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CSK-homologous kinase (CHK/MATK) is a potential colorectal cancer tumour suppressor gene epigenetically silenced by promoter methylation

Abstract

Hyperactivation of SRC-family protein kinases (SFKs) contributes to the initiation and progression of human colorectal cancer (CRC). Since oncogenic mutations of SFK genes are rare in human CRC, we investigated if SFK hyperactivation is linked to dysregulation of their upstream inhibitors, C-terminal SRC kinase (CSK) and its homolog CSK-homologous kinase (CHK/MATK). We demonstrate that expression of CHK/MATK but not CSK was significantly downregulated in CRC cell lines and primary tumours compared to normal colonic tissue. Investigation of the mechanism by which CHK/MATK expression is down-regulated in CRC cells uncovered hypermethylation of the CHK/MATK promoter in CRC cell lines and primary tumours. Promoter methylation of CHK/MATK was also observed in several other tumour types. Consistent with epigenetic silencing of CHK/MATK, genetic deletion or pharmacological inhibition of DNA methyltransferases increased CHK/MATK mRNA expression in CHK/MATK-methylated colon cancer cell lines. SFKs were hyperactivated in CHK/MATK-methylated CRC cells despite expressing enzymatically active CSK, suggesting loss of CHK/MATK contributes to SFK hyperactivation. Re-expression of CHK/MATK in CRC cell lines led to reduction in SFK activity via a non-catalytic mechanism, a reduction in anchorage-independent growth, cell proliferation and migration in vitro, and a reduction in tumour growth and metastasis in a zebrafish embryo xenotransplantation model in vivo, collectively identifying CHK/MATK as a novel putative tumour suppressor gene in CRC. Furthermore, our discovery that CHK/MATK hypermethylation occurs in the majority of tumours warrants its further investigation as a diagnostic marker of CRC.

Introduction

Hyperactivation of SRC-family tyrosine kinases (SFK), including SRC, YES and HCK, has been implicated in the initiation and progression of human colorectal cancers (CRCs) [1,2,3]. However, activating mutations of SFK genes are rare [4], suggesting that their hyperactivation in CRCs involves other mechanisms. In some CRCs, hyperactivation of SRC results from gene amplification leading to elevated SRC expression [5] or from increased expression of the upstream activator PTP1B [6]. Another mechanism that may drive SFK hyperactivation is the altered expression and/or dysregulation of their upstream inhibitors. However, the contribution of this mechanism to SFK hyperactivation in CRC is poorly understood.

Under physiological conditions, SFK activity in mammalian cells is restrained by their upstream inhibitors, C-terminal Src kinase (CSK) and CSK-homologous kinase (CHK, CTK or MATK, referred to as CHK/MATK herein) [7,8,9]. Dysregulation of these inhibitors can cause SFK hyperactivation, which may contribute to the development and progression of multiple types of cancer (reviewed in [10]). For example, expression of CSK-binding protein (Cbp/PAG1), a membrane-bound docking protein of CSK, is suppressed in several colorectal cancer cell lines [11]. Cbp/PAG1 recruits CSK from the cytosol to the plasma membrane, facilitating CSK phosphorylation and inhibition of SFKs [12]. Down-regulation of Cbp/PAG1 therefore attenuates the efficiency of CSK-mediated inhibition of SFKs. Besides dysregulation of CSK, down-regulation of CHK/MATK may contribute to the hyperactivation of SFKs in cancer cells [11].

The activity of human SFKs is regulated primarily by their conserved autophosphorylation sites (e.g. Y419 of SRC) in the activation loop of the kinase domain [13], and inhibitory phosphorylation sites (e.g. Y530 of SRC) in their C-terminal tail (Fig. 1A) [14]. Autophosphorylation stabilises the SFK kinase domain in the active conformation [13, 15]. In contrast, phosphorylation of the C-terminal tail tyrosine triggers its intra-molecular binding to the SH2 domain, thereby stabilising SFKs in the closed inactive conformation [16]. CSK and CHK/MATK are the major upstream kinases that phosphorylate this C-terminal tail tyrosine in SRC [9, 17]. Conversely, protein tyrosine phosphatase PTP1B (encoded by the PTPN1 gene) acts as an upstream activator of SFKs by dephosphorylating this C-terminal tail tyrosine [18]. Expression of PTP1B is increased in CRC and reported to contribute to CRC development and progression [6, 19]. In addition to phosphorylation, direct binding of CHK/MATK also suppresses the activity of all SFKs via a non-catalytic mechanism [17, 20, 21]. Thus, CHK/MATK is considered a versatile SFK inhibitor capable of inhibiting all active conformations of SFKs by direct binding and/or phosphorylation of the C-terminal tail tyrosine [10]. We previously demonstrated that CHK/MATK but not CSK expression is suppressed in the DLD-1 CRC cell line [20, 22], and that re-expression of CHK/MATK suppressed SRC activity in these cells [20] via the non-catalytic mechanism [20]. These findings provide preliminary evidence supporting the role of CHK/MATK as a potential tumour suppressor in CRC cells.

