1 Introduction
Primary liver cancer is one of the most common malignant tumors in the world [
1]. The main pathological type of primary liver cancer is hepatocellular carcinoma (HCC), accounting for over 80% of the total cases [
2]. The difficulty of early diagnosis contributes to high proportion of advanced-stage HCC cases [
3]. At present, targeted drugs like Sorafenib and Lenvatinib have become the first-line treatment for advanced HCC. However, the complex pathogenesis of HCC results in limited efficacy with single targeted drug [
4]. Therefore, it is necessary to search for new targets to further explore the mechanism of tumor progression and broaden selection of therapeutic drugs for HCC.
Tumor cells possess a unique metabolic feature, named “Warburg effect”, which result in increased level of glycolysis and more production of lactate [
5]. Various studies have confirmed that glycolysis plays a crucial part in the growth of different types of tumors, including HCC [
6‐
8]. The Warburg effect facilitates adaptation of hepatocellular carcinoma (HCC) cells to hypoxic and low-oxygen environments [
9]. Meanwhile, the hypoxic environment inside usually leads to the increased expression of hypoxia-inducible factors in tumor cells [
10]. Among them, Hypoxia-inducible factor 1α (HIF1α) is a well-studied transcription factor subunit which could regulate over 100 downstream genes required for glycolysis and tumor progression [
11]. Recent studies have reported that several signaling pathways, including Wingless/Integrated (WNT) pathway, Mitogen-activated protein kinase (MAPK) pathway, Phosphatidylinositol-3-Kinase/Protein Kinase B/Mammalian Target of Rapamycin (PI3K/AKT/mTOR) pathway, Nuclear Factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathway etc. could regulate the transcriptional of HIF1α [
12‐
16]. Besides, proline residue hydroxylation leads to the degradation of HIF1α regulated by von Hippel-Lindau tumor suppressor (pVHL) E3 ligase complex [
17]. However, there are still some molecules that affect HIF1α and cellular glycolysis waiting to be discovered.
Ubiquitination which mainly depends on ubiquitin, ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin ligase (E3) could regulate protein stability, activation of related signaling pathways and gene transcription [
18]. Ubiquitin conjugating enzyme E2 Q2 (UBE2Q2) contains a conserved ubiquitin conjugation (UBC) domain at its C-terminal, which can directly bind with ubiquitin, suggesting that it might play a role of ubiquitin conjugating enzyme to determine the ubiquitination modification type of the substrate protein and affect biological functions of the substrate protein [
19]. Researchers have demonstrated that UBE2Q2 is abnormally overexpressed in hypopharyngeal tumors and pediatric acute lymphoblastic leukemia [
20,
21]. In HeLa cells, UBE2Q2 antagonizes early mitotic checkpoints. The interference of UBE2Q2 may increase the sensitivity of tumor cells to chemotherapy drugs [
19]. However, there is no detailed research on the biological function of UBE2Q2 in HCC, or its role in the process of protein ubiquitination.
In this study, we found that UBE2Q2 promoted the progression of HCC. Besides, we discovered that UBE2Q2 could play a new role in NF-κB signaling pathway and regulate glycolysis of HCC. In consideration of the close association between glycolysis and tumorigenesis, this study provided a potential therapeutic target for HCC.
2 Materials and methods
2.1 Clinical HCC patients’ samples and information
Tumor and adjacent normal liver tissues of 80 HCC patients (68 male and 12 female patients) on whom the liver resections were performed during 2018 to 2020 in the Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University were collected. None of the patients received any pre-operative therapy like radiofrequency ablation, anhydrous alcohol injection, TACE or immunotherapy. The histopathological examination of samples was confirmed by two experienced pathologists. Related clinical data of 80 patients were recorded for statistical analysis.
2.2 Cell culture
The cell lines Huh-7, HCC-LM3, Hep3B, HepG2, HepG2.2.15, and SK-Hep-1 were obtained from the Shanghai Cell Bank of the Chinese Academy of Medical Sciences. These were cultured under standard conditions: Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin, maintaining a temperature of 37 °C and a 5% CO2 atmosphere. Cell line authenticity was verified through STR profiling and all were certified mycoplasma-free.
For specific experiments, Huh-7 and LM3 cell lines underwent treatment with distinct agents: 100 µM cobalt chloride for 12 h; 10 µM chlorhexidine, corynoxeine, or LY294002, each for a period of 24 h; 20 µM rapamycin for 24 h; 20 µM (-)-DHMEQ for 24 h and 2 mM 2-DG for 12 h. All aforementioned compounds were sourced from Sigma Aldrich (Germany) and MCE (USA).
