Background
Colorectal cancer (CRC) is the third most commonly diagnosed cancer and the second cause of cancer-related deaths among 36 cancer types globally in 2020 [
1]. The initiation and progression of CRC are commonly regarded as a complicated and heterogeneous process involving genetic mutations [
2] and dysregulated epigenetic modifications [
3,
4]. Histone methylation, a reversible modification associated with gene activation or silencing, is regulated by specific methyltransferases and demethylases. Global changes in histone methylation have been well-established in carcinogenesis and identified as prognostic biomarkers in a spectrum of human tumors, including CRC [
5‐
8].
The ubiquitously transcribed tetratricopeptide repeat on the X chromosome (UTX, encoded by
KDM6A located on the X chromosome) is a histone demethylase that catalyzes the removal of H3K27me2/3, promoting the transcription of target genes. UTX is involved in a variety of biological processes, comprising homeotic gene expression, embryonic development, and cellular reprogramming [
9]. UTY, a paralog sharing 83% sequence similarity with UTX, lacks detectable histone demethylase activity [
10]. Interestingly, the loss of UTX during the development could be compensated by UTY, suggesting the function of UTX during embryonic development might be independent of its demethylase activity between E9.5 and E13.5 [
11]. Recent studies have identified UTX as a highly mutated tumor suppressor, with reduced expression observed in several human malignancies [
12‐
17]. It has also been recognized as an “escape from X-inactivation tumor suppressor”, with a distinct dosage effect of
UTX copy number observed during tumorigenesis [
17]. The mutation or deletion of both copies of
UTX is required for the dysfunction of this tumor suppressor in females, while loss of one copy of
UTX achieves the same effect in males. UTY provides limited compensation for UTX loss during tumorigenesis, suggesting that the tumor suppressor function of UTX is demethylase activity-dependent. Accumulating evidence indicated that the oncogenic effect of UTX loss is mediated mainly through an increase in the EZH2 level in lung cancer [
16], and UTX loss sensitizes cells to EZH2 inhibition in multiple myeloma [
18]. Although a previous report suggested that UTX promotes CRC progression [
19], the functional and regulatory mechanisms of UTX in CRC is largely unclear.
The ubiquitin–proteasome system is a significant pathway that precisely governs protein stability [
20]. Among the Cullin-RING Ligase (CRL) family [
21], a typical CRL4 ligase is composed of a scaffold Cullin (CUL4A or CUL4B) protein, a linker protein-DNA Damage Binding Protein-1 (DDB1), a substrate recognition adaptor (DCAF), and a ring protein with intrinsic E3 activity (RBX1 or RBX2) [
22]. The substrate specificity of CRL4 is mainly dependent on the DCAF protein loaded on the specific CRL4 complex. Constitutive photomorphogenic 1 (COP1, also known as RFWD2) was initially identified as a negative regulator of photomorphogenesis in
Arabidopsis [
23], and its functions have been extensively studied in the context of light signaling in plants [
24]. Notably, mammalian COP1 possesses intrinsic E3 ubiquitin ligase activity, enabling it to either promote protein ubiquitination or serve as a DCAF protein that forms a CRL4 ligase complex to ubiquitinate substrates [
25]. Intriguingly, both classic oncoprotein and tumor suppressor proteins, such as c-Jun, ETS transcription factors, and P53, have been identified as ubiquitination-degradation substrates of COP1, indicating a complex and context-dependent role of COP1 in cancer [
26‐
28]. However, the role of COP1 in CRC has not yet been reported.
In the current study, we found that UTX is negatively correlated with clinical stage, and low UTX expression is associated with poor patient survival. Subsequently, we validated the tumor suppressor role of UTX in CRC by specifically depleting the Utx gene in intestinal epithelial cells and inducing de novo colorectal tumorigenesis. Our mechanistic study showed that UTX loss promoted colorectal oncogenesis partially via transcriptionally repression of EMP1 and AUTS2. Experiments performed with mouse CRC model and human CRC organoids further suggested that UTX deficiency confers enhanced sensitivity to EZH2 inhibitor GSK126 in CRC. Next, we certified that UTX is subject to CRL4-COP1 complex-mediated degradation, partially explaining the oncogenic role of COP1 in CRC.
Methods
Human CRC tissue microarray (TMA) construction
A human TMA was obtained from CRC patients who underwent radical surgery between January 2007 and November 2009 at Fudan University Shanghai Cancer Center (FUSCC), Shanghai, China. Human CRC TMA was carried out as described previously [
29]. The clinicopathological characteristics of patients, such as age, gender, tumor location, histological type, tumor-node-metastasis (TNM) stage, grade, venous and nervous invasion, pretreatment serum CEA level, and survival data, were collected from the FUSCC database.