Fig. 1: CHK/MATK expression is suppressed in colorectal tumours.
figure1

A Mechanisms of upstream regulation of SRC. SRC and other SFKs are activated by autophosphorylation at a consensus site (Y419 of SRC) in the kinase domain and inhibited by phosphorylation of a conserved site near the C-terminus (Y530 of SRC). Both CSK and CHK/MATK are endogenous inhibitors of SRC that phosphorylate Y530. PTP1B activates SRC by dephosphorylating Y530. Besides phosphorylating Y530, CHK/MATK also inhibits SRC by a non-catalytic inhibitory mechanism mediated by direct binding to the SRC kinase domain [17, 20, 21]. B mRNA expression levels of cell proliferation markers MKI67, measured with probe A (NM_002417) and probe B (NM_001145966); MYC, measured with the probe (NM_002467); and PCNA, measured with probe A (NM_002592) and probe B (NM_182649). C mRNA expression levels of CSK measured with probe A (NM_004383) and probe B (NM_001127190), and PTPN1 measured with the probe (NM_002827). D mRNA expression level of CHK/MATK measured with probe A (NM_139355), probe B (NM_002378) and probe C (NM_139354). Multiple probes were used to investigate the expression of MKI67, PCNA and CHK/MATK as there are more than one transcript variants to encode these proteins. The mRNA expression levels were determined by RNA-seq. E Log transformed copy number (CPM) of CHK/MATK, CSK and PTPN1 in CRC tumours versus normal biopsies of 50 tumour/normal pairs documented in TCGA. For the results shown in panels B, C and D, RNA was extracted from tissues obtained from 13 colorectal tumours and matched normal pairs and subsequently subjected to RNA-seq analysis. The expression levels of SRC upstream regulators and cell proliferation markers are presented as the number of copies per 10,000 copies of ACTB mRNA.

In the present study, we investigated the prevalence of CHK/MATK down-regulation in multiple CRC cell lines and patient tumour biopsies, and elucidated the mechanism driving the suppression of CHK/MATK expression in CRC cells. Specifically, we demonstrate that down-regulation of CHK/MATK expression is associated with promoter methylation, and that treatment of CHK/MATK-hypermethylated CRC cell lines with a DNA methylation inhibitor significantly increased CHK/MATK mRNA expression. Consistent with our previous observations in DLD-1 CRC cells [20], re-expression of CHK/MATK inhibited SRC activity in HCT116 CRC cells, and suppressed cell proliferation, anchorage-independent growth and migration in vitro, and tumour growth in vivo, supporting the notion that CHK/MATK exerts tumour suppressive activity in CRC cells. Taken together, our findings implicate CHK/MATK as a potential colorectal tumour suppressor that is epigenetically silenced in CRC cells. We also demonstrate CHK/MATK promoter hypermethylation as a common phenomenon in multiple solid tumours, suggesting that our findings may be relevant across a broad tumour spectrum.

Results

CHK/MATK mRNA expression is suppressed in primary colorectal cancers

To investigate if SFK hyperactivation in CRCs is associated with altered expression of their upstream regulators, we examined mRNA expression of CSK, CHK/MATK and PTPN1 (which encodes PTP1B protein) in a RNA-seq dataset generated from 13 colorectal tumours and matched normal samples (Fig. 1). Expression of the cell proliferation markers MKI67 and PCNA as well as that of MYC were also assessed to confirm the tumour samples were enriched for tumour cells. As expected, levels of MKI67, PCNA and MYC were highly elevated (~78, 23 and 19-fold respectively) in the tumour compared to adjacent normal tissue (Fig. 1B). Of the three upstream SFK regulators examined, a modest (~1.2-fold) but significant increase (p value < 0.01) in expression of PTPN1 mRNA was detected in the tumour as compared to normal samples, while no difference was observed for expression of CSK (Fig. 1C). In contrast, expression of all three CHK/MATK transcript variants was significantly reduced by an average of ~16-fold (p value < 0.05) in tumour compared to matched normal tissue, with down-regulation observed in the tumour in nine of the 13 (69%) tumour/normal pairs (Fig. 1D). To further verify these observations, we examined mRNA levels of CHK/MATK, CSK and PTPN1 in 50 CRC tumour/normal pairs documented in TCGA (The Cancer Genome Atlas Consortium). Consistent to what was found with our CRC patient cohort, CHK/MATK was significantly down-regulated in the tumours in ~76% of the CRC tumour/normal pairs while no difference in CSK expression was found between tumour and normal specimens in the TCGA CRC cohort (Fig. 1E). Taken together, these results indicate that reduced expression of CHK/MATK is a frequent event in human CRCs, suggesting that it potentially contributes to hyper-activation of SFKs in these tumours.

To examine the expression pattern of CHK/MATK in normal intestinal mucosa cells, immunohistochemical staining of tissue sections from macroscopically healthy human colonic epithelium was performed using a specific monoclonal antibody recognising CHK/MATK. Results from IHC analysis indicated that CHK/MATK protein expression is enriched in a small number of epithelial cells located in the lower half of human colonic crypts (Figure S1A). To further define the identity of these cells, we then analysed the single cell RNA-seq data from purified cell populations isolated from the mouse intestinal epithelium, as described by Yan et al. and Haber et al. [23, 24]. Interrogation of these data revealed CHK/MATK mRNA was highly expressed in tuft cells (Figure S1B, C and Tables S1 and S2), a rare population of secretory cells which act as chemosensory sentinels in the colonic epithelium, relaying signals from a range of luminal substances to trigger immunological or neuronal responses [25]. Besides expression in tuft cells, CHK/MATK mRNA expression was also detected in a small number of other normal colonic epithelial cell types, including enterocytes, enteroendocrine cells, goblet cells, transit amplifying cells, intestinal stem cells and Paneth cells (insets of Fig. S1B, C, and Tables S1, S2).