RNA from both tissue specimens and cultured cells was isolated using TRIzol Reagent (Invitrogen, USA). The quality and concentration of RNA were assessed with a NanoDrop ND2000 spectrophotometer (Thermo Scientific, Massachusetts, USA). Reverse transcription was conducted using the HiScript III 1st Strand cDNA Synthesis Kit for mRNA and the Mir-X miRNA First-Strand Synthesis Kit (Takara, USA), following the provided protocols. Quantitative real-time PCR was performed with a SYBR Green PCR kit (Vazyme, China) on a CFX96TM Real-time PCR Detection System (Bio-Rad, California, USA). Relative RNA expression levels were quantified using the 2^(-ΔΔCt) method, with the threshold cycle (Ct) being determined. Reproducibility was ensured by conducting all procedures in triplicate. Primer sequences used are detailed in Table S1 of the supplementary materials.
2.4 RNA interference and cell transfection
UBE2Q2 expression was targeted for knockdown using small interfering RNAs (siRNAs). Three distinct siRNAs aimed at UBE2Q2 (referred to as siRNA #1, siRNA #2, and siRNA #3) were custom-synthesized by Genecreate (Wuhan, China). Among them, siRNA #2 was subsequently labeled as siUBE2Q2 in Figs.
4 and
5 and Fig. S4. The details of these siRNA and shRNA sequences are provided in Table S2 of the supplementary materials. For the siRNA transfection, the Genmute transfection reagent (Signagen, Maryland, USA) was used, following the manufacturer’s protocol.
2.5 Construction of plasmid, lentivirus package and cell infection
The UBE2Q2 gene was synthesized and cloned into the pEZ-Lv105 vector to create an overexpression construct, hereafter referred to as UBE2Q2 plasmid. The empty pEZ-Lv105 vector was utilized as a control, designated as Vector. Both plasmids were products of GeneCopoeia (Rockville, USA). Additional plasmids, including pcDNA-HA-UBE2Q2, pcDNA-HIF1α, pcDNA-His-TRAF2, and pcDNA-Flag-cIAP1, were synthesized by Genecreate (Wuhan, China). Plasmids pCDEF-HA-Ub(K11), pCDEF-HA-Ub(K48), and pCDEF-HA-Ub(K63) were procured from Ke Lei Biological Technology (Shanghai, China). Transfections were carried out using Lipofectamine 3000 (Thermo Fisher Scientific, CA, USA) according to the manufacturer’s recommendations.
Stable UBE2Q2 knockdown and overexpression lines were established using lentiviral systems (Lv-shUBE2Q2 and UBE2Q2 respectively), also provided by Genecreate (Wuhan, China), with a virus titer of 6 × 108 TU/mL. For infection, a multiplicity of infection (MOI) of 10 was applied to Huh-7 cells, with 100 µL of viral suspension coupled with 100 µL of Hitrans P virus infection reagent (GeneChem, Shanghai, China) per 1 × 106 cells. After 24 h, the medium was replenished. Cells were collected 4 days post-infection and selected with puromycin. The knockdown efficiency was evaluated using qRT-PCR and Western blot analyses.
2.6 Cell viability assays
Cell viability was assessed using the Cell Counting Kit-8 (CCK-8, Biosharp, China) assay. Briefly, cells were seeded at a density of 5,000 per well in 100 µL of culture medium in a 96-well plate. Afterward, 10 µL of CCK-8 solution was added to each well. The plate was incubated at 37 °C for 1 h before measuring the absorbance at 450 nm using a microplate reader.
A colony formation assay was performed by plating 500 to 1,000 cells in a six-well plate and culturing for 14 days. The colonies were then fixed with 4% paraformaldehyde and stained for 1 h with 0.1% crystal violet (Sigma Aldrich, Germany). Post-staining, colonies were counted and imaged using a stereomicroscope.
2.8 Wound healing assay
Cell transfection and culture were performed in a six-well plate. Upon reaching confluence, a 100 µL pipette tip was used to create a straight scratch through the cell monolayer. Subsequently, cells were incubated in serum-free DMEM. Wound closure was documented at 0 h, 24 h and 48 h post-scratch, and analyzed using Image J software.
