The Molecular Balancing Act of P16 In

Author Manuscript Published OnlineFirst on October 17, 2013; DOI: 10.1158/1541-7786.MCR-13-0350 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.

The Molecular Balancing Act of p16INK4a in Cancer and Aging

Kyle M. LaPak1 and Christin E. Burd1,2†

1 Departments of Molecular Genetics and 2 Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio, 43210, USA.

†Address correspondence to C.E.B. Christin E. Burd Biomedical Research Tower, Rm 586 The Ohio State University Columbus, Ohio 43210, USA Phone: (614)688-7569 Fax: (614)292-6356 Email: [email protected]

Running Title: p16INK4a in Cancer and Aging Key Words: INK4/ARF, senescence, CDKN2A, polycomb Financial Support: This work was supported by NIH R00AG036817 (C.E.B) and American Cancer Society IRG-67-003-50 (C.E.B.). Conflict of Interest Disclosure: The authors declare no conflicts of interest.

Word Count: 8,619 Figure Count: 5 Figures

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Downloaded from mcr.aacrjournals.org on September 29, 2021. © 2013 American Association for Cancer Research. Author Manuscript Published OnlineFirst on October 17, 2013; DOI: 10.1158/1541-7786.MCR-13-0350 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.

1 Abstract

2 Located on chromosome 9p21.3, p16INK4a seems lost amongst a cluster of neighboring tumor

3 suppressor genes. While best known for inhibiting cyclin dependent kinase (CDK) activity, p16INK4a is not

4 a one trick pony. Long term p16INK4a expression pushes cells to enter senescence, an irreversible cell

5 cycle arrest that prevents the growth of would-be cancer cells, but also contributes to aging. Loss of

6 p16INK4a is one of the most frequent events in human tumors and allows pre-cancerous lesions to bypass

7 senescence. Therefore, precise regulation of p16INK4a is essential to tissue homeostasis, maintaining a

8 tight balance between tumor suppression and aging. Here, we outline the pathways required for proper

9 p16INK4a regulation and highlight the critical functions of p16INK4a in cancer, aging and human physiology

10 that make this gene special.

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1 Introduction

2 Every day we depend on our cells to make the right decision – to divide or not to divide.

3 Proliferation is essential for tissue homeostasis, but when deregulated can both promote cancer and

4 lead to aging. For this reason, the decision to replicate is tightly controlled by a complex network of cell

5 cycle regulatory proteins. In the early 1990s, it was clear that the catalytic activity of cyclin dependent

6 kinases (CDKs) was required to drive cellular division. Less obvious were the signals that regulate CDK

7 activity and how these became altered in neoplastic disease. In an attempt to address this very

8 question, Beach and colleagues made the observation that CDK4 bound a distinct, 16 kilodalton protein

9 in cells transduced with a viral oncogene (1). Biochemical characterization of this protein, later named

10 p16INK4a, placed it amongst the INK4-class of cell cycle inhibitors, which bind directly to CDK4 and CDK6,

11 blocking phosphorylation of the retinoblastoma tumor suppressor (RB) and subsequent traversal of the

12 G1/S cell cycle checkpoint ((2, 3); Fig. 1A). In the presence of various stressors (e.g. oncogenic signaling,

13 DNA damage), p16INK4a expression blocks inappropriate cellular division, and prolonged induction of

14 p16INK4a leads to an irreversible cell cycle arrest termed ‘cellular senescence’.

15 The gene encoding p16INK4a, CDKN2A, lies within the INK4/ARF tumor suppressor locus on

16 human chromosome 9p21.3 (Fig. 1B). CDKN2A encodes two transcripts with alternative transcriptional

17 start sites (4). Both transcripts share exons 2 and 3, but are translated in different open reading frames

18 to yield two distinct proteins: p16INK4a and ARF (p14ARF in humans, p19ARF in mice). In addition to CDKN2A,

19 the INK4/ARF locus encodes a third tumor suppressor protein, p15INK4b, just upstream of the ARF

20 promoter (3). Discovered through homology-based cDNA library screens, p15INK4b functions analogously

21 to p16INK4a, directly blocking the interaction of CDK4/6 with D-type cyclins (2, 3). In contrast to p15INK4b

22 and p16INK4a which function to inhibit RB phosphorylation, ARF expression stabilizes and thereby

23 activates another tumor suppressor, p53 (5, 6). Like the INK family of inhibitors, p53 functions to block

24 inappropriate proliferation and cellular transformation. Through a poorly understood mechanism, likely

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1 dependent upon cell type and transcriptional output, p53 activation can trigger either apoptosis or cell

2 cycle arrest (7). A fourth INK4/ARF transcript, ANRIL (Anti-sense Non-coding RNA in the INK4/ARF

3 Locus), was recently discovered in a familial melanoma kindred with neural system tumors (8). The

4 ANRIL transcript runs anti-sense to p15INK4b and encodes a long, non-coding RNA elevated in prostate

5 cancer and leukemia (9, 10). ANRIL is proposed to function as an epigenetic regulator of INK4/ARF gene

6 transcription, targeting histone modifying enzymes to the locus (See discussion below). In summary, the

7 INK4/ARF locus is a relatively small (110kb), but complex locus essential to the proper maintenance of

8 cell cycle control and tumor suppression. In this review, we focus on the founding member of the

9 INK4/ARF locus, p16INK4a, and discuss what is known and unknown about p16INK4a regulation in cancer

10 and aging.

12 CDK4/6-Independent Roles of p16INK4a

13 Several lines of evidence suggest that p16INK4a may function both through CDK4/6-dependent

14 and -independent mechanisms to regulate the cell cycle. CYCLIN D-CDK4/6 complexes are stabilized by

15 interactions with the CDK2 inhibitors, p21CIP1, p27KIP1 and p57KIP2, and serve to titrate these proteins

16 away from CDK2 (11-14). Subsequent expression of p16INK4a or p15INK4b causes these complexes to

17 disassociate, releasing sequestered CDK2 inhibitors (15). This process, known as ‘CDK inhibitor re-

18 shuffling’, has been documented in a growing list of cell lines, and several lines of evidence support the

19 biological relevance of this model. Mice harboring kinase-dead Cdk4 or Cyclin D1 alleles that retain

20 p27KIP1 binding capacity (Cyclin D1K112E, Cdk4D158N) display heightened CDK2 activity (16-18) and fewer

21 developmental defects than Cyclin D1 knockouts. The same observation holds true for a Cyclin D1

22 knock-in mutation incapable of binding RB (Cyclin D1∆LxCxE)(19). As such, it is not surprising that p27KIP1

23 deletion can rescue the retinal hypoplasia and early mortality phenotypes of Cyclin D1-null mice (20, 21).

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1 More recently the biological relevance of CDK inhibitor re-shuffling has come under scrutiny.

2 Knock-in mice harboring p16INK4a-insensitive Cdk4 and Cdk6 alleles still capable of binding p27KIP1

3 (Cdk6R31C and Cdk4R21C, respectively) do not display the phenotypes predicted by this model (18, 22).

4 The decreased p16INK4a binding capacity of these mutants should promote p27KIP1 sequestration and

5 enhanced CDK2 activity, but cells from the liver and testes of Cdk4R21C mice show no change in the

6 composition of CDK2-Cyclin complexes, nor do thymocytes harboring the Cdk6R31C allele (18, 22). These

7 data suggest that, in at least a subset of cell types, the kinase activity of CDK4/6 is predominantly

8 responsible for proliferative control. Knockout mice lacking a single CDK4/6 inhibitor (p16INK4a, p15INK4b

9 or p19INK4d) develop normally and are born at expected Medelian ratios ((23-25). In contrast, p18INK4c

10 knockouts are characterized by organomegaly, yet the association of p27KIP1 with CDK2 complexes is

11 unchanged in these animals (26). Work examining combined loss of p15INK4b and p18INK4c (24) or p27KIP1

12 and p18INK4c (26) in mice suggests that distinct mechanisms are used by each inhibitor to control cellular

13 proliferation. This result is in contrast to the CDK inhibitor re-shuffling model wherein co-deletion would

14 be predicted to concertedly promote CDK2 activity. However, it is important to note that none of these

15 publications contest the fact that CDK2 inhibitors bind CYCLIN D-CDK4/6 complexes and are released

16 upon p16INK4a expression. Moreover, recent findings suggest that p16INK4a may contribute to cell cycle

17 regulation through additional CDK-independent mechanisms. Specifically, expression of p16INK4a has

18 been reported to stabilize p21CIP1, and may inhibit the AUF1-dependent decay of p21CIP1, cyclin D1 and

19 e2f1 mRNA (27, 28). As a whole, these data provide evidence that the cell cycle-related functions of

20 p16INK4a may extend beyond CDK4/6 inhibition to include the regulation of other CDK-CYCLIN targets.

