JL: Assessment of oxidative base damage to isolated and cellular DNA by HPLC-MS/MS measurement. Free Radic Biol Med 2002, 33:441-449.

5.

Lindahl T: Instability and decay of the primary structure of DNA. Nature 1993, 362:709-715.

6.

Gates KS: An overview of chemical processes that damage cellular DNA: spontaneous hydrolysis, alkylation, and reactions with radicals. Chem Res Toxicol 2009, 22:1747-1760.

7.

Swenberg JA, Lu K, Moeller BC, Gao L, Upton PB, Nakamura J, Starr TB: Endogenous versus exogenous DNA adducts: their role in carcinogenesis, epidemiology, and risk assessment. Toxicol Sci 2011, 120(Suppl 1):S130-S145.

8.

Coppede F, Migliore L: DNA repair in premature aging disorders and neurodegeneration. Curr Aging Sci 2010, 3:3-19.


10. Niedernhofer LJ, Garinis GA, Raams A, Lalai AS, Robinson AR, Appeldoorn E, Odijk H, Oostendorp R, Ahmad A, van Leeuwen W et al.: A new progeroid syndrome reveals that genotoxic stress suppresses the somatotroph axis. Nature 2006, 444:1038-1043. 11. Dolle 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 et al.: Broad segmental progeroid changes in shortlived Ercc1(S/Delta7) mice. Pathobiol Aging Age Relat Dis 2011, 1. 12. Maccormick RE: Possible acceleration of aging by adjuvant chemotherapy: a cause of early onset frailty? Med Hypotheses 2006, 67:212-215. 13. Himmelstein MW, Boogaard PJ, Cadet J, Farmer PB, Kim JH, Martin EA, Persaud R, Shuker DE: Creating context for the use of DNA adduct data in cancer risk assessment. II: Overview of methods of identification and quantitation of DNA damage. Crit Rev Toxicol 2009, 39:679-694. 14. Hoeijmakers JH: Genome maintenance mechanisms for preventing cancer. Nature 2001, 411:366-374. 15. Iyama T, Wilson DM 3rd: DNA repair mechanisms in dividing and non-dividing cells. DNA Repair (Amst) 2013, 12:620-636. The authors describe the role of several DNA repair pathways in replicating and post-mitotic cells.

17. Sommariva M, De Cecco L, Tagliabue E, Balsari A: Modulation of DNA repair genes induced by TLR9 agonists: a strategy to eliminate ‘altered’ cells? Oncoimmunology 2012, 1:258-259. 18. Finkel T, Holbrook NJ: Oxidants, oxidative stress and the biology of ageing. Nature 2000, 408:239-247. 19. Boiteux S, Radicella JP: Base excision repair of 8hydroxyguanine protects DNA from endogenous oxidative stress. Biochimie 1999, 81:59-67. 20. Sale JE, Lehmann AR, Woodgate R: Y-family DNA polymerases and their role in tolerance of cellular DNA damage. Nat Rev Mol Cell Biol 2012, 13:141-152. 21. Plosky BS, Woodgate R: Switching from high-fidelity replicases to low-fidelity lesion-bypass polymerases. Curr Opin Genet Dev 2004, 14:113-119. 22. Cordonnier AM, Fuchs RP: Replication of damaged DNA: molecular defect in xeroderma pigmentosum variant cells. Mutat Res 1999, 435:111-119. 23. Wijnhoven SW, Hoogervorst EM, de Waard H, van der Horst GT, van Steeg H: Tissue specific mutagenic and carcinogenic responses in NER defective mouse models. Mutat Res 2007, 614:77-94. 24. de Wind N, Dekker M, van Rossum A, van der Valk M, te Riele H: Mouse models for hereditary nonpolyposis colorectal cancer. Cancer Res 1998, 58:248-255. 25. Zhang S, Lloyd R, Bowden G, Glickman BW, de Boer JG: Thymic lymphomas arising in Msh2 deficient mice display a large increase in mutation frequency and an altered mutational spectrum. Mutat Res 2002, 500:67-74. 26. Dolle ME, Busuttil RA, Garcia AM, Wijnhoven S, van Drunen E, Niedernhofer LJ, van der Horst G, Hoeijmakers JH, van Steeg H, Vijg J: Increased genomic instability is not a prerequisite for shortened lifespan in DNA repair deficient mice. Mutat Res 2006, 596:22-35. 27. Campisi J: Senescent cells, tumor suppression, and organismal aging: good citizens, bad neighbors. Cell 2005, 120:513-522. 28. Galluzzi L, Vitale I, Abrams JM, Alnemri ES, Baehrecke EH, Blagosklonny MV, Dawson TM, Dawson VL, El-Deiry WS, Fulda S et al.: Molecular definitions of cell death subroutines: Current Opinion in Genetics & Development 2014, 26:124–130