2.9 Cell invasion and migration assays
Migration and invasion assays were conducted using a 24-well plate with a Transwell insert (8 μm pore size, BD Biosciences, USA). Medium with 10% FBS (600 µL) was added to the lower chamber. For invasion assays, the upper insert was precoated evenly with Matrigel (Sigma Aldrich, Germany). Subsequently, 1 × 104 cells in 200 µL of serum-free medium were seeded into the upper chamber. Following a 48 h incubation period, non-invading or non-migratory cells were removed. Cells were fixed with 4% paraformaldehyde for 30 min and then stained with 0.1% crystal violet (Sigma Aldrich, Germany) for 1 h. After washed by sterile water, cells were observed using an inverted fluorescence microscope (Olympus, Japan). Results were examined and documented in three random fields of view.
2.10 Detection of cell cycle and apoptosis
Cell cycle and apoptosis analyses were performed utilizing the Annexin V FITC/PI Apoptosis and Cell Cycle Kit (MultiSciences, China) following the manufacturer’s protocol. Flow cytometric analysis was performed using a Beckman instrument (USA).
2.11 In vivo experiments
Four-week-old male athymic BALB/C-nude mice were acquired from SPF Biotechnology (Beijing, China). All experimental procedures and husbandry were conducted at the Center for Animal Experiment at Wuhan University. The mice were randomly assigned and identified in two groups, with five mice per group, for the establishment of a subcutaneous tumor model. A stable UBE2Q2 knockdown cell line (Lv-shUBE2Q2) was generated using Huh-7 cells. For tumor induction, 5 × 106 cells were injected subcutaneously into the right axillary region of each mouse. Commencing on day 7 post-inoculation, mice received 100 mg/kg of PX-478 in PBS by intraperitoneal injection bi-daily. Tumor sizes were measured tri-weekly. After 3–4 weeks, the mice were euthanized, tumors were excised, and preserved in formalin for further immunohistochemical analysis.
2.12 HE and immunohistochemical staining (IHC)
Tissues intended for hematoxylin and eosin (H&E) or immunohistochemical (IHC) staining were fixed in 4% paraformaldehyde solution. These were then dehydrated, embedded in paraffin, and sectioned to produce tissue slices. Then each section was stained with H&E or with primary antibody such as UBE2Q2 antibody, HIF1α antibody or Ki67 antibody etc. Detailed information of primary antibodies used in IHC is provided in Table S3 of the supplementary materials. Imaging was conducted using an Aperio VERSA 8 automatic digital scanning and analysis system (Leica Biosystems, Germany), and the images were quantitatively analyzed with Aperio ImageScope software.
2.13 Proteomics assay
The HCC-LM3 cells transfected with UBE2Q2 plasmids constituted the experimental group, while those transfected with empty vector plasmids served as the control. Cells were harvested 48 h post-transfection. Cell pellets were lysed using a protein lysis buffer containing 7 M urea, 2 M thiourea, 4% SDS, 40 mM Tris-HCl (pH 8.5), 1 mM PMSF, and 2 mM EDTA. The lysate was sonicated for 15 min, then centrifuged at 4 °C for 20 min to collect the protein precipitate. The resulting samples were submitted in triplicate for proteomic analysis at Singleronbio (Nanjing, China). Peptides were tagged using the iTRAQ-8 kit (SCIEX), and peptide detection was conducted with TripleTOF 5600plus mass spectrometry. ProteinPilot V4.5 software was utilized for protein identification and quantification. Differential protein expression was determined based on fold change and P-value; proteins exhibiting a fold change of ≥ 1.5 (upregulated) or ≤ 0.67 (downregulated) with a P-value of ≤ 0.05 were considered significant.
2.14 Co-immunoprecipitation (Co-IP) and mass spectrometry (MS)
Huh-7 cells were grown in 10 cm diameter culture dishes and co-transfected with various plasmids for subsequent co-immunoprecipitation experiments. The cells were harvested and placed into 2 mL centrifuge tubes. Each tube was treated with 1 mL of IP buffer (comprising 20 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1 mM EDTA (pH 8.0), 1% NP-40, and 1×Protease and Phosphatase Inhibitor Cocktail) to lyse the cells for 30 min. Pre-washed Protein A/G Magnetic beads from MCE (USA) were introduced into the tubes and the mixture was agitated on a disc rotator mixer for another 30 min. Target-specific antibodies were then added to the respective tubes and incubated for over 3 h at 4 °C. After the incubation, beads were collected by centrifugation at 5,000 rpm for 2 min at 4 °C and washed 4 times with ice-cold wash buffer (10 mM Tris/Cl pH 7.5, 150 mM NaCl, 0.5 mM EDTA). The beads were resuspended with 40 µl of 2× sample buffer and boiled for 3 min. Immunoprecipitates were separated by SDS-PAGE and sent for mass spectrometry analysis (Hangzhou Cosmos Wisdom Biotechnology).