Generation of genetically-modified mice
All mice were raised in a specific pathogen-free environment at the Shanghai Institute of Biochemistry and Cell Biology.
Utxf/f and
Villin-Cre mice were provided by Dr. Charlie Degui Chen and Dr. Anning Lin (Shanghai Institute of Biochemistry and Cell Biology, CAS), respectively. As described previously [
15], the exons 11 to 14 of
Utx were deleted using a targeting vector, which disrupts the
Utx H3K27 demethylase domain by triggering a frameshift mutation.
Cop1f/f mice were purchased from Laboratory Animal Center, East China Normal University.
Utx−/y or
Utx−/+ mice were generated by crossing
Utxf/f mice with
Villin-Cre mice, while
Utx−/− mice were embryonic lethal.
Cop1−/+ mice were generated by crossing
Cop1f/f mice with
Villin-Cre mice, while
Cop1−/− mice were embryonic lethal. All mice were maintained in a C57BL/6 background. The primers for genotyping are listed in Additional file
1: Table S1.
Induction of colitis, CRC, and treatments
We combined the carcinogen azoxymethane (AOM) treatment with repeated administration of dextran sodium sulfate (DSS) in drinking water to induce colorectal tumors. wild-type (WT), Utx−/y, and Utx−/+ mice were used for AOM/DSS treatment. 8–10-week-old mice were injected intraperitoneally with AOM (10 mg/kg, Sigma, A5486). After one week, DSS was solubilized into the drinking water to feed mice for 5 days (2%, MP Biomedicals, 160,110). Subsequently, regular drinking water was given for 14 days. The DSS treatment was repeated for another two cycles. Body weights were recorded during the DSS treatment. The mice were sacrificed 90 days after the AOM injection, and colorectums were obtained for further analysis. Gross inspection, total tumor number, tumor burden, and tumor size were recorded. The samples were fixed as ‘‘swiss-rolls,’’ and a histopathological examination was conducted.
For drug treatment, 2 weeks after AOM/DSS treatment, WT and Utx−/y mice were randomized into two groups. Then, the mice were treated with GSK126 (50 mg/kg, dissolved in SBE-β-CD) or vehicle control daily for additional 2 weeks before being sacrificed for analysis.
Immunoblotting (IB) and immunoprecipitation (IP)
Cells were lysed using EBC lysis buffer (50 mM Tris–HCl, pH 8.0, 120 mM NaCl, 0.5% Nonidet P-40) with protease inhibitors (1:100, Selleck) and phosphatase inhibitors (1:100, Selleck). Intestinal/tumor tissues from human or mice were lysed using Minute™ Total Protein Extraction Kit (Invent Biotechnologies, Inc.) with protease inhibitors (1:100, Selleck) and phosphatase inhibitors (1:100, Selleck). The protein concentrations of lysates were determined using the Bio-Rad protein assay kit on a spectrophotometer (Thermo Scientific). An equivalent of 30 μg total lysate from each sample was used for IB. The cell lysates were incubated with anti-FLAG M2 agarose beads or anti-HA agarose beads for 2–4 h for IP. The pellets were washed with NETN buffer (20 mM Tris–HCl, pH 8.0, 100 mM NaCl, 0.5% Nonidet P-40, 1 mM EDTA) before analysis by SDS-PAGE and IB with specific antibodies.
Immunohistochemistry (IHC)
IHC staining was performed with indicated antibodies using the standard protocol. The TMA was incubated with an anti-UTX antibody (1:400 dilution, 33510S, Cell Signaling Technology) and an anti-COP1 antibody (1:100 dilution, A300-894A, Bethyl). Mouse tissues were incubated with anti-UTX antibody (1:100 dilution, GTX121246, GeneTex), anti-COP1 antibody (1:100 dilution, A300-894A, Bethyl), Ki67 (1:100 dilution, ab15580, Abcam), anti-EZH2 antibody (1:200 dilution, ab191080, Abcam), and anti-H3K27me3 antibody (1:100 dilution, ab192985, Abcam; 1:100 dilution, A2363, Abclonal), respectively, as indicated. The IHC stained tissue sections were scored by two independent pathologists blinded to the clinicopathological features. The proportion of staining was graded as 0 (< 5%), 1 (5–25%), 2 (26–50%), 3 (51–75%), and 4 (> 75%) based on the percentages of the positive staining areas vs. the whole area. The staining intensity was graded as 0 (negative), 1 (weak), 2 (medium,) or 3 (strong). The immunoreactivity score (IRS) was calculated by multiplying the score of staining proportion with staining intensity. IRS ≤ 4 was considered as low, and > 4 was considered as high.
