Pancreatic Progenitor Commitment Is Marked by an Increase in Ink4a/Arf Expression

The identification of the molecular mechanisms controlling early cell fate decisions in mammals is of paramount importance as the ability to determine specific lineage differentiation represents a significant opportunity for new therapies. Pancreatic Progenitor Cells (PPCs) constitute a regenerative reserve essential for the maintenance and regeneration of the pancreas. Besides, PPCs represent an excellent model for understanding pathological pancreatic cellular remodeling. Given the lack of valid markers of early endoderm, the identification of new ones is of fundamental importance. Both products of the Ink4a/Arf locus, in addition to being critical cell-cycle regulators, appear to be involved in several disease pathologies. Moreover, the locus’ expression is epigenetically regulated in ES reprogramming processes, thus constituting the ideal candidates to modulate PPCs homeostasis. In this study, starting from mouse embryonic stem cells (mESCs), we analyzed the early stages of pancreatic commitment. By inducing mESCs commitment to the pancreatic lineage, we observed that both products of the Cdkn2a locus, Ink4a and Arf, mark a naïve pancreatic cellular state that resembled PPC-like specification. Treatment with epi-drugs suggests a role for chromatin remodeling in the CDKN2a (Cycline Dependent Kinase Inhibitor 2A) locus regulation in line with previous observations in other cellular systems. Our data considerably improve the comprehension of pancreatic cellular ontogeny, which could be critical for implementing pluripotent stem cells programming and reprogramming toward pancreatic lineage commitment.


Introduction
Alterations in PPCs (Pancreatic Progenitor Cells) homeostasis are fundamental to physiological processes, such as organ development and pathological events. In particular, PPCs are essential for the maintenance and regeneration of organs and tissues that exhibit high rates of cell turnover or regenerative reserve. Interestingly, events associated with an early epithelial-to-mesenchymal transition (EMT) phenotype closely resemble PPCs cellular transition that occurs during normal pancreas embryogenesis [1,2]. Experiments on genetically engineered mice revealed that depletion of progenitor cells leads to acute or delayed failure in tissue homeostasis, limited regenerative potential, and physiological aging [3]. Besides physiological aging, senescence is a growth-arrest mechanism triggered by different insults to protect cells from hyper-proliferative signals and various forms of stress, representing an important barrier against tumor formation [3].
The CDKN2A locus encodes two tumor suppressors, p16INK4a (INK4a) and p14ARF (ARF), and is among the most frequently mutated in human cancers [4]. Inactivation of Arf and Ink4a in mice induces tumors with complete penetrance, while in several human cancers, both epigenetic silencing and mutational inactivation of these genes have been described [5]. Interestingly, the locus is found mutated or epigenetically silenced in 30-70% of PanINs (pancreatic intraepithelial neoplasms), a percentage that becomes as high as 95% in full-blown tumors [6]. Asides from being involved in cancer, both INK4a and ARF are involved in differentiation, apoptosis, and senescence in a number of cellular contexts [7,8]. Interestingly, both INK4a and ARF are expressed during pancreas organogenesis and are tightly correlated with PPCs' quiescence [9]. Several lines of evidence suggested that increased transcription of INK4A and ARF provokes senescence in various cell types with a causative role in age-associated degenerative diseases. Hence, the comprehension of the mechanisms regulating the expression of these genes has major implications for both cancer and degenerative disorders. In beta cells, it is known that the lack of INK4a expression leads to the overexpression of CDK4 and consequently to an increase in cell proliferation, rising insulin secretion, and causes pancreatic hyperplasia [9]. Germline CDKN2A mutations have also been occasionally found in pancreatic cancer patients and families without familial melanoma, in which the locus involvement has been described in several systems [10][11][12]. Variants of CDKN2A/B are involved in susceptibility to type 2 diabetes highlighting its possible role in Beta-cell function and regeneration [13]. Besides their function as a barrier to tumor progression, a number of studies demonstrated that both proteins are implicated in developmental processes [7].
In this study, we followed the Ink4a/Arf locus expression during pancreatic commitment in mouse ESC. We provide data showing that upon mESCs differentiation in vitro, Ink4a/Arf expression sharply increases both at a transcriptional and protein level. In particular, both ARF and INK4a are expressed during the early stages of murine endoderm specification in a subset of cells marked by the expression of the Nepn (Nephrocan) gene at E7.5-11.5 of mouse development. Furthermore, mESCs treatment with 5-aza-2deoxyazacytidine (AZA) and trichostatin (TSA), in addition to allowing the expression of PPC markers, also induce an increase in Ink4a/Arf gene expression, thus suggesting that an epigenetic-dependent mechanism controls Cdkn2a locus remodeling activated during PPCs differentiation.

