Cdkn1a transcript variant 2 is a marker of aging and cellular senescence

Cdkn1a transcript variant 2 is preferentially induced with age

To assess expression levels of the individual Ckdn1a mRNA transcript variants, we designed two primer sets in which the forward primers hybridize with the variant-specific first exons (Figure 1A). To determine whether differential regulation occurs during aging in vivo, we analyzed liver samples from male mice at 2, 11, 23, 25 and 30 months of age. Relative to 2 month-old mice, p21var2, but not p21var1, increased after 20 months of age (Figure 1B). We then obtained additional tissues from 2 and 24 month-old male and female animals (n = 12-15 per sex and age). p21var2 levels were higher than p21var1 levels in aged liver, white adipose tissue, kidney, heart and lung (Figure 1C–1G). Steady-state levels of p21var1 remained unaltered with age, and were even slightly reduced with age in liver. On average, p21var2 abundance increased 3-fold with age in liver, kidney and adipose tissue, and 2-fold in heart and lung. Mice at 4 months of age used as young control yielded equivalent results (data not shown). The transcript encoding p16^Ink4a also increased with age in all these tissues (Supplementary Figure 1A–1E).

When males and females were analyzed separately, p21var2 increased with age in all tissues and in both sexes (Supplementary Figure 2A–2J), with the only exception of heart in male mice, where the upwards trend did not reach statistical significance (Supplementary Figure 2D). Of note, we detected higher p21var1 levels in the kidney of aged females (Supplementary Figure 2H). Despite the propensity of p21var2 to increase with age, overall, in all organs tested, p21var1 was more abundant than p21var2, as reported [10]. In sum, p21var2 expression is consistently elevated with age, in contrast with an absence of age-related change in p21var1 levels.

Both Cdnk1a transcript variants are induced in cellular senescence

To determine whether either transcript variant is preferentially upregulated in senescent cells, we induced senescence in primary mouse dermal fibroblasts (MDFs) using 15 GY ionizing radiation (IR), which induces a senescence response in virtually all the irradiated cells. Seven days later, irradiated, but not sham-irradiated, MDFs showed hallmarks of senescence, including increased levels of the mRNA encoding p16^Ink4a and lower levels of the mRNA encoding lamin-B1, as expected [12] (Supplementary Figure 3A–3B). The levels of both p21var1 and p21var2 also increased. However, as reported [10], p21var2 levels were 6- to 8-fold lower compared to p21var1 (data not shown). These data show that both of the murine Ckdn1a transcript variants are valid readouts to evaluate cellular senescence in cultured MDFs.

We then tested the dynamics of Cdkn1a variant expression in MDFs after irradiation. Expression of p21var1 increased 3 hours after irradiation, then progressively declined to a level twice that of baseline by 12 hours after irradiation. In contrast, p21var2 levels remained unaltered for the first 24 hours after irradiation (Figure 2A). Thereafter, both Cdkn1a variants steadily increased from day 3, without reaching a plateau by the end of the 12-day time course. Establishment of senescence was verified by increased p16^Ink4a and decreased lamin B1 mRNA levels (Figure 2B). Treatment of MDFs with 250 nM doxorubicin (doxo), a chemotherapeutic agent known to cause cellular senescence in culture and in vivo [13], increased p21var1 levels within the 24 hours, followed by a smaller increase in p21var2 levels (Figure 2C). Similar to the pattern in irradiated cells, from day 5 onwards both variants were coordinately and increasingly upregulated, concomitant with senescence-associated changes in p16^Ink4a and lamin B1 expression (Figure 2D). Together, our results show that p21var1 increases preferentially shortly after acute genotoxic stress, but both variants gradually rise as cells enter a senescent state.

Figure 2. Cdkn1a variant 2 increases as cells acquire senescent phenotypes in culture. Time course of (A) p21var1 and p21var2 levels and (B) p16^Ink4a and lamin B1 mRNA levels after 15 Gy irradiation. 2-way ANOVA test was applied. Time course of (C) p21var1 and p21var2 levels and (D) p16^Ink4a and lamin B1 levels after a 24 h exposure to 250 nM doxorubicin. 2-way ANOVA test was applied. (E) p21var1 and p21var2 levels in MDFs after treatment with 10 μM nutlin-3a. (F) mRNA levels 3 hours after treatment with increasing doses of nutlin-3a. (G) mRNA levels 3 hours after irradiation (15 Gy) and treatment with increasing doses of nutlin-3a. Mean ± SEM is shown. Note Y axes are log-2 scales. * p < 0.05, ** p < 0.01, *** p < 0.001.