2.15 Western blot (WB)
Tissue and cellular proteins were extracted using RIPA lysis buffer supplemented with 1×PMSF proteasome inhibitor, both sourced from Beyotime (China). Protein concentrations were quantified using a BCA assay kit provided by Thermo Fisher Scientific (CA, USA). Proteins were resolved by electrophoresis on 7-10% SDS-PAGE gels and subsequently transferred onto polyvinylidene fluoride (PVDF) membranes. The membranes were blocked with 5% non-fat milk for 1 h before overnight incubation at 4℃ with primary antibodies. Following a series of washes, the membranes were incubated with the corresponding secondary antibodies for 90 min at room temperature. Then membranes were dipped in ECL Substrate Luminol solution from Bio-Rad (CA, USA). Chemiluminescence detection was performed using the Tanon-5200 imager (Shanghai, China). Comprehensive antibody details were included in Table S3 of the supplementary materials.
2.16 Glucose uptake and lactate production
Designated cells were transfected with UBE2Q2 plasmids, HIF1α plasmids, empty vector plasmids, siUBE2Q2, and siRNA NC in line with the experimental protocol, and then seeded into 96-well plates. At the 24 h mark, glucose uptake and lactate secretion were quantified using the Glucose Uptake Colorimetric Assay Kit and the L-Lactate Assay Kit, respectively, both from Sigma Aldrich (Germany) and in strict accordance with the provided manufacturer’s protocols. Absorbance readings at 412 nm were captured using an enzyme-linked immunosorbent assay reader.
2.17 Immunofluorescence (IF)
Huh-7 and HCC-LM3 cells fixed in 4% paraformaldehyde were permeabilized using 0.5% Triton X-100 for 15 min. Subsequently, cells were blocked with 5% bovine serum albumin (BSA) for 1 h at room temperature before overnight primary antibody incubation at 4 °C. After thorough washing with PBS, the cells were incubated with fluorescently labeled secondary antibodies for 1 h at room temperature within a humidified chamber. Following this, cells were mounted with DAPI to stain nuclei and visualized with an Olympus FluoView™ FV1000 confocal microscope.
2.18 Seahorse bioanalyzer
Cells transfected with the appropriate plasmids or siRNA were plated at a density of 4 × 104 cells per well in XF24 microplates (Seahorse Agilent, USA). The assay cartridge was hydrated in a CO2-free incubator at 37 °C overnight. The next day, cells were switched to a specialized assay medium before the extracellular acidification rate (ECAR) or oxygen consumption rate (OCR) was measured using a Seahorse XF24 Analyzer’s sensor probe, adhering to the manufacturer’s guidelines. For ECAR, glycolysis stress tests were conducted with Seahorse XF cell glycolysis stress test kits, and the data were processed using Wave software. For OCR, oxygen consumption tests were conducted with Seahorse XF cell mito stress test kits, and the data were processed using Wave software.
2.19 In vivo ubiquitination assays
Following 48 h post-transfection, Huh-7 cells transfected with pEZ-UBE2Q2 or vector plasmids and treated with cobalt chloride were harvested. Additionally, Huh-7 cells co-transfected with pEZ-UBE2Q2 and mutant ubiquitin plasmids—pCDEF-HA-Ub(K11) (all lysine was mutant to arginine except from wild-type lysine 11), pCDEF-HA-Ub(K48) (all lysine was mutant to arginine except from wild-type lysine 48), or pCDEF-HA-Ub(K63) (all lysine was mutant to arginine except from wild-type lysine 63)—were collected after 48 h. Cell pellets from each group were lysed in IP lysis buffer. Subsequent procedures were coherent with those previously described for co-immunoprecipitation (Co-IP).
UBE2Q2 expression in paired tissue samples and associated Kaplan-Meier survival curves for hepatocellular carcinoma (HCC) patients were extracted from The Cancer Genome Atlas (TCGA) database. Additional analyses of overall survival curves and correlations with UBE2Q2 in HCC were conducted using the GEPIA platform (
http://gepia.cancer-pku.cn). The data for single-gene enrichment analysis were sourced from the Gene Set Enrichment Analysis (GSEA) website (
http://www.gsea-msigdb.org/gsea/index.jsp), with the analysis performed using GSEA-3.0 software.