SRC is hyperactivated in colorectal cancer cells despite the presence of active CSK

To further explore the mechanisms underlying SFK hyperactivation, we assessed mRNA levels of CSK and CHK/MATK in a panel of 35 human CRC cell lines using data from in-house Affymetrix gene expression arrays as well as those of a panel of 52 CRC cell lines determined by RNAseq (Figs. 2A and S2). CSK mRNA levels were much higher than those of CHK/MATK in all CRC cell lines examined (Figs. 2A and S2), suggesting that as in primary CRCs, expression of CHK/MATK but not CSK is selectively suppressed in CRC cell lines.

Fig. 2: Down-regulation of CHK/MATK expression correlates with activation of Src in colorectal cancer cell lines.
figure2

A Comparison of CHK/MATK and CSK mRNA levels in a panel of 35 colorectal cancer cell lines determined by our in-house Affymetrix gene expression array analysis. Cell pellets from each exponentially growing (>80% confluent) tumour cell line were pooled. RNA was extracted and subsequently subjected to Affymetrix gene expression array analysis. B The specific enzymatic activity of SRC immunoprecipitated from lysates of colorectal cancer cell lines including HCT116, SW620, CaCo2 and TC71 cells. The activity of SRC in the immunoprecipitates was determined by kinase assay using the SRC optimal peptide as substrate. The kinase activity of SRC in the immunoprecipitates are presented as mean specific enzymatic activity ± standard deviation. The dotted line shows the specific kinase activity of recombinant SRC (Recomb. SRC) (0.876 ± 0.19 pmol phosphate incorporated per min per ng of SRC) determined in the same assay with those of SRC isolated from the four cell lines. Its activity was also presented in our previously published manuscript [20]. Three technical replicates (n = 3) per cell line were used in the assay. C Western blots demonstrating expression of CSK in a panel of CRC cells and K562 leukemic cells. D Demonstration that CSK in colorectal cancer cells is catalytically active. Left panel: work flow. Right upper panel: ip: anti-CSK/WB: anti-CSK: Western blot confirming the presence of CSK in the immunoprecipitates derived from HCT116 and SW620 cells but not in the IgG-only precipitate (negative control). Right lower panel: autoradiogram (Autorad.) showing the time-dependent changes in phosphorylation of kinase-dead recombinant SRC (Recomb-SRC[KD]) by CSK immunoprecipitated (CSK ip) from HCT116 and SW620 cell lysates. Recomb-SRC[KD] (0.25 μM) was incubated with CSK ip in the presence of assay buffer and 250 μM of [γ-32P]ATP for 10, 20 and 60 min.

To establish if suppression of CHK/MATK expression contributes to hyperactivation of SFKs in CRC, we examined the activity and expression of the SFK member SRC, and the upstream inhibitory kinases CSK and CHK/MATK in four CRC cell lines. SRC was isolated from lysates of the four cell lines by immunoprecipitation, and its enzymatic activity was determined by in vitro kinase activity assay (Figs. 2B and S3A) as described in our previous report [20]. The specific enzymatic activities of SRC isolated from these CRC cell lines were compared with that of the active recombinant SRC. Figure 2B shows that the specific enzymatic activities of SRC isolated from CRC cell lines were 2 to 4-fold higher than that of active recombinant SRC, with the exception of TC71 cells. Even though the activities of SRC isolated from TC71 cells was about ≈80% of that of active recombinant SRC, it was still significantly higher than that of the recombinant SRC with Y530 phosphorylated by CSK (pY530-SRC), which was found to be less than 20% of that of recombinant SRC activity [26, 27]. Taken together, these results show that SRC activity in the selected CRC cell lines was significantly higher than that exhibited by pY530-SRC, which adopts a closed inactive conformation [16].

Aside from suppressed CHK/MATK expression, inactivation of CSK could also be a potential mechanism of SRC hyperactivation in CRC cells. To determine if CSK expressed in CRC cell lines is catalytically active, we isolated it from HCT116 and SW620 cell lysates by immunoprecipitation, and measured its ability to phosphorylate kinase-dead recombinant SRC mutant (recomb-SRC[KD]) in vitro (Figs. 2C, D and S3B). Since recomb-SRC[KD] cannot undergo autophosphorylation, its phosphorylation in the presence of the immunoprecipitated CSK measures the efficiency of CSK in phosphorylating the C-terminal tail tyrosine (Y530) of SRC. As shown in Fig. 2D, CSK immunoprecipitated from HCT116 and SW620 cells could readily phosphorylate the recomb-SRC[KD], indicating CSK is catalytically active in these cells. Hence, despite the presence of catalytically active CSK, SRC activity remained hyper-activated in CRC cell lines. These findings suggest that down-regulation of CHK/MATK could be a major cause of hyperactivation of SFKs in CRC cells.

The promoter of CHK/MATK is hypermethylated in human colorectal tumours and cell lines

Mutation, focal deletion or promoter hypermethylation-mediated epigenetic silencing are responsible for the inactivation or down-regulation of many tumour suppressor genes in cancer cells. Analysis of our previously generated Affymetrix SNP array data [28] revealed that deletions of the CHK/MATK gene locus are infrequent in CRC cell lines (Fig.S4), with only 4 out 31 cell lines (~13%) harbouring potential deletion events. In addition, interrogation of the publicly available TCGA dataset [29] revealed that >99% (255 out of 257) of primary CRCs displayed a normal copy number for CHK/MATK, demonstrating that focal deletion or loss of heterozygosity (LOH) are not the likely cause of CHK/MATK down-regulation in human CRCs.