p53 stabilization upregulates both Cdkn1a transcript variants

The basal expression of p21var1 and p21var2 is differentially regulated by p53, likely due to the proximity of the p21var2 transcription start site (TSS) to a p53-response elements (p53-Res) [10]. We performed a promoter analysis (TRANSFAC version 2018.3) for both Cdkn1a TSSs, spanning 2.5 kb upstream and 0.5 kb downstream of each TSS (Supplementary Information). Among a plethora of predicted transcription factor binding sites, p53-REs were detected within 500 bases upstream of both TSSs, even when we applied the most stringent algorithm. To understand the p53 responsiveness of the Cdkn1a transcript variants, we treated MDFs with 10 μM nutlin-3a, an MDM-2 inhibitor that stabilizes p53 [14]. The levels of both variants increased within 1 hour, reaching a plateau approximately 12 hours later (Figure 2E). Lower concentrations of nutlin-3a failed to reveal any sensitivity differences between the variants. Three hours after treatment, the dose-response curves were similar in shape for both Cdkn1a transcripts (Figure 2F). The same was true for senescent (irradiated) MDFs treated with 10 μM nutlin-3a (Figure 2G). These results suggest that p21var1 and p21var2 are equally sensitive to transcriptional upregulation upon p53 stabilization.

Circadian regulation of p21^Cip1/Waf1 does not involve transcript variant 2

To further explore the expression pattern of p21var2 in vivo, we asked whether it is subject to circadian regulation, as described for p21^Cip1/Waf1 [15]. We euthanized 2 month-old male mice at 3 hour intervals for 12 hours. In liver samples, p21var1 mRNA levels were highest at the end of the dark cycle (6:00 am Pacific time) and progressively decreased 8-fold to a minimum in the afternoon (Figure 3A). The p21var2 remained unaltered, at lower levels, throughout the same period. A similar pattern was observed in adipose and kidney tissue (Figure 3B, 3C). These results indicate that the circadian regulation of p21^Cip1/Waf1 is driven solely by expression of Cdkn1a transcript variant 1.

Figure 3. Cdkn1a variant 1 is circadian regulated, whereas variant 2 rises with senescence in vivo. (A) Cdkn1a variants expression throughout the light cycle (6 am to 6 pm) in the liver, (B) white adipose tissue and (C) kidney of 6 week-old male mice. (D–F) A cohort of 6 week-old mice were treated with doxorubicin or vehicle (n = 9-10 for either males or females, n = 9-10 for either vehicle or doxorubicin) and Cdkn1a variant levels were analyzed 6 weeks later. Results are shown for (D) liver, (E) adipose tissue and (F) kidney. (G–I) A cohort of 18 to 22 month-old mice were treated with ABT-263 or vehicle. Pooled results are shown for (G) liver, (H) adipose tissue and (I) kidney. 1-way ANOVA and Tukey post-tests were applied. * p < 0.05, ** p < 0.01, *** p < 0.001, ns = not significant.

Expression of p21var2 in vivo is increased by doxorubicin and decreased by ABT-263

To determine how Cdkn1a transcript variants are expressed when cellular senescence is induced in vivo, we induced cellular senescence in vivo by intraperitoneal injection of a single dose (10 mg/kg) of doxorubicin. After 6 weeks, p21var1 increased 3-fold while p21var2 increased 25-fold (reaching levels comparable to those of p21var1 at baseline) in the livers of treated mice (Figure 3D and Supplementary Figure 4A, 4B). Similar elevations were observed in the adipose tissue and kidneys (Figure 3E, 3F and Supplementary Figure 4C–4F) of male and female mice, consistent with the widespread luminescence reported in doxorubicin-treated p21-reporter mice [9]. Our data suggest that p21var2 is a more sensitive readout for doxorubicin-induced senescence in vivo than p21var1.

ABT-263 (navitoclax) has been shown to clear senescent cells by inhibiting Bcl-2 and related anti-apoptotic proteins [16, 17]. In a mixed cohort of 20-22 month-old male and female mice, ABT-263 specifically reduced p21var2 levels in adipose tissue and kidney, whereas p21var1 levels remained unaltered (Figure 3H–3L). There were no significant changes in the levels of either variant in liver (Figure 3G). Together, these results reinforce the idea p21var2 is a better marker than p21var1 for assessing the presence of senescent cells in vivo.

Mouse models

Animal husbandry

C56BL/6 mice were purchased from The Jackson Laboratory and allowed to acclimate to the Buck Institute facilities. The animals were group housed under controlled conditions of temperature (22-24° C), humidity (40-60%), and a 12 h light-dark cycle. All animal procedures were approved by the Buck Institute Institutional Animal Care and Use Committee (IACUC).