2.21 Statistical analysis
Statistical analysis was conducted using GraphPad Prism version 8.0 (GraphPad Software) and SPSS version 22.0 (SPSS, USA). Data are expressed as mean ± standard deviation (SD). The Student’s t-test and non-parametric test were utilized for comparing differences between two groups, while two-way ANOVA was employed for analyses involving more than two groups. Correlations between UBE2Q2 expression and clinical parameters were determined using the chi-squared (χ2) test, with two-tailed P values. Significance levels for all tests were set as follows: *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, with ns denoting ‘not significant’.
4 Discussion
Primary liver cancer ranks as one of the leading causes of cancer-related mortality globally. The high fatality rate stems chiefly from challenges in early detection, high postoperative recurrence, and limited treatment effectiveness [
27]. Malignant tumors commonly exhibit aerobic glycolysis, characterized by escalated glucose consumption and lactate production, bolstering tumor cell proliferation [
28]. Glycolytic inhibition has been implicated not only in suppressing tumorigenesis and angiogenesis but also in enhancing immune cell function [
29,
30].
Our investigation revealed overexpression of UBE2Q2, a putative ubiquitin-conjugating enzyme, in hepatocellular carcinoma (HCC), correlating with poorer patient prognosis. UBE2Q2 appears to drive HCC progression both in vitro and in vivo by facilitating HIF1α transcription. The mechanistic pathway entails UBE2Q2 binding with cIAP1 to trigger K63 ubiquitination of RIP1, thereby activating the NF-κB pathway, which in turn augments HIF1α transcription.
Previous research has linked abnormal UBE2Q2 overexpression to malignancies such as hypopharyngeal cancer, pediatric acute lymphoblastic leukemia, and breast cancer [
20,
21,
31]. HeLa cells exhibit increased chemotherapeutic sensitivity upon UBE2Q2 knockdown without altering cell cycle distribution [
19]. This study, however, demonstrated that UBE2Q2 knockdown in HCC cells leads to G2/M phase arrest and is associated with G2/M checkpoint and DNA damage repair pathways, as per gene set enrichment analysis of TCGA data. Our findings also suggest UBE2Q2’s involvement in glycolytic enhancement by upregulating key enzymes like PKM2, PFKL, and HIF1α. Multiple studies reveal a link between apoptosis, G2/M phase arrest, and the glycolytic activity of HIF1α, LDHA in tumor cells [
32‐
35], underscoring UBE2Q2’s oncogenic role in HCC.
The canonical NF-κB pathway is essential for inflammatory responses, cellular proliferation, differentiation, and survival [
36]. Persistent activation of this pathway can, however, drive tumor progression as seen in HBV-induced HCC [
37]. Moreover, NF-κB has been implicated in metabolic reprogramming towards glycolysis and increasing HIF1α transcription [
38,
39]. Our study corroborates UBE2Q2’s role in promoting HCC glycolysis and tumor growth through HIF1α transcriptional regulation, with (-)-DHMEQ inhibition indicating UBE2Q2’s possible mediation via the NF-κB pathway. Yet, the absence of numerous differentially expressed NF-κB proteins in the proteomic assay suggests UBE2Q2’s involvement might extend beyond direct NF-κB activation.
The NF-κB pathway and Warburg effect have deep interplay. For instance, the activation of the NF-kB pathway can lead to the increased expression of key enzymes involved in glycolysis, driving the Warburg effect [
40]. Pro-inflammatory cytokines released as a result of NF-kB activation can also indirectly support the Warburg effect by fostering a microenvironment conducive to metabolic alterations [
41]. In the same time, the metabolic reprogramming in cancer cells results in the accumulation of reactive oxygen species and other byproducts, which can further activate the NF-kB pathway, creating a positive feedback loop [
42]. Our study substantiated their crucial molecular cross-talk is pathogenic in HCC.
The exact role of UBE2Q2 within the ubiquitin system remains elusive, with prior research identifying its interaction with cIAP1/2’s RING domain [
24]. Our work not only substantiates cIAP1 as an interacting protein but also presents evidence of UBE2Q2-engaged K63 ubiquitination of RIP1, marking the first revelation of UBE2Q2 modifying protein ubiquitination. This K63 ubiquitination alteration suggests UBE2Q2’s activity within ubiquitin conjugation and its participation in NF-κB pathway activation.
In sum, UBE2Q2 propels HCC tumorigenesis and glycolysis by activating the NF-κB/HIF1α pathway, offering novel therapeutic avenues for tumor treatment.
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