qPCR Analysis
Total RNA was isolated from cells using Trizol (Sigma) according to the manufacturer's protocol and quantified by measuring absorption at 260 and 280 nm by Nanodrop. Purity was evaluated by gel electrophoresis and A260/A280 ratio calculation. One µg of total RNA was reverse transcribed into cDNA using iScript cDNA Synthesis Kit (Bio-Rad Laboratories, Hercules, CA, USA), according to manufacturer's protocol. Two µL of diluted cDNA preparation (equivalent to 20 ng of starting RNA) was used as a template for the qPCR analysis.
qPCR was performed in duplicate with the SYBR Green PCR Master Mix using a 7500 Real-Time PCR System machine (Applied Biosystems, Waltham, MA, USA). Quantitative relative expression was calculated according to the 2-DDCt method (Delta Ct method), normalizing to Gapdh. All the genes analyzed and primer sequences used in the reactions are listed in Table 1. Sry-Box transcription factor 9 GGTCTGCCTGGACTGTATGTGGATG CTGTCCGATGTCTCTCTGCAGGAG Sox17 Sry-Box transcription factor 17 GCCGATGAACGCCTTTATGGTG CATGCGCTTCACCTGCTTGC

Western Blot Analysis
Total proteins were extracted using 4× Laemmli Sample Buffer with the addition of 1 mM DTT (Dithiothreitol). Subcellular fractionation was carried out as described in [18]. Protein concentration was determined using the Bio-rad protein assay, and after denaturation at 90 • C for 10 min, equal amounts of proteins were electrophoretically separated through 13% SDS polyacrylamide gels transferred on polyvinylidene difluoride (PVDF) membranes. The membranes were blocked with 5% non-fat milk and probed with primary antibodies overnight at 4 • C with a gentle shaker, followed by incubation with HRP-conjugated secondary antibodies for 2 h at room temperature (RT). Proteins were detected by the ECL system (BioRad), and images were taken with ChemiDoc XRS System (Bio-Rad Laboratories) and quantified with densitometric analysis by Image J Software. Total protein extracts were normalized to Gapdh, while to verify the purity of the subcellular fractionation, Parp1 and Gapdh were used respectively as nuclear and cytoplasmic markers. The antibodies rabbit anti-p19Arf (Cayman Chemical, Ann Arbor, MI, USA), rabbit anti-p16Ink4a (Sigma Aldrich, Munich, Germany), anti-Parp1 (Cell Signalling, Danvers, MA, USA), and mouse anti-Gapdh (Santa Cruz Biotech, Dallas, TX, USA) were used in this study.

Statistics
All statistical analyses were performed using a one-way ANOVA test. Data are expressed as means ± standard deviation (SD). All experiments were repeated at least three times. A p value < 0.05 was considered to be statistically significant.