To determine if promoter hypermethylation is involved in CHK/MATK down-regulation, we examined the methylation status of the CHK/MATK promoter by bisulfite sequencing of DNA extracted from four representative CRC cell lines (HCT116, DLD1, HuTu80 and TC71). Bisulfite sequencing primers were designed to interrogate the methylation status of 38 CpG sites within a 277 bp region of the CHK/MATK gene promoter spanning −92 bp downstream of the transcription start site (TSS) to +185 bp upstream of the TSS (Fig. 3A and Table S3). These analyses demonstrated that the CHK/MATK promoter was heavily hypermethylated in all four CRC cell lines examined, with the average absolute methylation level ranging from 90.4 to 92.1% (Fig. 3B).

Fig. 3: The CHK/MATK promoter is heavily methylated in four representative colorectal cancer cell lines.
figure3

A Schematic diagram showing the location of the 38 CpG dinucleotides interrogated by bisulphite sequencing. All sites are located within the CHK/MATK promoter between positions −107 to +130, in relation to the transcription start site (i.e. +1 position). Each bar represents a CpG. The location of the four CpG sites interrogated by qMS-PCR are represented by red bars. B Results from bisulphite sequencing of four CRC cell lines presented as a lollipop diagram where each circle represented a CpG in the PCR product. Closed circles indicate methylated CpGs and open circles indicate unmethylated CpGs. Black arrow indicates location of the transcription start site and red arrows indicate CpGs examined by qMS-PCR. BS bisulphite sequencing, qMSP quantitative methylation specific PCR.

Based upon the patterns of hypermethylation of this region of the CHK/MATK promoter in these four CRC cell lines, we next developed a quantitative methylation specific-polymerase chain reaction (qMS-PCR) assay to interrogate the CHK/MATK promoter methylation status in a larger cohort of CRC cell lines and primary tumours (Fig. 4). As CHK/MATK is expressed at high levels in hematopoietic cells [30, 31], the human leukemic K562 cells were used as a positive control. The CHK/MATK promoter was found to be hypermethylated in all 22 CRC cells lines examined, but not in K562 cells (Figs. 4A and S5). We also analysed the PCR products generated from representative CRC cell lines by DNA agarose gel electrophoresis, which confirmed selective amplification of the methylated (M) allele in CRC cell lines, and the selective amplification of the unmethylated (U) allele in CHK/MATK-expressing K562 cells (Fig. 4B).

Fig. 4: Quantitative MS-PCR analysis showing CHK/MATK promoter hypermethylation in a panel of CRC cell lines and increased CHK/MATK promoter methylation in primary colorectal cancers.
figure4

A, B Mean methylation status of four CpG sites (depicted as red vertical lines in Fig. 4A) within the CHK/MATK promoter determined by qMS-PCR assay in 22 CRC cell lines and K562 leukemic cells. U: unmethylated, M: methylated. For LoVo, HuTu80, K562, only one data point is available because no amplification was detected in the second replicate. Amplified PCR fragments were run on 1% DNA agarose for the confirmation of successful PCR amplifications from the bisulphite treatment genomic DNA (panel B). U: unmethylated, M: methylated. C Methylation status of CHK/MATK promoter in primary CRCs and that of the matched normal tissues determined by bisulphite conversion and qMS-PCR analysis (p < 0.0001; two-tailed pair t-test, normal distribution).

Having established the robustness of the qMS-PCR assays, we next examined the relative methylation status of the CHK/MATK promoter in 15 human CRCs and matched normal tissues. A significant increase in CHK/MATK promoter methylation was observed in the tumour compared to the normal tissue in 13 of 15 (87%) cases (Fig. 4C), demonstrating that CHK/MATK promoter methylation is a common feature of human CRC.

Finally, we investigated methylation data available through the TCGA (The Cancer Genome Atlas Consortium) [29], where Illumina Infinium HumanMethylation450 BeadChips were used to profile 274 colorectal cancer and 25 normal colon mucosa specimens. Specifically, we interrogated multiple CpG sites that encompass and span the CHK/MATK promoter, as well those from neighbouring genomic regions (Fig. 5A), using the MethHC database [32]. Significantly increased methylation (30–40% increase) in tumours relative to normal colon mucosa was observed at the CHK/MATK promoter (CpG island, TSS 200 bp) and the immediate neighbouring regions (5′ UTR, first exon, TSS 1500 bp). Using the averaged CHK/MATK promoter methylation (CpG island or TSS 200 bp) from normal colon mucosa specimens as a reference, 94.5% and 92.3% of colorectal tumours harboured hypermethylation of the CpG island and TSS region of CHK/MATK promoter, respectively. Comparatively, no difference in methylation of CHK/MATK was observed in CpGs located within enhancer, 3′ UTR, CpG shore or shelf regions (Fig. 5B, C). In contrast to the hypermethylation of the CHK/MATK promoter, CSK promoter hypermethylation was not detected in the same colorectal tumour biopsies (Figure S6). Together, our results indicate that CHK/MATK promoter hypermethylation is a frequent event in human CRCs, with ≥90% of tumours hypermethylated.

Fig. 5: CHK/MATK hypermethylation in colorectal cancers occurs primarily at the gene promoter and flanking regions.
figure5

A Schematic diagram showing the location of CpG dinucleotides (represented as open lollipops) located in the different parts of the CHK/MATK gene. B The MethHC online bioinformatics tool was used to analyse (TCGA) CHK/MATK methylation status in 274 colorectal tumours and 25 normal colon tissues analysed by The Cancer Genome Atlas COAD (colon adenocarcinoma) project. The absolute methylation levels of CpG dinucleotides in each part of the CHK/MATK gene were averaged. Data points from individual tumour samples were subtracted from the averaged methylation level obtained from normal samples and plotted in a box-a-whisker plot (turkey). C CpG methylation in different parts of the gene. Individual data points from each colorectal tumour or normal sample were plotted in a box-and-whisker plot (Tukey). TSS transcription start site, UTR untranslated region, TSS 200 200 base pairs upstream to transcription start site, TSS 1500 1500 base pairs upstream to transcription start site.