Cell proliferation, colony formation, and soft agar colony formation assays
HCT116 cells were seeded into 96-well plates at a density of 3000 cells/well. Then, the cells were incubated with CCK-8 reagent (C0039, Beyotime Biotechnology, Shanghai, China) for 2 h, and absorbance was measured at 450 nm. For colony formation assay, HCT116 cells were seeded in the 96-well plates with 500 cells/well and incubated for 10 days. For the soft agar colony formation assay, 6-well plates were covered with lower agar (1.5 mL, 0.8%), and 500 cells were seeded in the upper agar (1.5 mL, 0.4%). After 2 weeks, the colonies were stained with 1% crystal violet (Beyotime).
ChIP-seq assay and data analysis
The distal colorectum samples of 2-month-old WT and Utx−/y mice (each sample mixed with three animals) were collected for ChIP-seq analysis service by Active Motif Inc. using the antibody against H3K27me3 (Active Motif). The data were deposited in the NCBI’s SRA (Accession: PRJNA752794).
RNA-seq analysis
The distal colorectum mRNAs from 2-month-old WT mice and Utx−/y mice (each RNA sample mixed with three animals) were obtained for transcriptome analysis service by Sangon Biotech. The data were deposited in the NCBI’s SRA (Accession: PRJNA734666).
siRNA screening for putative target genes
siRNA-based screening was performed for the selected 55 genes in HCT116 cells. The siRNAs were selected from Dharmacon Human ON-TARGET plus siRNA Library. To eliminate the off-target effects, four independent siRNAs (SMARTpools) were used for each gene. siNC and siTOX were selected as the negative and positive controls in the screening assay. 0.15 μL lipofectamine RNAiMAX reagent (Thermo) was added to the siRNA-loaded 96-well plates using Multidrop Combi (Thermo). Then, HCT116 cells were seeded in the 96-well plates at a density of 1500 cells/well. The number of cells was counted in the following 4 days using Ensight (Perkin Elmer). Subsequently, CTG (G756A, Promega) was added and measured on an Envision plate reader (Perkin Elmer).
Total RNA extraction and quantitative PCR
Total RNA was extracted from cells or tissues using TRIzol (Invitrogen) according to the manufacturer’s instructions. The cDNA was synthesized using ABScript II RT Master Mix (ABclonal Technology). Quantitative PCR was performed using a SYBR.
Kit (Takara) according to the manufacturer’s protocol. Human
GAPDH or mouse
β-
Actin was used as an internal control. The primer sequences are listed in Additional file
1: Table S1.
ChIP-qPCR assays
The ChIP assay was performed using truChIP Chromatin Shearing Kit (Covaris) and EZ-ChIP kit (Millipore). The procedure was according to the kit instruction manual provided by the manufacturer. Primer sequences can be found in Additional file
1: Table S1.
Plasmid construction
HA-UTX and different mutants were cloned into pcDNA3.1 vector. FLAG-UTX was generated by inserting UTX cDNA into pCMV-FLAG and pRLenti-CMV-MCS-3FLAG-PGK-Puro vectors. The Flag-tagged of DET1, DDB1, RBX1, Cullin1, Cullin2, Cullin3, Cullin4A, Cullin4B, and Cullin5 were generated by inserting cDNAs into pCMV-FLAG vector. The Flag-tagged and HA-tagged coding sequence of human COP1 WT or the relevant isoforms and the mutants were inserted into the lentiviral vector pLex-MCS-CMV-puro (Addgene, USA) to generate COP1 expression plasmids. Myc-Ub was provided by Dr. Cory Ronggui Hu (Shanghai Institute of Biochemistry and Cell Biology, CAS). pLKO.1-TRC cloning vector (Addgene: 10,878) was used to express shRNAs against COP1 or UTX. Briefly, the oligos targeting COP1, UTX, CUL1 and CUL4B were cloned into the pLKO.1-TRC vector to generate shRNA constructs.
Cell culture and transfection
HCT116, HT-29, SW620, SW480, LoVo, DLD1, and HEK293T cells were kindly provided by Cell Bank, Chinese Academy of Science and were cultured in DMEM containing 10% FBS (Invitrogen) at 37 °C in 5% CO2. Plasmids were transiently transfected with polyethylenimine (Sigma) or Lipofectamine 3000 (Invitrogen). Cells were transfected with siRNA using Lipofectamine 3000 (Invitrogen) according to the manufacturer’s protocol.