recommendations of the Nomenclature Committee on Cell Death. Cell Death Differ 2012, 19:107-120. 29. Chow J, Poon RY: DNA damage and polyploidization. Adv Exp Med Biol 2010, 676:57-71. 30. Rodier F, Coppe JP, Patil CK, Hoeijmakers WA, Munoz DP, Raza SR, Freund A, Campeau E, Davalos AR, Campisi J: Persistent DNA damage signalling triggers senescenceassociated inflammatory cytokine secretion. Nat Cell Biol 2009, 11:973-979. The authors demonstrate that persistent DNA damage leads to cellular senescence and a senescence-associated secretory phenotype of proinflammatory factors. 31. Jaskelioff M, Muller FL, Paik JH, Thomas E, Jiang S, Adams AC, Sahin E, Kost-Alimova M, Protopopov A, Cadinanos J et al.: Telomerase reactivation reverses tissue degeneration in aged telomerase-deficient mice. Nature 2011, 469:102-106. 32. Coppe JP, Desprez PY, Krtolica A, Campisi J: The senescenceassociated secretory phenotype: the dark side of tumor suppression. Annu Rev Pathol 2010, 5:99-118. 33. Tchkonia T, Zhu Y, van Deursen J, Campisi J, Kirkland JL: Cellular senescence and the senescent secretory phenotype: therapeutic opportunities. J Clin Invest 2013, 123:966-972. This paper presents potential therapeutic opportunities to reduce the negative side effects of senescent cells. 34. Baker DJ, Wijshake T, Tchkonia T, LeBrasseur NK, Childs BG, van de Sluis B, Kirkland JL, van Deursen JM: Clearance of p16Ink4apositive senescent cells delays ageing-associated disorders. Nature 2011, 479:232-236. 35. Clevers H: The intestinal crypt, a prototype stem cell compartment. Cell 2013, 154:274-284. 36. van der Wees CG, Vreeswijk MP, Persoon M, van der Laarse A, van Zeeland AA, Mullenders LH: Deficient global genome repair of UV-induced cyclobutane pyrimidine dimers in terminally differentiated myocytes and proliferating fibroblasts from the rat heart. DNA Repair (Amst) 2003, 2:1297-1308. 37. Maddukuri L, Speina E, Christiansen M, Dudzinska D, Zaim J, Obtulowicz T, Kabaczyk S, Komisarski M, Bukowy Z, Szczegielniak J et al.: Cockayne syndrome group B protein is engaged in processing of DNA adducts of lipid peroxidation product trans-4-hydroxy-2-nonenal. Mutat Res 2009, 666:23-31. 38. Jaruga P, Dizdaroglu M: 8,50 -Cyclopurine-20 -deoxynucleosides in DNA: mechanisms of formation, measurement, repair and biological effects. DNA Repair (Amst) 2008, 7:1413-1425. 39. Derheimer FA, O’Hagan HM, Krueger HM, Hanasoge S, Paulsen MT, Ljungman M: RPA and ATR link transcriptional stress to p53. Proc Natl Acad Sci U S A 2007, 104:12778-12783.

Beems R et al.: Impaired genome maintenance suppresses the growth hormone — insulin-like growth factor 1 axis in mice with Cockayne syndrome. PLoS Biol 2007, 5:e2. 45. Rapin I: Disorders of nucleotide excision repair. Handb Clin Neurol 2013, 113:1637-1650. 46. Ahmad A, Robinson AR, Duensing A, van Drunen E, Beverloo HB, Weisberg DB, Hasty P, Hoeijmakers JH, Niedernhofer LJ: ERCC1XPF endonuclease facilitates DNA double-strand break repair. Mol Cell Biol 2008, 28:5082-5092. 47. Jaarsma D, van der Pluijm I, van der Horst GT, Hoeijmakers JH: Cockayne syndrome pathogenesis: lessons from mouse models. Mech Ageing Dev 2013, 134:180-195. A clear and extensive overview of the various mouse models for Cockayne syndome is given by the authors. 48. Gorgels TG, van der Pluijm I, Brandt RM, Garinis GA, van Steeg H, van den Aardweg G, Jansen GH, Ruijter JM, Bergen AA, van Norren D et al.: Retinal degeneration and ionizing radiation hypersensitivity in a mouse model for Cockayne syndrome. Mol Cell Biol 2007, 27:1433-1441. 49. Jaarsma D, van der Pluijm I, de Waard MC, Haasdijk ED, Brandt R, Vermeij M, Rijksen Y, Maas A, van Steeg H, Hoeijmakers JH et al.: Age-related neuronal degeneration: complementary roles of nucleotide excision repair and transcription-coupled repair in preventing neuropathology. PLoS Genet 2011, 7:e1002405. 50. Parmar K, D’Andrea A, Niedernhofer LJ: Mouse models of Fanconi anemia. Mutat Res 2009, 668:133-140. 51. Houghtaling S, Timmers C, Noll M, Finegold MJ, Jones SN, Meyn MS, Grompe M: Epithelial cancer in Fanconi anemia complementation group D2 (Fancd2) knockout mice. Genes Dev 2003, 17:2021-2035. 52. Garaycoechea JI, Crossan GP, Langevin F, Daly M, Arends MJ, Patel KJ: Genotoxic consequences of endogenous aldehydes on mouse haematopoietic stem cell function. Nature 2012, 489:571-575. This study identified the driving lesions of the haematological phenotype in Fanconi anaemia. 53. Zhang QS, Marquez-Loza L, Eaton L, Duncan AW, Goldman DC, Anur P, Watanabe-Smith K, Rathbun RK, Fleming WH, Bagby GC et al.: Fancd2S/S mice have hematopoietic defects that can be partially corrected by resveratrol. Blood 2010, 116:5140-5148. 54. Weeda G, Donker I, de Wit J, Morreau H, Janssens R, Vissers CJ, Nigg A, van Steeg H, Bootsma D, Hoeijmakers JH: Disruption of mouse ERCC1 results in a novel repair syndrome with growth failure, nuclear abnormalities and senescence. Curr Biol 1997, 7:427-439.