Genetic or pharmacological inhibition of DNA methyltransferases (DNMTs) restores CHK/MATK mRNA expression in CRC cells

Having established an association between CHK/MATK promoter methylation and loss of expression, we next sought to restore CHK/MATK mRNA expression by reversing DNA methylation. To determine if expression of CHK/MATK is re-induced upon treatment with a DNA methyltransferase inhibitor, we treated four representative CRC cell lines with high CHK/MATK promoter methylation (HCT116, DLD1, RKO and LIM2405), with the DNA methyltransferase inhibitor 5-Aza-2′-deoxycytidine (5-Aza-dC) (Fig. 6A). In each case, 5-Aza-dC induced a dose-dependent increase in CHK/MATK expression, confirming the functional importance of DNA methylation-mediated epigenetic silencing as a cause in down-regulating CHK/MATK gene expression in CRC cells.

Fig. 6: Treatment of colorectal cancer cells with the demethylating agent 5-Aza-2′-deoxycytidine (Aza-dC) induces de-repression of CHK/MATK expression.
figure6

A Four colorectal cancer cell lines HCT116, DLD1, RKO and LIM2405 were treated with or without 5-Aza-dC for 72 h at the indicated doses (0.1–1.0 µM). Changes in mRNA expression of CHK/MATK were determined by qRT-PCR analysis. Data shown are mean ± SD of a single experiment analysed in triplicate. B Mean methylation status of four CpG sites (depicted as red vertical lines in Fig. 4A) within the CHK/MATK promoter determined by qMS-PCR assay in wild type (HCT116 PAR) and DMNT1/DMNT3B double knockout isogenic HCT116 cells (HCT116 DKO). U: unmethylated, M: methylated. C Determination of the methylation status of the loci of CHK/MATK promoter of HCT116 PAR and HCT116 DKO cells amplified as shown in Fig. 7A by DNA agarose gel electrophoresis analysis. U: unmethylated, M: methylated. D mRNA levels of CHK/MATK in HCT116 PAR and HCT116 DKO cells determined by quantitative real time PCR (qRT-qPCR) analysis and expressed as number of copies of CHK/MATK mRNA per 10,000 copies of ACTB mRNA. E Protein expression of endogenous CHK/MATK, recombinant CHK-GFP, CSK and Src in HCT116-PAR, HCT116-DKO, HCT116-GFP and HCT116-CHK-GFP cells.

We next used a genetic model of HCT116 colon cancer cells in which global DNA methylation is reduced by >95% by combined deletion of DNA methyltransferase 1 and 3B (DNMT1 and DNMT3B) (HCT116-DKO) [33]. Comparison of the CHK/MATK promoter methylation status in HCT116 parental (HCT116-PAR) and HCT116-DKO cells revealed complete promoter methylation in HCT116 PAR cells, while both the methylated and unmethylated alleles were detected in HCT116 DKO cells (Figs. 6B, C and S5), indicating knockout of DNMT1 and DNMT3B in HCT116 cells results in partial demethylation of the CHK/MATK promoter. Examination of corresponding CHK/MATK mRNA expression revealed a >50-fold increase in expression in HCT116-DKO cells relative to HCT116 PAR cells (Fig. 6D), although this was not sufficient to induce detectable CHK/MATK protein expression (Fig. 6E).

Hypermethylation of the CHK/MATK promoter occurs in multiple other tumours

As SFK hyperactivation is a common occurrence in other tumour types, we also examined the promoter methylation status of CHK/MATK in 18 common tumour types (including CRCs) using data deposited by the TCGA. In addition to CRCs, seven other tumour types (renal, pancreatic, liver, head and neck, breast, lung and bladder) displayed significantly increased CHK/MATK promoter methylation in tumours compared to their corresponding normal tissues (p value < 0.001) (Figure S7A). Furthermore, in each of these cases, CHK/MATK mRNA expression inversely correlated with the extent of promoter methylation (Figure S7B), suggesting gene promoter methylation also contributes to down-regulation of CHK/MATK expression in the cancer cells of these seven tumour types.

Re-expression of CHK/MATK inhibits SFK activity, anchorage-independent growth, cell migration and proliferation of CRC cells in vitro and growth and survival of CRC cells in vivo

To examine the functional consequences of suppressed CHK/MATK expression in CRC cells, we generated a pair of isogenic HCT116 cell lines, which expressed a GFP fusion protein of CHK/MATK (CHK-GFP) or GFP under the control of a doxycycline-inducible promoter. Expression of CHK-GFP was induced within 24 h of doxycycline treatment and sustained over 72 h (data not shown). Figure 7A shows expression of CHK-GFP in HCT116-CHK-GFP cells but not in HCT116-GFP cells at 48 h after Dox induction. Expression of CHK-GFP, but not GFP, significantly reduced the kinase activity of SRC (Fig. 7B). Notably however, the re-expression of CHK/MATK did not alter the level of SRC autophosphorylation (at Tyr-419) or the level of SRC phosphorylation at the C-terminal tail tyrosine (Tyr-530) (Fig. 7A), suggesting that the reduction in Src kinase activity was not caused by enhanced phosphorylation of Tyr-530 by CHK-GFP. Instead, the reduced Src kinase activity is likely caused by the non-catalytic inhibitory mechanism of CHK-GFP, which we have previously demonstrated in DLD-1 cells [17, 20].

