Elevated FUBP1 is associated with tumor progression in CRC
LoVo cells derived from metastatic tumor tissue exhibited the strong ability of tumor sphere formation compared to SW48 cells derived from the primary site with low expression of CD133/ALDH (Supplementary Figure. 1). To explore the critical functional molecules in tumor stemness and aggressiveness, we sorted CD133+ALDH1+ LoVo cells which accounted for a 9.6% ratio in total LoVo cells. We then analyzed differential protein expression between CD133+ALDH1+ LoVo cell and SW48 cells by iTRAQ protein mass spectrometry (Figure. 1A). Among the most changed proteins, a transcription factor, FUBP1, draws our attention. Since it is closely related to the maintenance and differentiation of stem cells, while the connection of FUBP1 with CRC was barely mentioned before (Figure. 1B-C).
Next, we verified the crucial role of FUBP1 in the progression of CRC. Impressively, compared to adjacent specimens (H-Score = 1.411), FUBP1 expression was remarkably increased in CRC specimens (H-Score = 4.089; p < 0.001; Figure. 1D-E) in a CRC Tissue Microarray (Supplementary Figure. 2). Meanwhile, we retrospectively studied the medical records of 143 patients in the CRC population and identified that FUBP1 expression increased along with the progression of CRC clinical stages (Figure. 1F-G). In addition, Correlation analysis demonstrated that elevated FUBP1 positively correlated with CRC lymph node metastasis and advanced clinical stages (Supplementary Table. 1). Accordingly, FUBP1 expression was negatively associated with overall survival (p < 0.001; Figure. 1H). The OS of the FUBP1 high expression group was even 30.25 months shorter than that of the low expression group (HR, 1.96; 95% CI, 1.291 to 2.974). Taken together, the upregulation of FUBP1 is associated with CRC metastasis and might be a potential prognostic factor for CRC.
Elevated Fubp1 Promotes Crc Cells Migration And Invasion
Similar to the results in CRC tissues, FUBP1 was significantly increased in CRC cell lines compared with normal intestinal epithelial cells (NCM460, CCD841). Moreover, CRC cells (LoVo, SW620) derived from tumor metastasis showed higher expression of FUBP1 than those (CaCO2, HCT116, SW48) derived from the primary site (Figure. 2A-B).
Furthermore, colony formation assay was performed to validate the cloning ability of CRC cells promoted by FUBP1. As shown in Figure. 2C-D, compared to the vector control cells, the numbers of the colony from FUBP1-transfected SW48 cells increased, and conversely decreased in FUBP1-silenced LoVo cells (Supplementary Figure. 3A-B). Moreover, Transwell and wound healing assay showed that the migration and invasion abilities were substantially enhanced in FUBP1 overexpressed SW48 cells, while were suppressed in FUBP1 knocked down LoVo cells (Figure. 2E-H; Supplementary Figure. 3C-F). These results suggested that the upregulation of FUBP1 promoted CRC cell migration and invasion.
Elevated FUBP1 promotes the stemness of CRC cells in vitro
CRC recurrence and distant metastasis arise from a subpopulation of CSCs, and FUBP1 expression was inversely correlated with tumor differentiation status (Supplementary Table. 1), which implied that cell migration and invasion enhanced by FUBP1 might be attributed to the regulation of stemness. To explore the oncogenic role of FUBP1 in the stimulation of stemness in CRC cells, firstly, the protein levels of the stemness-related markers, CD133, ALDH1, LGR5, and CD44, were examined between FUBP1 low expressing SW48 cells and FUBP1 high expressing LoVo cells. It showed that expression of stemness-related markers, especially CD133 and ALDH1, were elevated in the LoVo cell (Supplementary Figure.1A). Meanwhile, western blotting results revealed that CD133 and ALDH1, were up-regulated in FUBP1-transfected SW48 cells, and conversely downregulated in FUBP1-silenced LoVo cells (Figure. 3A; Supplementary Figure. 4A). In addition, Flow cytometry results further showed that overexpression of FUBP1 substantially increased the CD133+ALDH1+ percentage in SW48 cells from 0.34–3.27%, while knockdown of FUBP1 decreased the CD133+ALDH1+ percentage in LoVo cells from 7.06–3.28% (Figure. 3B-C; Supplementary Figure. 4B-C).