23 Transcriptional, Translational and Epigenetic Regulation of p16INK4a

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1 To maintain tissue homeostasis and prevent cancer, the ability of p16INK4a to inhibit cellular

2 proliferation must be tightly controlled. In this section, we discuss the role of chromatin, transcriptional

3 co-factors and RNAs in maintaining proper p16INK4a expression. In addition, we highlight the complexity

4 and redundancy of p16INK4a regulatory pathways required for proper proliferative control.

6 p16INK4a Repression by Polycomb Group Complexes

7 Chromatin modifications by the polycomb group complexes (PcGs), PRC1 and PRC2, are critical

8 to the homeostatic regulation of INK4/ARF gene expression (Fig. 2A). The PRC2 complex is made up of

9 four core components: EZH1/2, EED, SUZ12 and RBAp46/48. EZH1 or 2 serves as the catalytic subunit of

10 PRC2 and functions only in the presence of EED and SUZ12 to compact chromatin through the di- and

11 tri-methylation of histone H3 lysine 27 (H3K27me2/3) (29, 30). H3K27me3 is recognized by a

12 chromodomain-containing CBX protein family member associated with PRC1. In this manner, PRC1 is

13 recruited to the INK4/ARF locus, where it catalyzes the ubiquitylation of histone H2A lysine 119

14 (H2AK119ub), resulting in further chromatin compaction and gene silencing (31). Multiple variants of

15 the PRC1 complex have been identified in vivo, each containing homologs of the Drosophila Posterior

16 Sex Comb (Psc; NSPC1/PCGF1, MEL-18/PCGF2, RNF3/PCGF3, BMI1/PCGF4, RNF159/PCGF5,

17 RNF134/PCGF6), Polycomb (Pc; CBX2, CBX4, CBX6, CBX7, CBX8), Sex Combs Extra (RING1, RING2) and

18 Polyhomeotic proteins (Ph; HPH1, HPH2, HPH3) (32). PRC1 complexes contain a single Psc and Pc

19 homolog, yet Maertens et al. observed binding of MEL-18, BMI-1, CBX7 and CBX8 to the repressed

20 INK4/ARF locus (32). Further investigation revealed that multiple PRC1 variants bind to the p16INK4a

21 promoter, working in a concerted manner to control gene expression (32). It remains to be determined

22 whether recently reported non-canonical PRC1 complexes that lack a Pc homolog, contain RYBP/YAF2,

23 and are recruited to chromatin independent of H3K27me3 (33) can also function to regulate INK4/ARF

24 gene expression. However, regardless of their composition, PRC1 and 2 complexes clearly bind

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1 throughout the INK4/ARF locus, and repress p16INK4a expression in young, unstressed cells (31).

2 Maintenance of this repression may be partially dependent on the ubiquitin-specific protease, USP11,

3 which was also shown by Maertens et al. to bind and stabilize the PRC1 complex (34). In their work,

4 depletion of USP11 caused polycomb complexes to dissociate from the INK4/ARF locus leading to

5 subsequent de-repression of p16INK4a.

6 The importance of PRC1 and PRC2 for proper p16INK4a regulation may be best exemplified by the

7 phenotypes of polycomb knockout mice. Deletion of the PRC1 component, Bmi1, results in homeotic

8 skeletal transformations, lymphoid and neurological defects (35). Many of these phenotypes are

9 attributable to the deregulation of homeobox gene expression, however, the lymphoid and neurological

10 defects observed in Bmi1 knockout mice can be almost completely rescued by INK4/ARF deletion (36).

11 Here, INK4/ARF loss reverses the self-renewal defects of Bmi1-null hematopoietic and neuronal

12 progenitors (37, 38). Together, these data show that PRC1 regulation of p16INK4a expression is required

13 for proper development, stem cell maintenance and homeostasis. In contrast to PRC1-null animals

14 which survive gestation, deletion of the PRC2 members, Ezh2 or Suz12, is embryonic lethal (39, 40). For

15 this reason, conditional knockout alleles are required to assess the biological functions of PRC2. Using

16 such alleles to delete Ezh2 in the brain, pancreas and embryonic skin, phenotypic outcomes have been

17 observed. Specifically, loss of Ezh2 in murine pancreatic islets causes a diabetic phenotype associated

18 with increased β-cell expression of both p16INK4a and ARF (41). In contrast, Ezh2 deletion in the brain

19 and skin resulted in only mild differentiation defects (42, 43). The recent observation that EZH1 is

20 expressed in many adult tissues and also catalyzes histone H3 methylation led to the hypothesis that

21 EZH1 may compensate for EZH2 loss in some settings. Indeed, deletion of both Ezh1 and 2 caused

22 severe defects in murine skin morphogenesis associated with a >70-fold increase in p16INK4a/ARF

23 expression (43).

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1 Supporting a role for EZH2 in maintaining proliferative homeostasis, human germline mutations

2 in EZH2 give rise to Weaver syndrome, a congenital disorder characterized by uncontrolled and rapid

3 growth (44). While this phenotype could be attributed to p16INK4a silencing , few reports have attempted

4 to functionally characterize the EZH2 missense mutations commonly associated with Weaver syndrome

5 (44). Instead, work has focused on recurring point mutations reported in B-cell lymphoma. These

6 mutations localize to tyrosine 641 of the EZH2 SET domain, resulting in the production of a neomorphic

7 protein with enhanced H3K27 di- and tri-methylation activity (45). Of importance, not all cancer-

8 associated EZH2 mutants are gain-of-function alleles. In myleloid neoplasms, missense, nonsense and

9 frameshift mutations in EZH2 have been described which lack a catalytic SET domain (46). In addition,

10 the expression of wildtype EZH2 has been reported to cause p16INK4a silencing in SNF5-deficient

11 malignant rhabdoid tumors (MRTs) (47). Deletion or pharmaceutical inhibition of EZH2 activity in cells

12 from these tumors increases p16INK4a expression, resulting in cell cycle inhibition (47, 48). Together,

13 these observations suggest that EZH2 activity must be tightly controlled in order to maintain

14 proliferative homeostasis and proper p16INK4a regulation.

16 Recruiting Polycomb to CDKN2A

17 In Drosophila melanogaster, polycomb group proteins are recruited to defined DNA binding sites

18 termed, Polycomb repressive elements (PREs) (Reviewed in: (49)). In contrast, few mammalian PREs

19 have been identified to date, leading many to speculate that other DNA binding proteins or RNAs must

20 guide polycomb complexes to target genes like the INK4/ARF locus. Recent work suggests that long

21 non-coding RNAs (lncRNAs) can serve as scaffolds for polycomb recruitment and epigenetic gene

22 silencing. The discovery of disease-linked polymorphisms within ANRIL prompted investigation into

23 whether this lncRNA could function in a similar manner to regulate INK4/ARF gene transcription.