Fig. 7: Effects of expression of recombinant CHK/MATK on Src kinase activity and phosphorylation state of HCT116 CRC cells.
figure7

A HCT116-GFP and HCT116-CHK-GFP cells were treated with 5 μg/ml doxycycline (Dox) for 48 h to induce expression of CHK-GFP. The expression levels of CHK-GFP (~83.5 kDa), SRC and tubulin were monitored by Western blotting. The levels of phosphorylation of SRC at the autophosphorylation site (pY419) and at Tyr-530 (pY530) were monitored by the corresponding phosphospecific antibodies. B SRC was immunoprecipitated from the transduced HCT116 cell lines with and without induction by Dox (+Dox and −Dox). Its specific enzymatic activity in the immunoprecipitates was determined using Src-optimal peptide as the substrate.

Importantly, re-expression of CHK/MATK in HCT116 colon cancer cells inhibited cell migration (Fig. 8A), colony formation in soft agar (Figs. 8B and S8) and cell proliferation (Fig. 8C). Similar effects on SRC kinase activity, colony formation and proliferation were observed in DLD1 cells engineered to re-express CHK/MATK (Figure S9). To ascertain the effect of re-expression of CHK/MATK in vivo, HCT116-CHK-GFP cells were injected into the pericardial cavity of Casper zebrafish embryos prior to treatment with doxycycline for 72 h to induce expression of CHK-GFP. As shown in Fig. 8D, re-expression of CHK-GFP significantly reduced the number of surviving CRC cells at the injection site and in micrometastatic lesions that has seeded in caudal hematopoietic tissue in the tail region of the embryos.

Fig. 8: Effects of expression of recombinant CHK/MATK in HCT116 CRC cells on cell migration, anchorage-independent growth and proliferation in vitro and on growth and survival in vivo in zebrafish xenograft.
figure8

A Analysis of migration of HCT116-GFP and HCT116-CHK-GFP migration assessed by in vitro transwell assay. Cells were treated for 72 h with doxycycline to induce expression of GFP and CHK-GFP prior to the assay. Representative images of migrated crystal violet stained cells captured at 24 h after seeding. Inset: the number of migrated HCT116-GFP and HCT116-CHK-GFP cells. B Soft agar colony-formation assay of CHK-GFP-expressing HCT116 cells. Expression of GFP and CHK-GFP was induced by doxycycline for 48 h prior to the assay. Experiment was performed in triplicate (n = 3). Colonies were stained by 0.005% crystal violet for 1 h. Inset: Quantification of colony number (left) and colony size (right) of the data shown in panel B, using ImageJ software. Large colonies: ≥20 pixels, Medium colonies: 11–20 pixels, Small colonies: 1–10 pixels. The values represent the mean ± S.D. (n = 3 wells). *p < 0.05, **p < 0.005 and *** p < 0.001. C Comparison of proliferation rates of CT116-GFP and HCT116-CHK-GFP cells with and without Dox induction assessed by MTS assay. Doxycycline treatment and MTS assays were performed in quadruplicates for three independently seeded experiments (n = 3). All 12 data points for cell line with and without dox are shown and presented as pooled mean ± SD. D Representative images of the fluorescent Dil-labelled HCT116-CHK-GFP cells in Casper zebrafish embryos at 24 h after injection into the pericardial cavity (pre-treatment) and at 24 h after injection followed by treatment for an additional 72 h with (+Dox (72 h)) and without doxycycline (−Dox (72 h)). Inset: Total fluorescence intensity indicative of the number of Dil-labelled cells in the three different groups of embryos presented as mean ± S.D. The numbers of embryos used in the pre-treatment and the two treatment groups are shown. ***: p ≤ 0.001, ns no significant difference.

Discussion

Hyperactivation of SFKs plays an important role in the initiation and progression of CRC, however the mechanisms which lead to SFK activation remain poorly understood (reviewed in [34]). In this study we unveil a potential new mechanism for the hyperactivation of SFKs in CRCs mediated through the epigenetic silencing of CHK/MATK, one of its negative regulators. Specifically, we demonstrate that re-expression of CHK/MATK protein in CRC cell lines reduces SFK activity most likely via a non-catalytic mechanism, reduces anchorage-independent growth and cell migration and proliferation in vitro, and tumour growth in vivo, collectively indicating that CHK/MATK is a novel potential CRC tumour suppressor gene. Importantly, examination of previously reported datasets of methylated genes in CRC revealed that CRCs harbouring hypermethylation of the CHK/MATK promoter had more rapid recurrence after surgery, and shorter overall survival time [35], further supporting a role for CHK/MATK in tumour suppression.

Epigenetic alterations have been strongly implicated in the initiation of CRC [36]. Luo et al. demonstrated that there is a high degree of similarity in genome-wide DNA methylation changes in colon adenomas and colorectal cancers [36], suggesting that these changes occur prior to adenoma-to-carcinoma transition. Relevant to this, Luebeck et al. discovered a group of CpG islands exhibiting age-dependent changes in methylation state in normal human colon mucosa. Many of these CpG islands mapped to genes that undergo transcriptional changes in colorectal neoplasia [37], suggesting that epigenetic silencing of genes associated with CRC initiation occurs in premalignant colonic mucosal cells and adenomas, and that suppressed expression of some of these genes may contribute to CRC formation. While our study investigated the methylation status of CHK/MATK in advanced colorectal cancers, CHK/MATK was one of the genes identified in a global analysis of methylated genes in laterally spreading colonic mucosal adenomas [38], suggesting that CHK/MATK methylation may be an early event involved in CRC initiation and/or progression. Of relevance, CHK/MATK expression was also significantly lower in polyps located adjacent to colorectal cancers compared to the cancer-free polyps [39]. Since the former are likely to have given rise to colorectal carcinomas, the lower level of CHK/MATK expression in these polyps gives further support the notion that suppression of CHK/MATK expression is an early event in CRC progression.