Next, we conducted the tumor sphere formation assays to examine the effect of FUBP1 on the self-renewal ability of spherogenic CRC cells. After 10 days culture, the numbers and sizes of the formed spheres in the FUBP1-transfected SW48 group were more remarkable than that of the vector control group, and the FUBP1-silenced LoVo group exhibited the opposite effect (Figure. 3D-E; Supplementary Figure. 4D-E). Furthermore, FUBP1-transfected SW48 cells formed a more significant number of offspring spheres than the vector control cells, whereas FUBP1-silenced cells formed fewer offspring spheres (Figure. 3F).
To further confirm that FUBP1 played a considerable role in CRC CSCs, we investigated the expression of FUBP1 in CD133+ALDH1+ cells sorted from LoVo cells by flow cytometer. As expected, CD133+ALDH1+ LoVo cells expressed higher level of FUBP1 than the LoVo cells (Figure. 3G). Similarly, LoVo spheres sorted by tumor sphere formation also showed higher FUBP1 levels than the LoVo cells (Figure. 3H). while CD133 and ALDH1 were significantly down-regulated in FUBP1-silenced LoVo spheres (Figure. 3I). Notably, knockdown of FUBP1 in LoVo spheres substantially reduced the numbers and sizes of the formed spheres, and decreased the migration and invasion abilities (Figure. 3J-K; Supplementary Figure. 6). Collectively, these results indicated that the upregulation of FUBP1 promoted the stemness of CRC cells in vitro.
Elevated FUBP1 enhances the stemness and tumorigenicity of CRC cells in vivo
To explore the oncogenic role of FUBP1 in the promotion of stemness in CRC cells in vivo, BALB/c nude mice were subcutaneously inoculated different numbers of CRC cells mixed with Matrigel into the inguinal folds. The tumors formed by FUBP1-transfected SW48 cells had a larger size and obvious tumorigenicity than those formed by vector control cells after implantation of 1×106, 1×105, 1×104, or 1×103 cells (Figure. 4A-B; Supplementary Table. 2). Conversely, FUBP1-silenced LoVo cells formed smaller tumors and had blunt tumorigenicity (Figure. 4C-D; Supplementary Table. 2). Notably, the tumorigenicity of the sorted CD133+ALDH1+ LoVo cells was enhanced and fewer implantation of 1×105, 1×104, 1×103, or 1×102 cells were needed, meanwhile tumor size and tumorigenicity were quelled by FUBP1-silence (Figure. 4E-F; Supplementary Table. 3). Western blotting and Immunohistochemistry (IHC) results demonstrated that the expression of CD133 and ALDH1 in tumors originated from FUBP1-transfected SW48 cells were increased, compared with that from vector control cells (Figure. 4G; Supplementary Figure. 7). Notably, the expression of CD133 (p < 0.001; R2 = 0.519) and ALDH1 (p < 0.001; R2 = 0.588) in human CRC specimens were strongly positively correlated with FUBP1 in a CRC Tissue Microarray (Figure. 4H-I; Supplementary Figure. 8). Therefore, we concluded that elevated FUBP1 enhanced the stemness and tumorigenicity of CRC cells in vivo.
Elevated FUBP1 mediates stemness through the activation of the Wnt/β-catenin signaling
Wnt/β-catenin signaling is well accepted to be involved in the stemness in CRC8. To explore the mechanism related to the FUBP1-mediated stemness in CRC, we observed the Wnt/β-catenin signaling in the indicated FUBP1-transfected, FUBP1-silenced, or vector control cells. As expected, FUBP1 positively regulated the phosphorylation level of GSK-3β (Ser9) and non-phosphorylation levels of β-catenin (Figure. 5A). Next, nuclear extract and immunofluorescence assays showed that overexpression of FUBP1 substantially increased the β-catenin nuclear signals, whereas knockdown of FUBP1 reduced β-catenin nuclear translocation (Figure. 5B-D). Meanwhile, the mRNA transcription of the downstream targets of Wnt/β-catenin signaling, including COX2, MMP7, CCND1, c-MYC, and SOX2, were increased in FUBP1-transfected cells but were decreased in FUBP1-silenced cells (Figure. 5E). Collectively, these data suggested that FUBP1 overexpression activated the Wnt/β-catenin signaling pathway.