24 Through RNA binding assays, a study by Yap et al. showed that CBX7 interacts with both ANRIL and

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1 H3K27me3 to promote INK4/ARF gene silencing (Fig. 2A and (10)). Subsequently, ANRIL binding to

2 SUZ12, a component of the PRC2 complex, was reported to promote silencing of p15INK4b, but not

3 p16INK4a (50). Together with these data, a report showing that MOV10, a putative RNA helicase and PRC1

4 binding partner, is required for p16INK4a repression, supports a role for ANRIL in polycomb recruitment to

5 the INK4/ARF locus (51). Whether MOV10 binds ANRIL to facilitate PRC1 interaction with the INK4/ARF

6 locus has yet to be determined. However, together these data make a strong case for the role of ANRIL

7 in epigenetic silencing of p16INK4a.

8 ANRIL-independent mechanisms are also suggested to recruit PcG complexes to the p16INK4a

9 locus. Recently, H2.0-like homeobox 1 (HLX1), a homeobox (HOX) protein, was shown by Martin et al. to

10 facilitate PRC2 recruitment to the p16INK4a promoter (Fig. 2A and (52)). While the mechanism has yet to

11 be defined, six other homeobox-containing proteins (HOXA9, DLX3, HOXB13, HOXC13, HOXD3 and

12 HOXD8) were similarly reported to participate in p16INK4a silencing (52). Given the role of HOX genes in

13 developmental patterning, it is interesting to speculate that proteins like HLX1 and HOXA9 initiate

14 tissue-specific silencing of p16INK4a. Like HOX proteins, both TWIST1, a basic helix-loop-helix (bHLH)

15 transcription factor, and KDM2B, a histone demethylase, may also facilitate polycomb-mediated

16 silencing of the INK4/ARF locus. Ectopic expression of TWIST1 and KDM2B can cause cellular levels of

17 EZH2 to rise, resulting in an increase in PRC2 activity (53). KDM2B was further reported to function in

18 demethylating H3K36me2/3, a common marker for DNA polymerase II transcription (53). Furthermore,

19 TWIST1 appears to increase BMI1 expression (55), and subsequent recruitment of BMI1 to the p16INK4a

20 promoter has been linked to interactions with phosphorylated RB (pRB) and zinc finger domain-

21 containing protein 277 (ZFP277) (54, 55). In particular, the link between pRB and p16INK4a silencing is

22 intriguing as it suggests the presence of a feedback loop wherein cells entering S-phase repress p16INK4a

23 expression (54). ZFP277-mediated recruitment of BMI1 to the p16INK4a promoter may also be linked to

24 the cell cycle. A study by Negishi et al. showed that reductions in ZFP277 expression caused by oxidative

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1 stress could lead to PRC1 dissociation from the p16INK4a promoter and subsequent cell cycle arrest (55).

2 How these mechanisms of PRC recruitment interplay with ANRIL remains to be established, but certainly

3 the complexity of p16INK4a silencing is indicative of the importance of this gene in maintaining tissue

4 homeostasis.

6 Reversing Polycomb Silencing of the INK4/ARF locus

7 In order for normal cells to traverse the G1/S checkpoint, p16INK4a must be maintained in a

8 repressed state. At the same time, induction of p16INK4a expression in the presence of stress signals is

9 required to prevent inappropriate cell cycle progression. Linking proliferative control to epigenetic

10 regulation of the p16INK4a promoter, Bracken et al. first demonstrated that RB phosphorylation during

11 the G1 to S-phase transition releases E2F1 to transactivate EZH2 and EED (56). Later, these data were

12 confirmed by an independent group who showed that p53 activation represses EZH2 expression through

13 RB-mediated inhibition of E2F1 activity (57). While these results explain how the activity of PRC2 might

14 be curbed in the presence of stress, they do not explain how epigenetic silencing of the p16INK4a

15 promoter is reversed. One mechanism of removing repressive histone marks is via the activity of

16 histone demethylases. In response to oncogenic stressors, levels of the H3K27me3 demethylase, Jmjd3,

17 increase, removing repressive histone marks from the p16INK4a promoter (Fig. 2B; (58, 59)). Following

18 histone demethylation, the Yokoyama lab showed that Jun dimerization protein 2 (JDP2) may help

19 maintain p16INK4a in an active state by binding and sequestering H3K27 away from the actions of PRC2

20 (60). These findings suggest that the activity of JDP2 and JMJD3 establishes a permissive state for

21 p16INK4a expression. Furthermore, unmethylated H3K27 is no longer recognized by PRC1, and chromatin

22 surrounding the p16INK4a promoter is decondensed. Based upon this activity, it is not surprising that

23 JMJD3, like p16INK4a, serves as a barrier to induced pluripotency (61, 62) (See: “p16INK4a as a Barrier to

24 Pluripotency”). Clearly, interplay between PRC1, PRC2 and histone demethylases is required for

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1 homeostatic regulation of the p16INK4a promoter, yet how this crucial balance is maintained is still in

2 question. Moreover, it is possible that other histone demethylases, such as lysine-specific demethylase

3 6A (KDM6A/UTX), may also play a role in p16INK4a regulation.

4 In Drosophila, the SWI/SNF chromatin remodeling complex serves as a trithorax group activator,

5 opposing the actions of polycomb-mediated silencing. Similarly, SWI/SNF functions to counteract PcG

6 silencing of p16INK4a in mammals. Cancer cell lines deficient in the SWI/SNF component, SNF5, induce

7 high levels of p16INK4a upon the restoration of SNF5 expression (63). In untransformed cell lines, SNF5

8 binds and directly inhibits the transcription of EZH2, resulting in decreased polycomb occupancy at the

9 p16INK4a promoter (47). Tumor cells lacking SNF5 overexpress EZH2 and are dependent upon the activity

10 of PRC2 to silence p16INK4a expression and drive proliferation (47, 64).

12 Chromatin Regulation of p16INK4a by Non-Polycomb Proteins

13 Epigenetic modification of the INK4/ARF locus extends beyond polycomb-mediated silencing.

14 The well-conserved genomic insulator, CCCTC-motif binding factor (CTCF), binds throughout the

15 INK4/ARF locus (65, 66) and functions to regulate both chromatin compaction and gene expression (Fig.

16 2B). Witcher et al. first reported interaction of CTCF with a chromosomal boundary ~2kb upstream of

17 the p16INK4a promoter (65). In their studies of cancer cell lines, knockdown of CTCF resulted in the

18 spread of heterochromatin DNA into the INK4/ARF locus leading to epigenetic silencing of p16INK4a (65).

19 In contrast to this model, Hirosue et al. recently reported that decreases in CTCF expression associated

20 with oncogene induced senescence promote decondensation of the INK4/ARF locus and lead to

21 heightened levels of p16INK4a mRNA (66). Reconciliation of these two results is possible as rapid p16INK4a

22 induction following CTCF knockdown would place enormous pressure on would-be cancer cells to

23 epigenetically silence the INK4/ARF locus. In fact, the observation that epigenetic silencing of p16INK4a in

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1 breast cancers is accompanied by CTCF disassociation from the locus (65) is consistent with a role for

2 CTCF in proper epigenetic regulation of INK4/ARF.

4 Transcriptional Activators and Repressors of p16INK4a

5 Opposing Transcriptional Regulators

6 The presence of a permissive chromatin state alone is insufficient for p16INK4a expression.

7 Binding of activation factors and the subsequent recruitment of RNA polymerase is required to initiate

8 p16INK4a transcription (Fig. 3). Similar to the interplay between PRC2 and JMJD3, transcriptional

9 regulation of the p16INK4a promoter is tightly controlled by antagonistic pathways. Serving as a classic

10 example, induction of p16INK4a by the E-box binding transcription factors E-26 transformation-specific 1

11 (ETS1), E-26 transformation-specific 2 (ETS2) and E47, is directly opposed by Inhibitor of DNA Binding 1

12 (ID1) (67). In response to oncogenic and senescent signaling, ETS1, ETS2 and/or E47 bind to E-box

13 motifs (CANNTG) within the p16INK4a promoter to stimulate gene expression (67, 68). This action is

14 directly antagonized by ID1 which prevents interaction of ETS1, ETS2 and E47 with the p16INK4a promoter

15 (67, 68). As such, it is not surprising that Id1 null MEFs undergo premature senescence in culture (69),

16 and that age-related increases in p16INK4a expression correlate directly with ets-1 levels in mice and rats

17 (70).

