High expression of ELFN1 is a prognostic biomarker and promotes proliferation and metastasis of colorectal cancer cells

doi:10.12122/j.issn.1673-4254.2025.07.22

Abstract

Abstract:

Objective To explore the correlation of ELFN1 expression level with prognosis of colorectal cancer and its regulatory role in colorectal cancer cell proliferation and metastasis. Methods We analyzed the expression levels of ELFN1 across 33 cancer types using publicly available databases and identified differential genes related to ELFN1 in colorectal cancer. Gene function annotation and enrichment analysis were used to identify the involved signaling pathways. Logistic analysis, Kaplan-Meier analysis and Cox regression analysis were performed to evaluate the correlation between ELFN1 expression and clinicopathological parameters and survival of colorectal cancer patients. qPCR and Western blotting were used to validate the expression levels of ELFN1 in different colorectal cancer cell lines and tissues, and Transwell and EDU experiments were carried out to assess the effect of ELFN1 knockdown on biological behaviors of SW480 cells. Results ELFN1 was highly expressed in 14 cancers, and its expression was significantly higher in colon cancer tissues than in adjacent tissues. A high expression of ELFN1 mRNA was associated with a poorer overall survival of colorectal cancer patients. Cox regression analysis indicated that ELFN1 expression was an independent prognostic factor for overall survival of the patients. ELFN1 was significantly enriched in tumor metastasis and proliferation and participated in several tumor signaling pathways. The colon cancer cell lines showed significantly higher expression levels of ELFN1 than normal cells, ELFN1 knockdown obviously inhibited proliferation and migration of SW480 cells in vitro. Conclusion ELFN1 is overexpressed in colorectal cancer and is associated with poor clinical prognosis of the patients. A high ELFN1 expression is associated with malignant phenotypes of colorectal cancer and promotes cancer cell proliferation and metastasis, suggesting its potential as a prognostic biomarker for colorectal cancer.

Key words: colorectal cancer, ELFN1, ECM signaling pathway, clinical prognosis, bioinformatics

Kang WANG, Haibin LI, Jing YU, Yuan MENG, Hongli ZHANG. High expression of ELFN1 is a prognostic biomarker and promotes proliferation and metastasis of colorectal cancer cells[J]. Journal of Southern Medical University, 2025, 45(7): 1543-1553.

Figures/Tables 9

Fig.1 Data from the TCGA database show high expression of ELFN1 in a variety of tumors, which has different prognostic implications. A: TCGA diffuse carcinoma analysis. B: TCGA pan-cancer pairing analysis. C: Forest map of the prognostic value of ELFN1 in different tumors. *P<0.05, **P<0.01, ***P<0.001.

Fig.2 ELFN1 has a high diagnostic value in colon cancer and is highly expressed in colon cancer. A: Venn diagram of ELFN1 expression patterns and its prognosis and diagnostic value of colon cancer. B: ROC curve analysis showing an AUC value of ELFN1 in COAD of 0.851. C: High expression levels of ELFN1 in paired samples of TCGA. D-F: Multiple datasets in the GEO database indicate that the expression level of ELFN1 is higher tumor tissues than in normal tissues. *P<0.05, **P<0.01, ***P<0.001.

Fig.3 Prognostic and clinical significance of ELFN1 in colon cancer. A-C: Kaplan-Meier survival analysis reveals that COAD patients with high ELFN1 expression have shorter overall survival (A), disease-specific survival (B) and progression-free interval (C) than those with low ELFN1 expression. D-I: mRNA expression level of ELFN1 in COAD patients with different clinicopathological features. *P<0.05, **P<0.01, ***P<0.001.

Tab.1 Univariate and multivariate Cox regression analyses of overall survival of COAD patients based on ELFN1 expression levels