To further validated the targets of FUBP1 in the Wnt/β-catenin signaling pathway, we used Real-time PCR to detect the change of receptors and ligands which played essential roles in this pathway, including LRP5, LRP6, FZD1, WNT3A, and WNT5A, as FUBP1 had been proved to be an important transcription factor. However, none of these molecules are significantly altered (Supplementary Figure. 9). Then, we detected mRNA levels of the critical scaffold molecules in the upstream of β-catenin, including DVL, GSK-3β, APC, AXIN, and CK1. Impressively, we found that DVL1 mRNA levels were significantly up-regulated by FUBP1, while other molecules remained unchanged (Figure. 5F). Moreover, FUBP1 increased DVL1 protein expression levels in CRC cells and tumor specimens, whereas silencing FUBP1 had the opposite effects (Figure. 5G; Supplementary Figure. 7). Furthermore, FUBP1 expression was positively correlated with the expression of DVL1 in CRC tissues (p < 0.001; R2 = 0.541; Figure. 5H-I). These data indicated that FUBP1 activates the Wnt/β-catenin signaling through transcriptionally regulating DVL1.
Fubp1 Up-regulates Dvl1 Through Direct Binding To Its Promoter
To investigate how DVL1 was transcriptionally regulated by FUBP1, promoter assays were undertaken. As shown in Figure. 6A, luciferase reporters containing the full-length of the human DVL1 promoter were transiently transfected into LoVo cells and overexpressed FUBP1 vector or empty vector as a control. Overexpression of FUBP1 significantly increased DVL1 promoter-driven reporter activity. To identify the specific binding site, we constructed five truncation fragments of DVL1 promoter, as indicated in Supplementary Figure. 11A. Our results demonstrated that FUBP1 is bound to DVL1-P3 fragments (Figure. 6B). After carefully searching, we found a potential binding site (TTCCCCTGATTT) in DVL1-P3 fragments was identical to the c-Myc FUSE binding site. The candidate FUBP1 binding site, TTCCCCTGATTT, was shown in the − 1178 to − 1167 region of the DVL1 promoter sequence (Figure. 6C). To confirm whether FUBP1 can directly bind to this site, we constructed a mutation of DVL1-P3 (C to G substitution and T to A substitution, underlined), and the mutation abolished FUBP1 mediated up-regulation of DVL1-P3 promoter reporter activity. Chromatin immunoprecipitation (ChIP) assays further confirmed that FUBP1 could directly bind to DVL1-P3 fragments (Figure. 6D; Supplementary Figure. 10A).
Next, we investigated whether DVL1 activation was required for the stemness in CRC cells. Silencing DVL1 substantially reduced the sphere-forming ability of FUBP1-overexpressing cells, the stemness-related markers expressions (CD133 and ALDH1), as well as Wnt/β-catenin signaling (Figure. 6E-F; Supplementary Figure. 10B). The increased abilities of CRC cell migration and invasion induced by overexpression of FUBP1 were also dramatically abrogated by knockdown of DVL1 (Supplementary Figure. 11B-C). Moreover, to address the key role of DVL1 in the FUBP1-induced effect of CRC in vivo, we generated a cell line-derived xenograft model using SW48-Vector, SW48-FUBP1, SW48-FUBP1 with DVL1 knockdown, and SW48-FUBP1 with NSC668036 treatment (DVL inhibitor). It showed that SW48-FUBP1 with DVL1 knockdown and treatment with NSC668036 in SW48-FUBP1 xenografts inhibited the tumor volume and tumorigenicity significantly(Figure. 6G-H; Supplementary Table. 4). On the contrary, LoVo-FUBP1 with DVL1 overexpression xenografts recovered the tumor volume and tumorigenicity compared with LoVo-shFUBP1 xenografts (Figure. 6I-J; Supplementary Table. 5). Taken together, our results indicated that FUBP1 activated the Wnt/β-catenin signaling to promote the stemness of CRC cells through up-regulating DVL1 by direct binding to DVL1's promoter.