18 Similar to ID1, TWIST1 is reported to oppose transcriptional activation of p16INK4a. The

19 relationship between ID1 and TWIST1 was initially suggested in studies examining the progression of

20 benign human nevi to melanoma. In general, nevi are non-proliferative and express elevated levels of

21 p16INK4a; yet, upon progression to melanoma these lesions frequently silence p16INK4a (71). Analysis of

22 TWIST1 and p16INK4a expression in nevi and melanomas revealed an inverse correlation between these

23 two proteins, putting forth the hypothesis that they function in antagonistic pathways (72). Preliminary

24 work suggested that this antagonism might be mediated through direct interaction of TWIST1 with ETS2

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1 (72), however, in a recent publication by Cakouros et al., TWIST1 was reported to inhibit p16INK4a

2 transcription by decreasing E47 expression (73). Clearly, further work is required to fully understand the

3 physiological relationship between p16INK4a and TWIST1. In addition, it will be of interest to assess the

4 potential role of p16INK4a in classical TWIST1 pathways including epithelial to mesenchymal transition,

5 stem cell maintenance and tumor metastasis.

6 In line with the relationship between TWIST, ID1 and E-box binding transcription factors,

7 antagonistic interplay has also been described between members of the Activator Protein-1 (AP-1)

8 family of transcription factors, c-JUN and JUNB. While JUNB serves to activate p16INK4a transcription by

9 binding to three identified AP1-like sites within the p16INK4a promoter (74), c-JUN limits p16INK4a

10 expression (75). Certainly, a delicate balance between inhibitory (ID1, TWIST, c-JUN) and stimulatory

11 (JUNB, ETS, E47) pathways is required for proper regulation of p16INK4a. Upsetting this balance through

12 the overexpression of inhibitors or repression of p16INK4a activators promotes the bypass of senescence

13 and can lead to cancer (72, 73, 76-78).

14 The HOX family of proteins could also be viewed as antagonistic p16INK4a regulators. Above, we

15 discussed the potential role of HLX1, HOXA9, DLX3, HOXB13, HOXC13, HOXD3 and HOXD8 in polycomb-

16 mediated repression of the INK4/ARF locus. In contrast, the HOX proteins, VENTX, MEOX1 and MEOX2

17 have each been reported to bind the p16INK4a promoter and activate gene transcription (79-81). This

18 proposed interplay between HOX genes and p16INK4a regulation is suggestive of a role for CDK4/6

19 inhibition in embryonic development. In spite of this, developmental defects are not observed in

20 p16INK4a knockout mice or melanoma-prone kindreds harboring germline p16INK4a deficiencies (25, 82).

21 Whether compensatory mechanisms are required to combat the functional loss of p16INK4a during

22 development is still to be determined.

24 Role of Acetyltransferases and Deacetylases in p16INK4a Regulation

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1 Histone acetylation facilitates chromatin decondensation and subsequent gene transactivation.

2 As such, transcriptional coactivators often harbor or recruit histone acetyltransferase (HAT) activity to

3 target gene promoters. In a pair of recent publications, Wang et al. describe how the transcription

4 factors, SP1 and HMG box-containing protein 1 (HBP1), recruit p300, a well-known HAT, to the p16INK4a

5 promoter (83, 84). In their studies, acetylation of local chromatin as well as HBP1, promoted

6 decondensation of the p16INK4a promoter and subsequent gene transactivation. However, numerous

7 targets of p300 acetylation have been identified to date, including B-MYB, a putative repressor of

8 p16INK4a transcription (83, 85, 86). Therefore, the p300-p16INK4a relationship is likely complex and may be

9 dependent upon the available pool of transcriptional co-factors within a given cell type.

10 HAT activity is opposed by histone deacetylases (HDACs) which promote transcriptional

11 silencing. In human cell lines, HDACs 1-4 have all been reported to bind and repress transcription from

12 the p16INK4a promoter (52, 87-89). Most of these interactions have been linked to bridging transcription

13 factors such as Lymphoid Specific Helicase (LSH), HLX1 and ZBP-89 (87, 89); albeit one report suggested

14 that HDAC2 may directly bind the p16INK4a promoter (88). While loss of Hdac1, 2, 3 or 4 causes

15 developmental abnormalities and lethality in mice, none of these phenotypes have been attributed to

16 defects in p16INK4a regulation (90).

18 Age-related Signaling Pathways Influence p16INK4a Expression

19 The observation that p16INK4a levels are high in senescent cells has prompted several

20 investigations into the connection between pro-senescent signaling and p16INK4a regulation. For

21 example, age-related metabolic pathologies have long been associated with activation of the

22 peroxisome proliferator-activated receptors (PPARs). It is now known that these nuclear receptors

23 directly bind and activate the p16INK4a promoter leading to subsequent cell cycle arrest (91, 92).

24 Similarly, alterations in TGF-β signaling have been linked to a variety of age-related diseases including

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1 cancer, osteoarthritis, cardiovascular disease and Alzheimer’s (93). Work by the Conboy lab has

2 demonstrated that elevated TGF-β signaling reduces the capacity of muscle stem cells to regenerate

3 (94). Here, phospho-SMAD3 has been shown to directly bind the p16INK4a promoter, stimulating gene

4 transcription and cell cycle arrest (95). Due to crosstalk between the TGF-β and β-CATENIN/WNT

5 signaling pathways, it is not surprising that aberrant WNT signaling is also associated with age-related

6 disease (95). β-CATENIN can directly bind and activate the p16INK4a promoter in both human and murine

7 cells (96-98), and recent evidence links the induction of p16INK4a by reactive oxygen species (ROS) to β-

8 CATENIN/WNT signaling (99). Together these findings suggest a strong association between age-

9 promoting, ‘gerontogenic’ signals and p16INK4a expression.

11 Cellular Structure and p16INK4a Expression

12 An emerging theme in p16INK4a regulation is the potential for cytoskeletal rearrangements to

13 influence INK4/ARF gene transcription. In an siRNA screen of over 20,000 genes, Bishop and colleagues

14 recently identified GLI2, a member of the Hedgehog signaling pathway, as an activator of p16INK4a

15 expression (100). Interestingly, GLI2 partially localizes to a non-motile cytoskeletal protrusion called the

16 primary cilium, and cultured human mammary epithelial cells with a primary cilium expressed lower

17 levels of p16INK4a than those without (100). Upon ablation of p16INK4a, the number of cells with a primary

18 cilium increased, suggesting a link between cellular structure and p16INK4a expression (100). Supporting

19 this observation, the ACTIN nucleating enzymes ARP2 and 3 have been implicated in a second

20 connection between cytoskeletal structure and Ink4/Arf gene transcription. Here, the generation of

21 stable ARP2/3 knockdown cells required concomitant Ink4/Arf deletion (101). These data suggested

22 that lamellipodial dysfunction triggers growth inhibitory Ink4/Arf gene transcription; however the

23 specific role of p16INK4a in this process has yet to be examined.