The siRNAs targeting indicated genes were synthesized by Biotend (Shanghai, China), and the sequences are listed in Additional file
1: Table S2.
Human primary CRC organoid culture
Organoids were cultured in Advanced DMEM/F12 medium (GIBCO, 12,634–010), containing 500 ng/mL R-spondin 1 (Sino Biological, 11,083-HNAS), 100 ng/mL Noggin (Sino Biological, 50,688-M02H), 50 ng/mL EGF (Sino Biological, 50,482-MNCH), 100 ng/mL FGF-10 (Sino Biological, 10,573-HNAE), 1X HEPES (GIBCO, 15,630,080), 1X Glutamax (GIBCO, 35,050,061), 100 μg/mL Normocin (InvivoGen, ant-nr-1), 1X Gentamicin/amphotericin B (GIBCO, R01510), 1X B27 (Invitrogen, 17,504–044), 1X N2 (Invitrogen, 17,504–048), 1 mM n-Acetylcysteine (Sigma-Aldrich, A9165), 10 mM nicotinamide (Sigma-Aldrich, N0636), 0.5 μM A-83–01 (Tocris, 2939), 10 μM Y-27632 (Sigma-Aldrich, Y0503), 10 nM Gastrin, 1 μM prostaglandin E2 (Sigma-Aldrich, P6532), and 3 μM SB202190 (Sigma-Aldrich, S7067). The culture medium was refreshed every 3 days.
Organoid cytotoxicity assay
Organoids were harvested, passaged, and seeded in a 48-well cell culture plate. Each well contained about 100 ± 50 organoids in 20 μL Matrigel with 300 μL culture medium. Once the organoids grew to 100 μm in diameter, the organoids culture medium was replaced with 300 μL drug-containing culture medium with GSK126. The drug-containing culture medium was refreshed every 3 days. Organoids were photographed every 3 days during the 9-day drug treatment period. The size of live organoids was measured using ImageJ 1.53a (National Institutes of Health, USA).
TdT-UTP nick end labeling (TUNEL) assay
TUNEL assay was performed with a colorimetric TUNEL apoptosis assay kit according to the manufacturer’s instructions (C1091, Beyotime).
5-ethynyl-2’-deoxyuridine (EdU) assay
EdU assay was conducted using BeyoClick™ EdU Cell Proliferation Kit with DAB (C0085S, Beyotime).
Xenograft tumorigenesis assay
HCT116 cells expressing ectopic COP1, ectopic COP1 plus UTX mutant (V607A/P608A/V1205A/P1206A), and empty vector were injected into the flank of each nude mouse (1 × 107 cells each mouse) to evaluate the tumorigenesis. Tumor volumes were measured and recorded every 3 days.
Antibodies and chemical inhibitors
Primary antibodies used in this study are as follows: UTX (33510S, Cell Signaling Technology; GTX121246, GeneTex), COP1 (A300-894A, Bethyl), CUL1 (SC-17775, Santa Cruz Biotechnology), CUL2 (A5308, Abclonal), CUL3 (2759, Cell Signaling Technology), CUL4A (AB60215a, Abgent), CUL4B (A6198, Abclonal), CUL5 (SC-373822, Santa Cruz Biotechnology), EMP1 (ab230445 and ab202975, Abcam), AUTS2 (25,001–1-AP, Proteintech), Ki67 (ab15580, Abcam), EZH2 (ab191080, Abcam), VEGFC (A2556, Abclonal), Caspase-9 (A0281, Abclonal), Bcl2 (15,071, Cell Signaling Technology), DDB2 (ab181136, Abcam), DCAF7 (ab138490, Abcam), DCAF13 (ab195121, Abcam), H3K27me3 (ab192985, Abcam; A2363, Abclonal), H3 (ab1791, Abcam), P27 (610,241, BD), HA-Tag (51,064–2-AP, Proteintech; SC-7392, Santa Cruz Biotechnology), Flag-Tag (F7425-0.2MG, Sigma; F3165-1MG, Sigma), GFP (66,002–1-Ig, Proteintech), Myc-Tag (16,286–1-AP, Proteintech), α-tubulin (SC-23948, Santa Cruz Biotechnology), and Vinculin (V4505, Sigma). The chemical inhibitors MG132 (S2619), MG101 (S7386), MLN4924 (S7109), Baf-A1 (S1413), and GSK126 (S7061) were purchased from Selleck.