FUBP1 is ubiquitinated by Smurf2 in CRC regardless of KRAS genotype
The above data suggest that FUBP1 plays a crucial role in the stemness and metastasis in CRC. The critical question arose up that the intrinsic mechanism by which FUBP1 was up-regulated in CRC. KRAS mutations are the most frequent alterations, occurring in 30–50% of CRC cases. Further investigation of 54 CRC specimens identified that FUBP1 was highly expressed in KRAS mutation CRC specimens (n = 14) compared with KRAS wild-type specimens (n = 40; p < 0.001; Figure. 7A-B). The proportion of high FUBP1 expression (H-Score ≥ 6) in the KRAS mutation group (85.71%, 12/14) was higher than that of the KRAS wild-type group (25.00%,10/40; Figure. 7C). Moreover, KRAS mutation significantly increased FUBP1 protein expression levels in CRC cells, whereas silencing KRAS exhibited the opposite effects (Supplementary Figure. 12C). Unexpectedly, the RNA level of FUBP1 was unchanged in the tumor section than adjacent sections from the TCGA-COAD database, and remain consistent in the LoVo cell compared to the SW48 cell (Supplementary Figure. 12A-B).
Interestingly, we found that the proportion of high FUBP1/KRAS wild-type specimen remained as 18.52% of total CRC pathological samples (10/54; Figure. 7C). The survival outcomes of patients with high FUBP1 expression in both KRAS wild-type (HR, 2.369; 95%CI, 0.923 to 6.080; p = 0.013) and KRAS mutation (HR, 5.201; 95%CI, 1.612 to 16.78; p < 0.001) were much poorer compared with simultaneous low FUBP1 /KRAS wild-type patients (Figure. 7D). While the survival outcomes of patients had no statistical difference between high FUBP1/KRAS wild-type and high FUBP1/KRAS mutation groups (p = 0.066; Figure. 7D). While FUBP1 RNA levels were not statistically different in CRC specimens between KRAS mutation, KRAS wild-type, and adjacent CRC specimens (Supplementary Figure. 12D). These results suggest that FUBP1 might be post-transcriptionally regulated in CRC regardless of KRAS mutation.
Recently studies showed that Smurf2 was responsible for the ubiquitination of FUBP1. Excitingly, lower expression of Smurf2 was found only in the high FUBP1/ KRAS wild-type group (Figure. 7E-F). Silencing Smurf2 substantially increased the expression of FUBP1 and the stemness-related markers, CD133 and ALDH1, conversely decreased in Smurf2 overexpressed cells (Figure. 7G). Consistently, we found Smurf2 effectively shorten protein half-lives of FUBP1 via proteasomal degradation pathway (Figure. 7H-I). Furthermore, ectopically expressed Smurf2 with MG132 treatment markedly promoted the polyubiquitination levels of FUBP1 (Figure. 7J). These data indicated that the FUBP1 level was post-transcriptionally by Smurf2 in KRAS mutation and part of KRAS wild-type CRC.
FUBP1 is also up-regulated by caspase3 inactivation driven by KRAS signaling in KRAS mutation CRC
Moreover, Previous research demonstrated that FUBP1 was the hydrolyzed substrate of caspase311, which is mainly suppressed by the anti-apoptosis AKT and ERK signaling. KRAS mutation, which directly activates ERK and AKT pathways, has been recently linked to CSCs-like phenotypes16. Therefore, we hypothesized that inhibition of caspase3 activity through activating the anti-apoptosis AKT and ERK signaling mediated by KRAS mutation also contributed to the abnormal increase of FUBP1.
Next, we observed the protein expression induction of FUBP1 in SW48 treated with SC79 (AKT activator), LM22B-10 (ERK activator), Nocodazole (apoptosis activator) or KRAS mutation, along with FUBP1 expression in LoVo treated with MK2206 (AKT inhibitor), AZD0364 (ERK inhibitor), Z-VAD-FMK (apoptosis inhibitor) or KRAS knockdown (Figure. 8A). It showed that AKT and ERK activators increased the expression of FUBP1 in SW48 almost close to that of SW48 KRASG13D, while apoptosis agonist could block this induction. On the contrary, AKT and ERK inhibitors decreased the expression of FUBP1 in LoVo almost close to that of LoVo-shKRAS, while apoptosis inhibitor rescued this inhibition. Silencing FUBP1 substantially reduced the stemness inducing by KRAS mutation (Figure. 8B-D). All these data confirmed that FUBP1 was post-transcriptionally up-regulated by caspase3 inhibition through AKT and ERK activation driven by KRAS mutation. The conclusion of the mechanism study fully revealed the reason for the increase of FUBP1 in colorectal cancer, providing another target for treatment (Figure. 8E).