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1 The Role of microRNAs and RNA Binding Proteins in p16INK4a Regulation

2 While literature defining transcriptional and epigenetic regulators of p16INK4a is extensive, far

3 fewer studies have examined post-transcriptional mechanisms of p16INK4a regulation. Discovered in an

4 unbiased search for miRNAs silenced during senescence (102), two independent groups have reported

5 that miR-24 binds and inhibits p16INK4a translation (102, 103). Consistent with this observation,

6 antagonists of miR-24 cause a moderate decrease in the proliferation of normal human keratinocytes

7 (103). In a similar manner, knockdown of miR-31 has been proposed to regulate cell cycle progression in

8 murine embryo fibroblasts with altered nuclear structure (104). Here, loss of Lamin B1 was associated

9 with increased miR-31 expression and p16INK4a instability (104). This work suggests another possible

10 connection between cellular structure and p16INK4a regulation, linking changes in nuclear integrity to

11 p16INK4a expression. Together, the associations between miR-31, miR-24 and p16INK4a suggest that

12 miRNAs function to control proliferation via interactions with p16INK4a mRNA; however, it is important to

13 note that other cell cycle regulators have been identified as miR-24 targets (e.g. cdk4, cyclin A2, cyclin

14 B1, myc, e2f2, p14ARF and p27KIP1; (103, 105, 106)) and miR-31 (e.g. ets1, cdk1; (107)). Therefore, cell

15 cycle defects caused by perturbations in miRNA expression likely reflect the outcome of both p16INK4a-

16 dependent and -independent pathways.

17 The let-7 family of microRNAs has also been implicated in p16INK4a regulation, proliferative

18 control and stem cell aging. The Morrison group first reported that murine let-7b expression increased

19 with age in neuronal stem cells (108). Although let-7b did not bind p16INK4a mRNA directly,

20 overexpression of let-7b reduced the expression of High-Mobility Group AT-Hook 2 (HMGA2), causing

21 p16INK4a levels to increase (108). In addition to hmga2, a growing number of RNAs involved in growth

22 and proliferative control have been identified as let-7b targets, and therefore, it is not surprising that

23 the levels of most let-7 family members decrease during tumor progression (109).

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1 In addition to miRNAs, RNA binding proteins can also regulate p16INK4a translation. Interaction

2 of the Hu RNA binding protein, HuR, with the p16INK4a 3’UTR have been reported to destabilize the

3 transcript in an miRNA-independent fashion (110). Work by Zhang et al. suggests that this action is

4 opposed by the tRNA methyltransferase, NSUN2, which methylates the 3’UTR of p16INK4a to prevent HuR

5 binding and subsequent mRNA degradation (111). In this way, interplay between HuR and NSUN2 may

6 tightly control p16INK4a translation. For example, in the presence of oxidative stress, NSUN2 levels

7 appear to increase, tipping the balance towards mRNA stability, p16INK4a expression and subsequent cell

8 cycle arrest (111).

12 The Function and Significance of p16INK4a Expression in Cancer

14 In the absence of p16INK4a, both mice and humans are predisposed to cancer (25, 82). Loss of

15 p16INK4a function can occur through gene deletion, methylation or mutation, and therefore,

16 comprehensive genetic analyses are required to determine the frequency of p16INK4a silencing in cancer.

17 Adding to the challenge of assessing p16INK4a status in human tumors, few studies distinguish between

18 the two CDKN2A transcripts: p16INK4a and ARF. Here, we compiled data from the Cancer Genome Atlas

19 (TCGA) to reveal that functional inactivation of CDKN2A is a frequent event in most tumor types ((112-

20 118); Fig. 4). We probed 16 tumor types to determine the percent of cases wherein mutational and/or

21 copy number changes disrupted genes critical to the p16INK4a tumor suppressor pathway (i.e. RB1,

22 CDKN2A, CCND1 (CYCLIN D1), CCND2 (CYCLIN D2), CCND3 (CYCLIN D3), CCNE1 (CYCLIN E1), and CCNE2

23 (CYCLIN E2)). Tumor types displaying a high percentage of p16INK4a tumor suppressor pathway

24 alterations included urothelial carcinoma (BLUCA; 77%), glioblastoma multiforme (GBM; 77%), head and

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1 neck squamous cell carcinoma (HNSC; 63%), lung squamous cell carcinoma (LUSC; 58%) and cutaneous

2 melanoma (SKCM; 58%) (Fig. 4A). Examination of individual tumor profiles revealed infrequent overlap

3 between CDKN2A and RB1 deletion, implying that these are often mutually exclusive tumorigenic events

4 (Fig. 4B). In support of these data, an inverse correlation between p16INK4a and RB inactivation was

5 previously described in lung cancer cell lines (119) and human tumors (120). In contrast to RB, we

6 frequently noted alterations within other components of the p16INK4a tumor suppressor pathway (i.e.

7 Cyclin amplification) in CDKN2A mutant tumors from the TCGA dataset (Fig. 4B). However, in cases

8 where the p16INK4a tumor suppressor pathway appeared genetically intact, high levels of RB1 or CDKN2A

9 methylation were observed (e.g. kidney cancers (KIRP, KIRC), colorectal adenocarcinomas (COAD/READ),

10 low grade glioma (LGG), and acute myeloid leukemia (AML); Fig. 4C). Combining these genetic and

11 epigenetic data suggests that functional inactivation of the p16INK4a-RB axis approaches 100% in many

12 cancer types. A prior study by Schutte et al. supports this claim, demonstrating inactivation of the

13 p16INK4a/RB-axis in 49 of 50 pancreatic carcinomas (121). However, further comprehensive assessment

14 of p16INK4a functionality in a wide variety of tumors will require thorough experimental and bioinformatic

15 analyses.

17 p16INK4a Expression in Tumors

18 In most tumor types, p16INK4a inactivation occurs early in tumorigenesis. For example,

19 pancreatic intraepithelial neoplasias frequently inactivate p16INK4a upon progression to invasive disease

20 (122). Pressure to silence p16INK4a presumably stems from oncogenic engagement of the RB tumor

21 suppressor pathway. Therefore, tumors with early defects in RB signaling continue to express p16INK4a

22 independent of progression (Reviewed in: (123)). Intense activation of the p16INK4a promoter is believed

23 to represent a futile attempt by the cell to curb oncogenic proliferation in the absence of a functional

24 G1/S checkpoint. In the clinic, immunohisotchemical p16INK4a staining is used to identify cervical and

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1 head and neck tumors driven by oncogenic human papilloma virus (HPV) infection. Here, the HPV viral

2 oncoprotein, E7, functionally inactivates RB leading to increases in p16INK4a expression (124). Although it

3 is believed that RB inactivation is requisite for the elevation of p16INK4a expression in cancer, aberrations

4 in the RB pathway are not obvious in every tumor. The RB checkpoint is deregulated by multiple

5 mechanisms independent of RB1 mutation, deletion or methylation. Viral oncogene expression and

6 cyclin gene amplification represent just two possible forms of alternative RB inactivation.

7 Unfortunately, there is a paucity of studies that comprehensively examine the status of the RB pathway

8 in multiple human tumor types. Therefore, the critical role of this p16INK4a-induced checkpoint may be

9 underestimated.

10 Limited analyses of the RB pathway in human tumors have revealed that p16INK4a expression can

11 be predictive of both tumor subtype and therapeutic response. Elevated p16INK4a levels discern small

12 cell lung cancer from lung adenocarcinoma (119, 125) and characterize the basal-like breast cancer

13 subtype (126). Given that tumor subtypes often show distinct therapeutic response profiles, it is not

14 surprising that p16INK4a expression can predict therapeutic efficacy. For example, elevated p16INK4a levels

15 predict a higher initial response to radiation therapy in prostatic adenocarcinoma (127). However, these

16 same p16INK4a positive tumors are the most likely to fail androgen-deprivation therapy (128). In

17 oropharyngeal cancer, p16INK4a serves as a marker of oncogenic HPV infection and is predictive of

18 improved therapeutic response and patient survival (129). While p16INK4a expression clearly serves as a

19 relevant clinical marker, combined analysis of multiple RB pathway members may be of additional value.

20 Likewise, recent data suggests that the localization of p16INK4a staining within a tumor may provide

21 further clinical insight (see below).