Interestingly, interrogation of published single-cell transcriptomic datasets of mouse intestinal epithelium revealed CHK/MATK is expressed in a subset of enterocytes, LGR5+ and BMI+ stem cells, and transit amplifying cells, but is also highly expressed in tuft cells. Tuft cells are low abundant epithelial cells located in colon crypts and the crypts villus axis [25], which play a role in chemosensing as well as the initiation of T helper, type 2 (Th2) immune responses to parasites. Intriguingly, long lived tuft cells have also been proposed to act as cancer initiating cells [40]. Whether CHK/MATK is required for the differentiation of tuft cells or whether its epigenetic silencing in tuft cells, LGR5+ or BMI+ stem cells is required for CRC initiation remains to be determined.

With regards to the mechanism driving CHK/MATK promoter methylation in CRC, the E3 ubiquitin-like containing PHD and RING finger domain 1 (UHRF1) was recently discovered as an upstream regulator directing abnormal hypermethylation in CRC cells by forming a protein complex with DNMT1 and HDAC1 [35]. Notably, CHK/MATK was one of the genes found to be demethylated and re-expressed in CRC cells following UHRF1 knockdown, demonstrating its methylation and silencing in CRC cells is either directly or indirectly regulated by UHRF1 [35]. In this regard, it is notable that while genetic inactivation of DNA methyltransferases was able to induce a modest increase in CHK/MATK mRNA expression, it was not sufficient to restore CHK/MATK expression to endogenous levels. It is possible that inhibition of both DNMTs and UHRF1, as well as potentially other regulatory factors, is required to re-induce CHK/MATK expression to physiological levels.

A further implication of our finding that CHK/MATK promoter is methylated in the majority of CRCs is its potential as a biomarker for the early detection of CRC. The early detection of CRC is currently based upon Faecal Occult Blood Testing (FOBT) and colonoscopy, which while effective, has inherent limitations associated with sensitivity and costs (reviewed in [41]). In this regard, the diagnosis of CRC using molecular biomarkers, including methylated loci has gained interest due to its potential for detection using non-invasive and inexpensive MS-PCR testing. For example, MS-PCR of the Vimentin gene promoter has been developed as a diagnostic test for population-based screening for early detection of CRC [41]. Furthermore, in 2014, the US Food and Drug Administration approved the use of the multi-target stool DNA test for population-based screening of CRC, which interrogates KRAS mutation status as well as the methylation status of the NDRG4 and BMP3 promoters [42]. Our finding that the CHK/MATK promoter is methylated in ~90% of CRCs (Fig. 5C) underscores its potential as a reliable biomarker of the disease.

Importantly, we also extend these findings to other solid tumours, where we observed frequent CHK/MATK promoter methylation in seven other tumour types (Figure S7). Several of these tumours (e.g. breast cancer) are known to harbour SFK hyperactivation, suggesting that in addition to CRC, epigenetic silencing of CHK/MATK may also contribute to SFK activation in these tumours. CHK/MATK methylation may also serve as a potential biomarker for early detection of these tumour types, a possibility worthy of investigation in future studies.

While we observed consistent down-regulation of CHK/MATK in CRC cells, CSK expression was maintained in most CRCs and CRC cell lines, raising the important question of why CSK cannot compensate for the loss of CHK/MATK in CRC cells. One possible explanation may relate to the ability of SFKs to adopt an inactive conformation as well as multiple active conformations [43]. The inactive conformation of SFKs is stabilised by the intramolecular interactions of the phosphorylated C-terminal tail tyrosine (e.g. Tyr-530 of SRC) with the SH2 domain and those of SH2-kinase linker with the SH3 domain [44]. SFKs in the inactive conformation can be activated by many mechanisms to form multiple active conformations. For example, the inactive SFKs can be activated by disruption of these intramolecular interactions by exogenous ligands of the SH2 and SH3 domains while the C-terminal tail tyrosine remains phosphorylated [45, 46]. Furthermore, the activated SFKs undergo autophosphorylation, which further stabilise them in the active conformations [13]. In CRC cells, CSK can phosphorylate the C-terminal tail tyrosine of SFKs. However, the phosphorylation cannot inhibit SFKs so long as SFKs are autophosphorylated and/or the SH2 and SH3 domains still remain bound to their exogenous ligands. Hence, SFKs are hyperactivated even in the presence of active CSK (Fig. 2) [20]. Unlike CSK, CHK/MATK can inhibit all active conformations of SFKs both by phosphorylation of the C-terminal tail tyrosine and by a non-catalytic allosteric mechanism that involves direct binding of the CHK/MATK kinase domain with the kinase domain of SFKs [17, 20, 21]. Its re-expression effectively suppresses SFK activity in CRC cells (Fig. 7) [20, 22].