Ink4a/Arf Gene Expression Increases in mESCs Induced to Differentiate towards Pancreatic Lineage
Using an established differentiation protocol [15], E14 mouse ESCs were induced to differentiate into pancreatic progenitors. In particular, mESCs cells expressing Oct4 and Nanog marked as D0 were grown in matrigel and activin A until the expression of the DE markers Foxa2 and Sox17 (typically 4 days, indicated herein as D4). These cells were further treated for 4 days with RA and FGF10 to induce the expression of molecular markers such as such as Hnf6, Sox9, and Nkx6.1 that are typical of the PFE. These cells are highly enriched in PPCs (herein indicated as D8) and represent a good in vitro model to investigate the molecular mechanisms that occur during pancreatic differentiation ( Figure 1). We thus analyzed the level of expression of the Ink4a/Arf locus' products evaluating both the mRNA and protein levels of Ink4a and Arf by qPCR and Western blot. A transcriptional analysis of Ink4a and Arf genes showed that their expression increases as long as the cell's differentiation proceeds toward the PPC's lineage. The Ink4a gene expression We thus analyzed the level of expression of the Ink4a/Arf locus' products evaluating both the mRNA and protein levels of Ink4a and Arf by qPCR and Western blot. A transcriptional analysis of Ink4a and Arf genes showed that their expression increases as long as the cell's differentiation proceeds toward the PPC's lineage. The Ink4a gene expression significantly increased at DE (D4) by around 20 times compared to the control (D0), while in PFE (D8), its transcriptional expression was increased by nearly 200 times compared to the control (Figure 2A).  Arf gene expression mirrors the kinetics of Ink4a. While remaining similar between D4 and D0, the transcript's level is significantly increased by 20 times in D8. Quantification of Ink4a and Arf immunoblots showed a sharp increase of both proteins in D8 compared to D0 (see graphs in Figure 2B). The immunofluorescence staining confirmed an increased expression of both proteins in D8 ( Figure 2C and Figure S2). These results were further confirmed for both proteins by nuclear/cytoplasmic fractionation in D0 and D8 ( Figure 2D). Ink4a appeared poorly expressed in D0, acquiring a clear cytoplasmic localization in D8 ( Figure S1). On the other end, Arf showed a sharp increase both in the nucleus and cytoplasm in D8 ( Figure 2D and Figure S3).

Ink4a/Arf Gene Expression Correlates with Endoderm-Nepn Cells
It has been shown that the Nepn gene marks the early stages of murine endoderm specification and is required for correct endoderm differentiation [14,15]. To further characterize the kinetics of the Ink4a and Arf expression in our cellular system, we differentiated ES cells as described before and analyzed the locus' expression in a pure subpopulation of Nepn expressing cells. Differentiating cells were sorted by FACS in order to obtain a population enriched in Nepn expressing progenitor cells. When we analyzed Cdkn2a's transcript levels by qPCR, we found a significant enrichment of both Ink4a and Arf expression in Nepn-sorted cells. Moreover, a comparison of the expression level dynamics strongly suggests that the locus expression is confined in the Nepn+ cell state (Figure 3). Arf gene expression mirrors the kinetics of Ink4a. While remaining similar between D4 and D0, the transcript's level is significantly increased by 20 times in D8. Quantification of Ink4a and Arf immunoblots showed a sharp increase of both proteins in D8 compared to D0 (see graphs in Figure 2b). The immunofluorescence staining confirmed an increased expression of both proteins in D8 (Figures 2c and S2). These results were further confirmed for both proteins by nuclear/cytoplasmic fractionation in D0 and D8 ( Figure  2d). Ink4a appeared poorly expressed in D0, acquiring a clear cytoplasmic localization in D8 ( Figure S1). On the other end, Arf showed a sharp increase both in the nucleus and cytoplasm in D8 (Figures 2d and S3).

Ink4a/Arf Gene Expression Correlates with Endoderm-Nepn Cells
It has been shown that the Nepn gene marks the early stages of murine endoderm specification and is required for correct endoderm differentiation [14,15]. To further characterize the kinetics of the Ink4a and Arf expression in our cellular system, we differentiated ES cells as described before and analyzed the locus' expression in a pure subpopulation of Nepn expressing cells. Differentiating cells were sorted by FACS in order to obtain a population enriched in Nepn expressing progenitor cells. When we analyzed Cdkn2a's transcript levels by qPCR, we found a significant enrichment of both Ink4a and Arf expression in Nepn-sorted cells. Moreover, a comparison of the expression level dynamics strongly suggests that the locus expression is confined in the Nepn+ cell state (Figure 3).