23 The Significance of Stromal p16INK4a Expression

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1 While a myriad of signals are linked to p16INK4a regulation, most of these are triggered by

2 intrinsic, cell-autonomous events. Employing a recently developed luciferase reporter mouse, p16LUC,

3 we have observed a second, cell-non-autonomous mechanism of p16INK4a activation (130). The p16LUC

4 allele expresses firefly luciferase from the endogenous p16INK4a promoter, allowing investigators to

5 dynamically track p16INK4a transcription in live animals. When the p16LUC allele was crossed with

6 genetically engineered mouse models (GEMMs) of human cancer, a luminescent signal appeared only in

7 the location of future tumor formation (130). These luminescent foci were visible weeks before tumors

8 could be visualized or palpated, providing a significant detection advantage over traditional monitoring

9 methods. This incredible sensitivity, along with the observation that tumors maintained luciferase

10 activity during progression, led to the hypothesis that p16INK4a transcription is activated in the

11 surrounding tumor stroma. Indeed, this was the case as syngeneic transplantation of six p16LUC-negative

12 tumor cell lines harboring a wide variety of oncogenic drivers caused stromal induction of p16LUC (Fig.

13 5A and (130)). Although the specific stromal cell types responsible for this observation have yet to be

14 identified, bone marrow transplantation studies suggest that the p16LUC signal originates in part from

15 bone marrow-derived cells. Therefore, it appears that alterations in the milieu surrounding a growing

16 neoplasm can promote the expression of p16INK4a in a cell-non-autonomous fashion (Fig. 5B).

17 Mounting evidence supports a role for stromal p16INK4a expression in tumor initiation and

18 progression. Fibroblasts ectopically expressing p16INK4a have altered cellular metabolism and over-

19 produce high-energy mitochondrial fuels such as L-lactate (131). In xenograft studies, co-injection of

20 these fibroblasts with MDA-MB-231 breast cancer cells increased tumor size 2 fold, suggesting that

21 altered stromal metabolism caused by p16INK4a expression promotes tumor growth (131). In support of

22 this observation, elevated p16INK4a levels in the stroma of human mammary ductal carcinoma in situ

23 (DCIS) lesions are predictive of disease recurrence independent of other histopathological markers such

24 as ER positivity (132). It remains to be determined whether the promotion of tumorigenesis by p16INK4a-

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1 positive stromal cells is solely a reflection of altered local metabolism. Studies from the p16LUC mouse

2 model suggest that p16INK4a induction in tumor infiltrating immune cells may also promote cancer

3 progression by dampening the anti-tumor response. Regardless of the mechanism, these data make it

4 clear that p16INK4a expression in the tumor stroma should not be ignored.

6 Therapeutic Mimicry of p16INK4a

7 Pharmaceutical efforts to mimic the function of p16INK4a arose after the anti-tumor effects of

8 flavopiridol were linked to CDK inhibition (Reviewed in: (133)). Flavopiridol (alvocidib) was originally

9 touted as an inhibitor of epidermal growth factor receptor (EGFR), but later shown to inhibit the growth

10 of a wide range of cancer cells at an IC50 much lower than that required to block EGFR activation. Broad

11 inhibition of cyclin dependent kinases (CDKs), including CDK4 (IC50 <120nM), was later identified as the

12 mechanism of flavopiridol action (134). After several promising phase I trials, flavopiridol failed in phase

13 II, showing significant activity only in cases of relapsed chronic lymphocytic leukemia (135). Based upon

14 these disappointing results, Sanofi-Aventis halted production of flavopiridol in 2010. For other non-

15 selective CDK inhibitors, multiple toxicities and poor solubility prevented successful transition to the

16 clinic. However, recent efforts to generate potent and selective CDK inhibitors appear more fruitful.

17 Of particular interest to the pharmaceutical industry, selective CDK4/6 inhibitors have shown

18 promise in early clinical trials (Reviewed in: (136)). Knowledge of p16INK4a regulation and function has

19 bolstered these efforts by providing biomarkers of therapeutic efficacy and identifying patient

20 populations wherein response is likely. Often clinical trials of CDK4/6 inhibitors now exclude RB null

21 tumors, which are naturally resistant to the effects of ectopic p16INK4a expression. In addition, the

22 observation that p16INK4a is markedly upregulated in response to RB-inactivating viral oncoproteins (e.g.

23 E7, T-Antigen) has prompted the exclusion of tumors expressing high levels of p16INK4a. Finally, studies

24 of CDK knockout mice are assisting these efforts, identifying cell and tumor types which are more reliant

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1 upon the activity of CDK4/6 to drive proliferation than that of CDK2. Employing this knowledge, CDK4/6

2 inhibitors are showing efficacy, and a number of drugs have now entered phase II and III clinical trials

3 (Phase 2- LEE011(Novartis) and Ly2835219(Lilly); Phase 3- MK-7965/dinaciclib (Merck) and PD-

4 0332991/palbociclib (Pfizer)) (137).

5 p16INK4a selectively binds CDK4 and 6 in vitro (2), however achieving such therapeutic specificity

6 is more challenging. In fact, Merck attributes the success of dinaciclib in chronic lymphocytic leukemia

7 to inhibition of CDK9, not CDK4/6 (137). Moreover, the observation that p16INK4a may contribute to

8 CDK4/6-independent cell cycle regulation (i.e. through CDK inhibitor reshuffling) suggests that

9 pharmaceutical CDK4/6 inhibitors may not fully recapitulate the potency of p16INK4a. While adverse

10 effects associated with CDK4/6-selective inhibitors are mild (i.e. limited bone marrow suppression)

11 (136), concerns about the long-term efficacy of such therapeutics is rising. In particular, mechanisms to

12 bypass the requirement for CDK4/6 are already known including: RB loss and increased CDK2 activity.

13 How quickly tumors will exploit these pathways to subvert therapeutic treatment is unknown. Initial

14 trials of PD-0332991 in mantle cell lymphomas speak to this concern. While 89% of study participants

15 showed reduced phospho-RB staining at 3 weeks, only 18% of tumors responded to therapy, suggesting

16 that resistance was rapidly acquired (138). In addition to concerns about resistance, the role of p16INK4a

17 expression in the tumor stroma remains undefined and inhibition of the local immune response or

18 altered cellular metabolism may function to promote growth and metastasis. In fact, fibroblasts

19 exposed to PD-0332991 adapt a tumor promoting, metabolic phenotype similar to that of fibroblasts

20 overexpressing p16INK4a (131). Therefore, therapeutic mimetics could have similar, detrimental

21 consequences on the tumor microenvironment. A final concern is the long-term effects of CDK4/6

22 inhibition on cellular senescence. Prolonged expression of p16INK4a promotes senescence and decreases

23 regenerative capacity (See below). In a similar manner, CKD4/6 inhibitors may influence tissue aging.

24 However, under normal physiological conditions, stem cell populations are by and large quiescent and

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1 thus unlikely altered by CDK4/6 inhibitors. It may be that stress and/or mitogenic signaling, which often

2 accompany p16INK4a induction in vitro, is required to elicit senescence, and therefore the effects of

3 CDK4/6 inhibition on aging will be minimal. As more than half of all cancers are diagnosed in people 65

4 and older, determining whether CDK4/6 therapeutics exacerbate age-related disease will be of

5 significant interest.

9 The Role of p16INK4a in Senescence and Aging

11 p16INK4a Marks Biological Senescence

12 As noted first by Sherr and colleagues (139), p16INK4a levels increase with aging. In fact, detailed

13 quantification has demonstrated a direct increase in p16INK4a expression with chronological age in all

14 mammalian species tested to date (140). Such increases in p16INK4a are exponential, rising ~16 fold

15 during the average human lifespan and making p16INK4a one of the most robust aging biomarkers

16 characterized to date (141). The induction of senescence and p16INK4a expression is traditionally

17 associated with a wide variety of intrinsic cellular stressors including: DNA damage, telomere erosion,

18 reactive oxygen species, and stalled replication forks (Reviewed in: (142)). However, use of the p16LUC

19 reporter mouse has provided evidence that undefined, extrinsic signals can also trigger p16INK4a

20 transcription in a cell non-autonomous fashion (130). Using this same reporter to compare the

21 dynamics of p16INK4a expression in mice with that observed in humans showed a direct correlation

22 between the rate of p16INK4a accumulation and lifespan (130). Furthermore, data from progeroid and

23 calorically restricted rodents suggest that p16INK4a serves as a marker of biological rather than

24 chronological aging (70, 143, 144). Supporting this observation in humans, smoking and chemotherapy

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1 are associated with elevated p16INK4a expression in the human population (141, 145). Moreover, skin

2 biopsies from long-lived nonagenarian cohorts have fewer p16INK4a positive cells than their age-matched

3 partners (146). Clinically, use of p16INK4a as a marker of biological aging could provide quantitative

4 measures of patient fitness including immune function and chemotherapeutic tolerance (145, 147).