40. Conforti G, Nardo T, D’Incalci M, Stefanini M: Proneness to UVinduced apoptosis in human fibroblasts defective in transcription coupled repair is associated with the lack of Mdm2 transactivation. Oncogene 2000, 19:2714-2720.

55. Prasher JM, Lalai AS, Heijmans-Antonissen C, Ploemacher RE, Hoeijmakers JH, Touw IP, Niedernhofer LJ: Reduced hematopoietic reserves in DNA interstrand crosslink repairdeficient Ercc1S/S mice. EMBO J 2005, 24:861-871.

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

56. Spoor M, Nagtegaal AP, Ridwan Y, Borgesius NZ, van Alphen B, van der Pluijm I, Hoeijmakers JH, Frens MA, Borst JG: Accelerated loss of hearing and vision in the DNA-repair deficient Ercc1(delta/S) mouse. Mech Ageing Dev 2012, 133:59-67.

42. Garinis GA, Uittenboogaard LM, Stachelscheid H, Fousteri M, van Ijcken W, Breit TM, van Steeg H, Mullenders LH, van der Horst GT, Bruning JC et al.: Persistent transcription-blocking DNA lesions trigger somatic growth attenuation associated with longevity. Nat Cell Biol 2009, 11:604-615. The authors show that the transcriptional landscape of natural and accelerated aging by a nucleotide excision repair defect resembles the cellular response to transcription-blocking lesions. 43. Schumacher B, van der Pluijm I, Moorhouse MJ, Kosteas T, Robinson AR, Suh Y, Breit TM, van Steeg H, Niedernhofer LJ, van Ijcken W et al.: Delayed and accelerated aging share common longevity assurance mechanisms. PLoS Genet 2008, 4:e1000161. 44. van der Pluijm I, Garinis GA, Brandt RM, Gorgels TG, Wijnhoven SW, Diderich KE, de Wit J, Mitchell JR, van Oostrom C,


57. Borgesius NZ, de Waard MC, van der Pluijm I, Omrani A, Zondag GC, van der Horst GT, Melton DW, Hoeijmakers JH, Jaarsma D, Elgersma Y: Accelerated age-related cognitive decline and neurodegeneration, caused by deficient DNA repair. J Neurosci 2011, 31:12543-12553. 58. de Graaf EL, Vermeij WP, de Waard MC, Rijksen Y, van der Pluijm I, Hoogenraad CC, Hoeijmakers JH, Altelaar AF, Heck AJ: Spatiotemporal analysis of molecular determinants of neuronal degeneration in the aging mouse cerebellum. Mol Cell Proteomics 2013, 12:1350-1362. 59. Durik M, Kavousi M, van der Pluijm I, Isaacs A, Cheng C, Verdonk K, Loot AE, Oeseburg H, Bhaggoe UM, Leijten F et al.: Nucleotide excision DNA repair is associated with age-related vascular dysfunction. Circulation 2012, 126:468-478.


Not all research is equal.

Not all information is created equal.

All cervical sonography is not created equal.

Controlling for Socioeconomic Status in Pain Disparities Research: All-Else-Equal Analysis When "All Else" Is Not Equal.

All cravings are not created equal.

All Purkinje cells are not created equal.

Obesity and renal disease: not all fat is created equal and not all obesity is harmful to the kidneys.

Not All NSTEMIs Are Created Equal.

All surgical site infections are not equal.

Not all convective dialysis therapies are equal.

All contraceptives are not created equal.

Is all chronic kidney disease created equal?

Upstream stiffness, downstream problems: not all arteries are equal.

All things not being equal: readmission associated with procedure type.

Obesity: adipocyte development-all fat cells are not created equal.

Vascular response after percutaneous sympathectomy: not all devices are equal.

Tumor Cell Invasion-Not All Barriers Are Created Equal.

Postoperative radiotherapy: not all thymic malignancies are created equal.

Resistance training: not all programs are created equal.

Platelet function assays--not all are created equal.

Not all β-lactams are equal regarding neurotoxicity.

Searching for Trichinella: not all pigs are created equal.

Not all extracellular vesicles were created equal: clinical implications.

All low-density lipoprotein particles are not created equal.