DNA Methylation and Chromatin Acetylation Affect Ink4a and Arf Gene Expression in ESCs
It is known that the Cdkn2a locus is not expressed in ES and in iPS (induced Pluripotent Stem) cells but acquires the epigenetic marks of a bivalent chromatin domain, thus retaining the ability to be reactivated if required after differentiation onset [19,20]. Epigenetic suppression of the INK4A-ARF locus has been widely shown, and greatly promotes survival and cloning efficiency in individualized human ESCs via deposition of the H3K27me3-mark to INK4A-ARF locus [21,22]. In order to verify if epigenetic modifications, specifically DNA methylation and chromatin deacetylation, were responsible for the Ink4a and Arf regulation in ESCs, we performed treatments of cells with widely used

DNA Methylation and Chromatin Acetylation Affect Ink4a and Arf Gene Expression in ESCs
It is known that the Cdkn2a locus is not expressed in ES and in iPS (induced Pluripotent Stem) cells but acquires the epigenetic marks of a bivalent chromatin domain, thus retaining the ability to be reactivated if required after differentiation onset [19,20]. Epigenetic sup-pression of the INK4A-ARF locus has been widely shown, and greatly promotes survival and cloning efficiency in individualized human ESCs via deposition of the H3K27me3mark to INK4A-ARF locus [21,22]. In order to verify if epigenetic modifications, specifically DNA methylation and chromatin deacetylation, were responsible for the Ink4a and Arf regulation in ESCs, we performed treatments of cells with widely used epidrugs. In particular, we used either the demethylating agent AZA or the HDAC inhibitor TSA. mESCs were treated with 25 µM AZA or with 100 nM TSA. Twenty-four hours post-treatments, Ink4a and Arf expression in mESCs cells was simultaneously analyzed by qPCR and Western blot. Before lysis, cells were observed by phase-contrast microscopy, and we noticed that cells treated with TSA, in contrast to AZA treated cells, acquired an elongated morphology (Figure 4A left). The analysis of pluripotency markers such as Oct4 and Nanog [23,24] and differentiation markers such as Nkx6.1 and Pdx1 [25] are in line with the epigenetic pattern of regulation of these genes suggesting the priming of a differentiation program ( Figure 4A right). epidrugs. In particular, we used either the demethylating agent AZA or the HDAC inhibitor TSA. mESCs were treated with 25 µ M AZA or with 100 nM TSA. Twenty-four hours post-treatments, Ink4a and Arf expression in mESCs cells was simultaneously analyzed by qPCR and Western blot. Before lysis, cells were observed by phase-contrast microscopy, and we noticed that cells treated with TSA, in contrast to AZA treated cells, acquired an elongated morphology (Figure 4a left). The analysis of pluripotency markers such as Oct4 and Nanog [23,24] and differentiation markers such as Nkx6.1 and Pdx1 [25] are in line with the epigenetic pattern of regulation of these genes suggesting the priming of a differentiation program (Figure 4a right).  While we found that both treatments significantly increase both Ink4a and Arf transcriptional levels, analysis by Western blot revealed a significant increase only upon TSA treatment ( Figure 4B,C and Figure S4).