5 Assessment of p16INK4a levels prior to organ transplantation may also aid in the identification of

6 biologically ‘younger’ donor tissues with increased potential for success (148-150).

8 A Causal Role for p16INK4a in Aging

9 Several lines of evidence suggest that p16INK4a is not only a biomarker of aging, but also causes

10 aging in many cell types. Using p16INK4a transgenic and knockout mice, the cell-autonomous role of

11 p16INK4a in aging has been investigated. In murine hematopoietic stem cells, T-cells, pancreatic β-cells

12 and neural progenitors of the subventricular zone, age-related p16INK4a expression causes a decline in

13 regenerative capacity (151-154). A caveat to these initial studies was the use of germline knockout

14 mice; however strategies employing conditional p16INK4a loss or siRNAs have since confirmed these

15 findings in T-cells and pancreatic β-cells (154, 155). Supporting the idea that tissues expressing less

16 p16INK4a are more biologically fit, kidney transplant success is higher in p16INK4a-low donor organs (148-

17 150). These data put forth the hypothesis that p16INK4a expression drives cellular senescence, resulting

18 in decreased regenerative potential. As a proof of principal, work from the Van Deursen lab showed

19 that deletion of p16INK4a-expressing cells from a BubR1 deficient, progeroid mouse model reduced many

20 aging phenotypes (e.g. sarcopenia, cataracts, loss of adiposity) (144). Further work by this group

21 showed that both muscle and adipocyte progenitors from these mice express high levels of p16INK4a,

22 suggesting that even the deletion of senescent stem cells can promote improved regenerative capacity

23 (156). Unfortunately, these animals did not live longer, owing to the development of cardiac

24 pathologies, and a similar experiment has yet to be reported in wild type mice (144). One explanation

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1 for why these animals were not long-lived is that the gerontogenic effects of p16INK4a expression are

2 tissue-specific. Indeed, p16INK4a levels do not seem to influence the regenerative capacity of murine

3 melanocyte stem cells or neuronal progenitors of the dentate gyrus (unpublished observation and (153,

4 157)). Other mechanisms of curbing age-related p16INK4a induction have been reported in mice. For

5 example, activation of platelet-derived growth factor receptor (PDGFR) signaling in elderly murine

6 pancreatic β-cells increased the regenerative capacity of these cells via repression of p16INK4a expression

7 (158). Likewise, administration of fibroblast growth factor 7 (FGF7) reduced p16INK4a levels and

8 increased the number of early T-cell progenitors in 15-18 month-old mice, thereby partially rescuing the

9 known decline in thymopoiesis with age (159). Apart from these studies, analyses of p16INK4a-mediated

10 regenerative decline are limited to a small number of tissues; therefore the potential outcome of

11 p16INK4a-directed therapies remains uncertain. Clearly, further characterization of the relationship

12 between p16INK4a expression, senescence and regenerative capacity in vivo would have broad

13 implications for the therapeutic treatment of age-related disease.

15 The Role of p16INK4a in Intrinsic vs. Extrinsic Aging

16 Senescence is typically viewed as a response to detrimental, intrinsic cellular events; however,

17 recent evidence suggests that extrinsic signals also contribute to tissue aging. Above, we discussed the

18 potential for neoplastic transformation to initiate cell non-autonomous p16INK4a expression. Although

19 the extracellular mediators of stromal p16INK4a induction are undefined, several signaling pathways have

20 been linked to the expression of p16INK4a in aging tissues. In muscle satellite cells, age-associated

21 increases in local TGF-β production activate SMAD3, which in turn binds to the p16INK4a promoter to

22 initiate gene transcription (94). Notch signaling antagonizes TGF-β, and in doing so can alleviate age-

23 related declines in satellite cell function (94). Similar to TGF-β signaling, changes in thymic and bone

24 marrow structure are reported to promote aging in local progenitor cell populations (142). Together,

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1 these findings put forth the model of “niche aging” wherein stromal changes influence the regenerative

2 capacity of local progenitors. However, parsing the role of the senescent cell versus the niche in aging

3 biology becomes somewhat of a chicken and egg question. After all, senescent cells themselves secrete

4 a large number of pro-inflammatory cytokines associated with age-related disease (Reviewed in: (160)).

5 Future studies aimed at identifying cell non-autonomous p16INK4a activation signals are clearly needed to

6 better understand the induction of senescence during physiological aging.

8 p16INK4a as a Barrier to Pluripotency

9 Work with induced pluripotent stem cells (iPS) also implicates p16INK4a as a modulator of

10 regenerative capacity. During iPS generation, senescence induced by the four factor cocktail of OCT4,

11 SOX2, KLF4 and c-MYC serves as a barrier to efficient reprogramming (161). In cells where

12 reprogramming is effective, silencing of INK4/ARF gene transcription is observed concomitant with the

13 induction of molecular markers indicative of stem cell phenotypes (61). Therefore, it is not surprising

14 that iPS production efficiency is increased by cellular immortalization (162), or shRNA knockdown of

15 INK4/ARF genes (61, 161). Currently, efficient generation of iPS from older patients represents a major

16 hurdle for regenerative medicine. Therefore, novel reprogramming approaches aimed at curbing the

17 senescent phenotype, may improve iPS technology for the future (163).

19 Genome-Wide Association Studies (GWAS) Linking p16INK4a to Age-Related Disease

20 Meta-analysis of genome-wide association studies (GWAS) suggests that we have only begun to

21 scratch the surface in understanding the role of p16INK4a in age-related disease. Single nucleotide

22 polymorphisms (SNPs) in chromosome 9p21.3 have been linked to cancer, atherosclerosis, diabetes,

23 frailty, cataracts and late onset Alzheimer’s disease (Fig. 1B and (164)). In many cases, expression of

24 p16INK4a correlates directly with SNP genotype, suggesting a causal role for p16INK4a in diverse, age-

Page | 26

1 associated diseases (164). Several mechanistic models have been suggested to explain how SNPs, some

2 of which are more than 100 kb from the gene promoter, influence p16INK4a expression. One model

3 proposes that the activity of distal enhancer elements is modified by SNP genotype (165). Another

4 provides evidence that ANRIL expression and splicing is directly influenced by 9p21 SNPs (166). We

5 believe that these models are not mutually exclusive.

6 While mechanisms by which 9p21.3 SNPs influence p16NK4a transcription have been proposed,

7 the link between p16INK4a expression and age-related diseases is not always apparent. For example,

8 atherosclerosis is frequently associated with lipid metabolism, yet 9p21.3 SNPs have emerged as robust

9 indicators of atherosclerotic risk in some of the most widely replicated GWASs conducted to date (167).

10 Evidence from animal models suggests that 9p21.3 SNPs may reduce INK4/ARF gene transcription,

11 leading to altered cellular proliferation and apoptosis which exacerbate disease progression (168-170).

12 However, transgenic mice carrying multiple copies of the INK4/ARF locus are equally susceptible to

13 atherosclerosis (171). Therefore, the mechanisms by which 9p21.3 SNPs influence a large number of

14 age-related human disease remain a subject of ongoing investigation.