Aging cohorts

C56BL/6 were aged at the Buck Institute vivarium and male and female littermates derived from the same colony were used as young controls.

Doxorubicin treatment

6-week old male and female C57BL/6 littermates were intraperitoneally (IP) injected with a single dose of doxorubicin (10 mg/kg) to induce widespread senescence [13]. After 6 weeks, the animals were euthanized by CO₂ inhalation followed by cervical dislocation, and tissues were harvested and flash frozen in liquid nitrogen.

ABT-263 treatment

ABT-263 or vehicle (5% DMSO, 95% corn oil) was delivered to 20-month old C57BL/6 littermates via IP injection at 50 mg/kg for 7 consecutive days per cycle for two cycles, with a 2-week interval between cycles. Animals were sacrificed one week after the last treatment cycle and tissues were collected and flash frozen in liquid nitrogen.

Cell culture

Mouse dermal fibroblasts

Primary mouse dermal fibroblasts (MDF) were obtained from postnatal day 2-3 C57BL/6 mice. Skin was excised from the mice and incubated overnight in 0.25% trypsin-EDTA. The dermis was mechanically disengaged and incubated with 10 mg/ml collagenase for 30 min at room temperature. The mixture was filtered and plated. MDF were cultured in 3% oxygen in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum and 100 U/ml streptomycin and penicillin.

Irradiation and doxorubicin treatment

MDFs were induced to senesce by X-irradiation (15 Gy), as described [23], or mock-irradiated (control). Alternatively, MDF were treated with 250 nM doxorubicin or vehicle (DMSO, control) for 24 h, then washed and cultured in fresh complete medium. Senescence markers were tested at different times (1, 3, 6, 9, 12 h and 1, 3, 5, 7, 9, 12 days) after treatment.

Nutlin-3a treatment

MDFs were incubated with 10 μM nutlin-3a or vehicle (DMSO, control) and RNA was collected 1, 3, 6, 9, 12 and 24 h later. MDFs were also treated with different nutlin-3a concentrations (0.6-10 μM), irradiated (15 Gy X-rays) or mock-irradiated and RNA collected 3 h later.

RNA extraction and RT-qPCR

RNA was extracted using Tri-reagent and isolated with the Direct-Zol RNA miniprep kit (Genesee Scientific). For adipose tissue, the RNeasy Lipid Tissue mini kit (Qiagen) was used. cDNA was synthesized using the High Capacity cDNA RT kit (Life Technologies). Transcripts were analyzed using a Roche LightCycler 480 II in 384-well plates and the UPL probe system. Bioline SensiFast Probe No-ROX was used as a master mix. Primer sequences and respective probes were as follows: Cdkn2a (p16), forward 5’-TCCTCGCAGTTCGAATCTG, reverse 5’-AACTCTTTCGGTCGTACCCC, with a custom designed probe (5'- /56-FAM/AGG TGA TGA /ZEN/TGA TGG GCA ACG TTC AC/3IABkFQ/ -3'); Cdkn1a (p21) variant 1, forward 5’-TCCACAGCGATATCCAGACA, reverse 5’-GGACATCACCAGGATTGGAC, with UPL probe 21; Cdkn1a (p21) variant 2, forward 5’-TTGCCAGCAGAATAAAAGGTG, reverse 5’-TTTGCTCCTGTGCGGAAC, with UPL probe 9; β-actin: forward 5’- CTAAGGCCAACCGTGAAAAG, reverse 5’- ACCAGAGGCATACAGGGACA, with UPL probe 64; tubulin: forward 5’- CTGGAACCCACGGTCATC, reverse 5’- GTGGCCACGAGCATAGTTATT, UPL probe 88. Results were normalized to β-actin and tubulin. ΔΔCt values prior to logarithmic transformation were used for statistical analyses.

Promoter analysis

Transcription factor binding sites were analyzed using TRANSFAC version 2018.3 (geneXplain) and sequences between -2500 and +500 for each variant. For each variant, two analyses were performed, either minimizing false positives (minFP) or balancing false positives and false negatives (minSUM), using algorithms provided by the software.

Statistical analysis

Unless otherwise noted, results are shown as individual data points with geometric means and 95% CIs. Comparisons between multiple groups were analyzed using 1-way ANOVA with Tukey post-tests, or 2-way ANOVA with Bonferroni post-tests if a second variant (usually time) was present. No statistical outliers were removed.