Discussion
In this study, by using mouse embryonic stem cells induced to differentiate as a model system, we analyzed the expression of the Cdkn2a/Arf locus during pancreatic lineage commitment. Western blot and immunofluorescence analysis confirmed an increase in both protein products. Interestingly, we found that Cdkn2a locus activation mainly takes place in cells expressing Nepn, a factor that marks the genesis of pancreas bud being expressed in a naïve pancreatic cellular state resembling PPC-like specification. To further confirm our data, we used data obtained by mRNA expression profiles of hPSCs differentiating along the pancreatic beta-cell linage [26]. Using repository data from GEO (http://www.ncbi.nlm.nih.gov/geo (accessed on 1 January 2021)) (GSE42094), we performed a bioinformatic analysis looking for both ARF and INK4a expression. This analysis showed the activation of the locus, in agreement with our results in mice, although with different kinetics (data not shown).
Physiological expression of ARF during development has been described in a precise time frame during the differentiation of several tissue types, such as the developing eye, spermatogonia [27], differentiating keratinocytes [28], epithelial derivative, and the yolk sac [29]. The transcriptional activation of these two tumor suppressors has been related to their function of monitoring and restricting aberrant mitogenic signals arising during cell differentiation. Several studies highlighted the importance of proper heterochromatin establishment to promote cell differentiation and the maintenance of cell identity during embryogenesis. Epigenetic regulation of chromatin structure has a key role in the control of cell differentiation and cell identity in embryogenesis. The INK4-ARF locus is epigenetically silenced thanks to the function of the Polycomb group of proteins [19,21] Importantly, repression of the Ink4a/ARF locus represents a roadblock during iPS (induced Pluripotent Stem Cells) generation [20,29], in line with the role of epigenetic regulation of this locus in ES cells homeostasis. While p16Ink4a and p19Arf induction in cultured primary cells cause senescence [30], Bmi-1 overexpression can prevent senescence and extend their replicative lifespan by reducing p16Ink4a and p19Arf expression [31]. Our results are in line with the epigenetic regulation of the locus. We observed that the treatment of undifferentiated cells with epigenetic drugs such as AZA and TSA, in addition to inducing some features of endoderm's differentiation, also induces the expression of both p16Ink4a and p19Arf, thus suggesting that an epigenetic remodeling of the locus could take place during pancreatic differentiation, in line with studies in other cellular systems [32]. Interestingly, ARF expression upon TSA treatment is characterized by the acquisition of an elongated cellular morphology. This observation, together with previously published data about ARF's role in cytoskeleton remodeling [18], suggests that ARF expression in pancreatic progenitors could have a role in this phenomenon. Besides, Ink4a and Arf ectopic expression correlates with a NeuroD1 increase, mainly involved in beta cells differentiation of pancreatic development [33], and p16Ink4a activation has been reported in human pluripotent stem cells (hPSCs) induced to differentiate into cardiomyocytes [34]. The CDKN2A locus has been shown to affect cell metabolism by influencing glucose homeostasis, β-cell functions and mass, hepatic gluconeogenesis, and lipid storage [35]. Genome-wide association studies (GWASs) have unequivocally linked the CDKN2A locus with human diabetes risk, although the mechanisms remain uncertain [21,[36][37][38][39]. Moreover, it is known that CDKN2A mutation occurs in early PDAC (pancreatic ductal adenocarcinoma) [40,41] and, CDKN2A promoter hypermethylation is related to malignant tumor development [42].
Our data are in agreement with those found in human ES during endodermalpancreatic differentiation, prompting us to think that the expression of Ink4a and Arf in PPC is due either to an organ regeneration mechanism or to a stress response. Given that alteration in PPCs homeostasis, besides being fundamental to physiological processes such as organ development, are also a key step in pathological events such as cancer, elucidation of the mechanisms governing tissues development is critical to understand the cause of organ disorders and essential for the development of new therapies focused on tissue and organ regeneration.
Supplementary Materials: The following are available online at https://www.mdpi.com/article/ 10.3390/biom11081124/s1, Figure S1: Full-length Western blots images of cropped immunoblots of Figure 2B, Figure S2: Immunofluorescence assays for Ink4 and Arf subcellular localization of Figure 2C, Figure S3: Full-length Western blots images of cropped immunoblots of Figure 2D, Figure