18 Conclusions

20 Since the discovery of p16INK4a more than 20 years ago, numerous advances have led to an

21 increasingly complex view of p16INK4a regulation and function. The role of p16INK4a clearly extends

22 beyond cancer and aging. Dynamic induction of p16INK4a is observed during mammary involution, wound

23 healing, nerve regeneration and infection (unpublished data and (130, 172-174)). It has been proposed

24 that the induction of p16INK4a during these highly proliferative events is critical to the maintenance of

Page | 27

1 proper tissue homeostasis. Whether the same signals that trigger p16INK4a expression under

2 physiological conditions play a role in tumorigenesis or aging is still unclear. However, p16INK4a

3 expression is only transient during processes like mammary involution and wound healing (130, 172,

4 173). Are p16INK4a positive cells cleared by the immune system or can they revert to a phenotype

5 conducive to proliferation? Understanding the role of p16INK4a in normal physiology will be critical to the

6 development of ‘senolytic’ therapies, which aim to lengthen our healthspan by eliminating senescent

7 cells in the body.

8 p16INK4a is different than the other INK4/ARF family members. The dynamics of p16INK4a

9 expression during senescence make it a robust biomarker of mammalian aging. Human tumors silence

10 p16INK4a with greater frequency than ARF or p15INK4b (140), suggesting that the tumor suppressor

11 function of p16INK4a is somehow more critical than the other INK4/ARF family members. As such, the

12 therapeutic restoration of p16INK4a activity appears to be a promising avenue for anti-neoplastic

13 development. Ironically, while drug development teams in the field of oncology work fervidly to move

14 CKD4/6 inhibitors into the clinic; aging biologists aim to block the accumulation of p16INK4a-positive cells.

15 Oddly, the key to longevity likely lies in the hands of both groups, as a careful balance of p16INK4a

16 expression is required to stave off cancer and prevent aging.

19 Acknowledgements

21 The authors thank M. Waqas, J. Gillahan, S.T. Nguyen and Drs. D. Beach (Barts, UK), C. J. Burd (OSU) and

22 N. Sharpless (UNC) for critical reading of the manuscript. Dr. K. Hoadley (UNC) provided advice and

23 guidance regarding the analysis of TCGA data. This work was supported by NIH R00AG036817 (C.E.B)

24 and American Cancer Society IRG-67-003-50 (C.E.B.).

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1 Figure Legends

3 Figure 1. Function, Structure and Polymorphisms of the INK4/ARF Locus. A, p15INK4b and p16INK4a both

4 function in the RB tumor suppressor pathway through inhibition of CDK4/6 activity. Expression of p14ARF

5 inhibits the E3 ubiquitin ligase activity of MDM2, leading to stabilization of p53. The p53 and RB

6 pathways play integral roles in blocking inappropriate cellular proliferation. B, Packed into 35 kilobases

7 of chromosome 9p21.3 are three well-characterized tumor suppressor genes: p14ARF, p15INK4b and

8 p16INK4a. GWAS have implicated 9p21.3 SNPs in cancer, heart disease, glaucoma, type II diabetes, autism

9 and endometriosis. The majority of the SNPs lie outside of transcript and coding regions in a recently

10 discovered long, non-coding RNA, ANRIL. Of the identified SNPs, those that have been shown to

11 correlate with CDKN2A expression in at least one study are filled with grey. Other SNPs that have not

12 been correlated with CDKN2A expression in validation studies, or have yet to be examined are filled with

13 black or white, respectively.

15 Figure 2. Mechanisms of p16INK4a Regulation by Chromatin Modification. A, p16INK4a is negatively

16 regulated by the histone modifying complexes, PRC1 and PRC2, which combine to lay down repressive

17 marks (e.g. H3K27me3, H2AK119ub) throughout the INK4/ARF locus. Several associated proteins (APs),

18 including RNA binding proteins (RBPs), are reported to facilitate PRC1/2 interaction with the p16INK4a

19 promoter. APs and RBPs discussed in the text are shown. Elevated expression of the PRC2 component,

20 EZH2, is also reported to enhance INK4/ARF gene silencing. Proteins reported to transactivate EZH2,

21 leading to PRC-mediated silencing of p16INK4a are depicted above. B, Activation of p16INK4a is associated

22 with decreases in PRC1/2 levels and the removal of repressive histone marks. JMJD3 demethylates

23 H3K27me3 and subsequent chromatin decondensation promotes access by transcription factors and

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1 p16INK4a transcription while JDP2 binds H3K27 and prevents further methylation. CTCF maintains

2 chrosomal boundaries and 3-dimension structure of the chromatin surrounding p16INK4a.

5 Figure 3. Transcriptional Regulation of p16INK4a. Expression of p16INK4a requires the action of

6 transcription factors that recruit and/or facilitate RNA polymerase association with the promoter

7 (shown in green). Opposing this action are transcriptional repressors (shown in red). Direct interactions

8 with the p16INK4a promoter are depicted by a solid line, indirect interactions with a dotted line. The

9 numbers below each binding site indicate the position of protein interaction relative to the p16INK4a

10 transcriptional start site. All locations correspond to the human genome unless designated by an ‘(m)’,

11 which signifies the mouse genome. Proteins predicted to share a common binding site are depicted

12 over top of one another.

14 Figure 4. Alterations in the p16INK4a Tumor Suppressor Pathway are Frequent in Human Cancer. A, Data

15 from TCGA was obtained and analyzed using cBioPortal (112, 113). The tumors analyzed are as follows:

16 Bladder Urothelial Carcinoma (BLUCA), Glioblastoma Multiforme (GBM), Head and Neck Squamous Cell

17 Carcinoma (HNSC), Lung Squamous Cell Carcinoma (LUSC), Skin Cutaneous Melanoma (SKCM), Ovarian

18 Serous Cystadenocarcinoma (OV), Lung Adenocarcinoma (LUAD), Stomach Adenocarcinoma (STAD),

19 Breast Invasive Cancer (BRCA), Uterine Corpus Endometrial Carcinoma (UCEC), Brain Lower Grade

20 Glioma (LGG), Colon and Rectum Adenocarcinoma (COAD/READ), Prostate Adenocarcinoma (PRAD),

21 Kidney Renal Papillary Cell Carcinoma (KIRP), Kidney Renal Clear Cell Carcinoma (KIRC), Acute Myeloid

22 Leukemia (AML). The percent of tumors with mutations or copy number changes in the p16INK4a tumor

23 suppressor pathway are shown. For the purposes of this analysis the p16INK4a tumor suppressor pathway

24 was defined to contain: CDKN2A (p16INK4a), RB1 (RB), CCND1 (CYCLIN D1), CCND2 (CYCLIN D2), CCND3

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1 (CYCLIN D3), CCNE1 (CYCLIN E1), and CCNE2 (CYCLIN E2). B, OncoPrints from cBioPortal show

2 aberrations in individual tumors across the X-axis. C, Methylation of CDKN2A (black bars) and RB1 (grey

3 bars) was quantified using HM27 or HM450 TCGA data. Genes were considered methylated if β-values

4 exceeded 0.2.

6 Figure 5. Extrinsic Versus Intrinsic Activation of p16INK4a. A, Injection of Lkb1 null endometrial cancer

7 cells into a syngenic mouse heterozygous for the p16LUC reporter causes stromal luciferase expression

8 upon tumor growth. Injection of Matrigel vehicle on the opposite flank does not alter p16INK4a

9 expression. See also: (130) B, Intrinsic signals induces p16INK4a expression in damaged, senescent or

10 transformed cells. Alterations in surrounding the cellular milieu can trigger the induction of p16INK4a in

11 nearby undamaged cells through an unknown pathway.

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The Molecular Balancing Act of p16INK4a in Cancer and Aging

Kyle M LaPak and Christin E Burd

Mol Cancer Res Published OnlineFirst October 17, 2013.

Updated version Access the most recent version of this article at: doi:10.1158/1541-7786.MCR-13-0350

Author Author manuscripts have been peer reviewed and accepted for publication but have not yet been Manuscript edited.

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