Statistical analysis
Statistical evaluation was conducted using SPSS 25.0 (SPSS Inc., Chicago, IL, USA) and GraphPad Prism v.8 (La Jolla, CA, USA). The experimental data were analyzed using a two-tailed Student’s t-test, one-way analysis of variance (ANOVA) with Dunnett’s multiple comparisons test, Pearson’s correlation coefficients test, and log-rank test. P < 0.05 was considered significant.
Discussion
The oncogenic function and regulation of EZH2, the major H3K27 methyltransferase, in CRC have been well-documented [
37‐
40]. Conversely, the functional and regulatory mechanism of the H3K27me3 histone demethylase UTX in CRC is yet unclear. In the present study, we found that UTX protein levels were downregulated in advanced stages of CRC as examined by immunostaining. Moreover, low UTX expression was associated with poor patient survival, indicating a putative tumor suppressor role of UTX in human CRC (Fig.
1). Next, we observed that UTX loss significantly increased tumor numbers and burden in the AOM/DSS-induced CRC model. These results suggested that UTX functions as a tumor suppressor in CRC, and reduced UTX may drive the progression of the disease. Since reduced UTX expression in intestinal tissue significantly increased the H3K27me3 levels, which are enriched in CRC with more advanced disease stages, we speculated that targeting H3K27me3 may be an effective way to treat UTX loss-related CRC. Typically, spontaneous colorectal tumors derived from UTX-deficient intestines or human CRC organoids with low UTX expression exhibited sensitivity to EZH2 inhibitors, consistent with previous reports in other cancer types [
16,
18]. Therefore, the EZH2 inhibitor could be a promising therapeutic option for CRC patients with UTX deficiency.
The combined analysis of
UTX-depleted mice intestine and human CRC cells identified
EMP1 and
AUTS2 as the target genes modulated by UTX since their expression decreased upon
UTX depletion and increased upon treatment with the EZH2 inhibitor GSK126. Notably, the depletion of
EMP1 and
AUTS2 promoted CRC cell proliferation, a phenotype similar to
UTX knockdown. Reportedly, EMP1 has a possible cross-talk with the EGFR signaling pathway [
41] and negatively regulates cell growth and metastasis in CRC [
35], and its downregulation is observed in multiple cancers [
36,
42]. In contrast, AUTS2 is frequently disrupted in patients with neurological disorders [
30] but is less studied in cancer. Here, we characterized UTX as the epigenetic regulator of
EMP1 and
AUTS2 expression. Furthermore, the increased protein level of VEGFC and BCL2 as well as reduced cell apoptosis caused by depletion of
UTX could be rescued by ectopic expression of
EMP1, suggesting that
EMP1 is a significant effector gene mediating the tumor-suppressing function of UTX in CRC. However, during our screening process, we only focused on putative target genes mutually modulated by UTX in human CRC cells and mice intestines, particularly those that affect cell growth. Other putative UTX target genes (
FRMPD1,
HPSE2,
SELL,
IFIT2,
SLC8A1,
SLC44A5, and
LIMCH1) were identified in ChIP-seq and RNA-seq analyses. These genes may also modulate CRC via various mechanisms other than regulating cell growth. Some specific human UTX target genes that mediate its tumor suppressor function in CRC might not have been discovered in the mouse model.
According to the COSMIC (the Catalogue of Somatic Mutations in Cancer) database and previous reports, genomic deletion or mutation of UTX is not a frequent event in CRC. Therefore, it is essential to understand how UTX expression is impaired in CRC. The current study indicated that the CUL4B-DDB1-COP1 E3 ligase complex governs UTX protein stability. Depletion of COP1 in human CRC cells or mice intestinal tissue caused a marked increase in UTX expression and restricted tumorigenesis. The expression of COP1 was inversely correlated with UTX expression in human CRC specimens. Furthermore, we observed a remarkably enhanced growth of tumors upon ectopic expression of COP1 in the in vivo tumorigenesis assays. Importantly, ectopic expression of a non-degradable UTX mutant reversed the tumor-promoting effect of COP1 overexpression. Mechanistically, we have characterized that UTX is a substrate for the CUL4B-DDB1-COP1 E3 complex, but not for the COP1 intrinsic RING motif. We also identified two putative “VP” degron motifs in UTX that mediate COP1 recognition. Thus, the current study revealed the oncogenic role of COP1 in CRC, at least partially, by degrading UTX and inducing epigenetic changes. Additionally, it uncovers a critical layer of UTX regulation in CRC.
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