The role of hyperactivation of SFKs in promoting CRC invasiveness and anchorage-independent growth is well documented [47]. In agreement with these roles, we observed that re-expression of CHK/MATK in HCT116 or DLD-1 CRC cells suppresses SFK activation, anchorage-independent growth and cell migration. Furthermore, we also observed that CHK/MATK overexpression inhibited the proliferation of colon cancer cells. Notably, treatment with SFK inhibitors has previously been reported to have little or no impact on cell proliferation of CRC cells in vitro [47,48,49,50]. It is possible therefore that the reduced proliferation of both HCT116 and DLD1 cells induced by re-expression of CHK/MATK (Fig. 8) may be driven by a mechanism independent of SFK inhibition [49]. In this context, as a protein tyrosine kinase, CHK/MATK may also exert its anti-proliferative effects by phosphorylating non-SFK proteins in CRC cells. Identification of the non-SFK direct substrates of CHK/MATK will shed new light on the molecular mechanism of its tumour suppressive action in CRC cells. In this regard, the HCT116 and DLD-1 cell lines we have generated in which CHK/MATK expression can be induced by doxycycline, represent useful tools to further define the tumour suppressive mechanisms of CHK/MATK [20].

In summary, our findings demonstrate that epigenetic inactivation of CHK/MATK, is a frequent event in CRC, which may contribute to enhanced cell proliferation and invasiveness by SFK-dependent and independent mechanisms.

Materials and methods

Bisulfite conversion and sequencing

Cell pellets (2–3) from each exponentially growing tumour cell line were pooled. Genomic DNA from CRC cell lines were extracted using QIAamp DNA Mini Kit (Qiagen) and bisulfite converted using the EpiTect Bisulfite Kit (Qiagen). PCR was performed using Platinum™ Taq DNA Polymerase High Fidelity (ThermoFisher Scientific). The primer sequences used to amplify CHK/MATK gene promoter are provided in Table S1. The locations of primers and target CpG dinucleotides relative to the CHK/MATK gene promoter are shown in Fig. 3A. PCR products were ligated into the pCR4-TOPO vector using the TOPO TA Cloning Kit (ThermoFisher Scientific) followed by bacterial transformation using TOP10F′ competent cells. Ten clones were randomly selected per cell line and subjected to sanger sequencing using the M13 primer. Chromatograms were visually inspected, then aligned with reference sequences to determine the methylation status for each CpG site within the amplicon. In total, 38 CpG sites were investigated within the CHK/MATK gene promoter. Methylation status of individual CpG site was assessed across all clone sequenced and % methylation was calculated. Mean % methylation of CHK/MATK was determined by averaging the % methylation calculated for each of the 38 CpG sites investigated.

Single cell RNA-seq analysis

Analyses of single-cell RNA-seq data were performed using R (version 3.6.1). We analysed the raw count data from Yan et al. [24], which included Bmi1+, Prox+, Lgr+ and Lgr5- cells, as well as two raw count data from Haber et al. [23], including regional data (duodenum, ileum and jejunum) and large cell data. The count data were converted to Seurat objects using the Seurat (version 3.1.1) R/Bioconductor package [51]. Gene IDs were mapped to mouse Entrez IDs using the Mus musculus.gene info file from the NCBI. Genes only expressing in less than three cells or genes with no valid official gene symbols or duplicated official symbols were removed. We removed cells if they expressed less than 200 genes or more than 5000 genes, or if they had more than 20% mitochondrial UMI counts. Following these filtration steps, 3554 cells in Yan et al. study [24], 11,665 cells in the regional data and 9924 cells in the large cell data in Haber et al. study [23] were analysed. We used the SCTransform() function in the Seurat package to normalise count data by setting the vars.to.regress to be the percentage of mitochondrial reads. We used RunPCA() function on highly variable genes and used the top 30 principal components for Uniform Manifold Approximation and Projection (UMAP) dimensional reduction using RunUMAP() function with default parameters.

Marker gene discovery was performed using differential expression analysis to identify genes that characterised CHK/MATK-expressing cells vs all other cells using FindMarkers() function from the Seurat package with test.use = “wilcox”, only.pos = TRUE. Heatmaps were generated using the ComplexHeatmap (version 2.2.0) R/Bioconductor package [52] for the top 30 significant genes that were highly expressed in CHK/MATK-expressing cells vs others.

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Funding

O. Sieber is a NHMRC Senior Research Fellow (GNT1136119); grant support to H.-J. Zhu: NHMRC project grant #628727, grant support to H.-C. Cheng: NHMRC project grant # 1050486 and Australian Brain Foundation, grant support to A. Dhillon: NHMRC project grants #1141906. J. Mariadason was supported by a NHMRC Senior Research fellowship (GNT1046092). F. Hollande received grants from the Tour de Cure Foundation, Australia (Senior Project grant) and the National Health and Medical Research Council of Australia (Grant #1164081).

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Conception, experimental design and data analysis: ACC, GA, NN, H-CC, H-JZ, HV, HN, JB, DJF, DM, OS, FH, AD, FB and JM. Performing experiments: ACC, GA, NN, MF, JS, DSL, H-JZ, JB, IL, AS and FB. Preparation of the manuscript: ACC, Y-PC, JPL, GA, NN, H-CC, H-JZ, HV, HN, JB, DJF, OS, FH, FB, AD and JM.

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Correspondence to Anderly C. Chüeh or Heung-Chin Cheng.

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Chüeh, A.C., Advani, G., Foroutan, M. et al. CSK-homologous kinase (CHK/MATK) is a potential colorectal cancer tumour suppressor gene epigenetically silenced by promoter methylation. Oncogene 40, 3015–3029 (2021). https://doi.org/10.1038/s41388-021-01755-z

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