Characteristics	Total (n)	Univariate analysis		Multivariate analysis
Characteristics	Total (n)	Hazard ratio (95%CI)	P	Hazard ratio (95%CI)	P
Age (year)	477
≤65	194	Reference
>65	283	1.610 (1.052-2.463)	0.028	3.417 (1.309-8.920)	0.012
T stage	476
T1&T2	94	Reference
T3&T4	382	3.072 (1.423-6.631)	0.004	0.661 (0.120-3.637)	0.634
N stage	477
N0	283	Reference
N1&N2	194	2.592 (1.743-3.855)	<0.001	0.174 (0.016-1.839)	0.146
M stage	414
M0	348	Reference
M1	66	4.193 (2.683-6.554)	<0.001	5.463 (1.807-16.518)	0.003
Pathologic stage	466
Stage I&Stage II	267	Reference
Stage III&Stage IV	199	2.947 (1.942-4.471)	<0.001	14.791(1.177-185.875)	0.037
Perineural invasion	181
No	135	Reference
Yes	46	1.940 (0.982-3.832)	0.056	0.736 (0.280-1.935)	0.534
Lymphatic invasion	433
No	265	Reference
Yes	168	2.450 (1.614-3.720)	<0.001	1.408 (0.557-3.556)	0.470
ELFN1	477
Low	238	Reference
High	239	1.683 (1.135-2.496)	0.010	3.284 (1.154-9.339)	0.026

Tab.2 Logistic regression analysis of ELFN1

Characteristic	Total (n)	OR (95%CI)	P
Pathologic T stage (T3&T4 vs T1&T2)	477	1.831 (0.975-3.600)	0.069
Pathologic N stage (N1&N2 vs N0)	478	1.743 (1.078-2.851)	0.025
Pathologic M stage (M1 vs M0)	415	2.425 (1.286-4.572)	0.006
Pathologic stage (Stage III&IV vs Stage I&II)	467	1.787 (1.104-2.936)	0.020
Primary therapy outcome (PD&SD vs PR&CR)	250	2.834 (1.120-7.152)	0.025
Perineural invasion (Yes vs No)	181	2.675 (0.984-7.424)	0.044
Lymphatic invasion (Yes vs No)	434	2.823 (1.653-4.934)	<0.001

Fig.4 Analysis of differentially expressed genes related to ELFN1 and construction of the PPI network. A: Volcano plot of differentially expressed genes (DEGs, |log2(FC)|>1, P.adj<0.05). B: The co-expression chord diagram showing the top 10 genes positively and negatively correlated with ELFN1. C: Molecular protein interaction network of ELFN1.

Fig.5 ELFN1 interaction protein identification and gene function annotation analysis. A: GO functional annotation analysis of biological process (BP), cellular component (CC) and molecular function (MF). B: Analysis of 10 KEGG signaling pathways related to ELFN1. C, D: The 10 GSEA pathways associated with ELFN1 in COAD.

Fig.6 Expression and function of ELFN1 in COAD cell lines. A, B: ELFN1 expression levels in NCM460, SW480, SW620, RKO, HCT116, LOVO, and CACO2 cells detected by qRT-PCR (A) and Western blotting (B). *P<0.05, **P<0.01, ***P<0.001 vs NCM460 cells. C: Expression levels of ELFN1 in 10 pairs of colon cancer tissue samples (*P<0.05, **P<0.01, ***P<0.001 vs NATs). D: Transwell assay of SW480 cells transfected with si-ELFN1. E: EDU proliferation assay of SW480 cells transfected with si-ELFN1. **P<0.01, ***P<0.001.

Fig.7 Molecular mechanism of ELFN1 in the oncogenic signaling pathway of colorectal cancer. A: Analysis of relevant carcinogenic pathways of ELFN1 in COAD. B: Western blotting for detecting protein expressions in COAD cells with ELFN1 knockdown. *P<0.05, ***P<0.001.

References 34

[1]	Stachniak TJ, Sylwestrak EL, Scheiffele P, et al. Elfn1-induced constitutive activation of mGluR7 determines frequency-dependent recruitment of somatostatin interneurons[J]. J Neurosci, 2019, 39(23): 4461-74. doi：10.1523/jneurosci.2276-18.2019
[2]	Dunn HA, Patil DN, Cao Y, et al. Synaptic adhesion protein ELFN1 is a selective allosteric modulator of group III metabotropic glutamate receptors in trans [J]. Proc Natl Acad Sci USA, 2018, 115(19): 5022-7. doi：10.1073/pnas.1722498115
[3]	Tomioka NH, Yasuda H, Miyamoto H, et al. Elfn1 recruits presynaptic mGluR7 in trans and its loss results in seizures[J]. Nat Commun, 2014, 5: 4501. doi：10.1038/ncomms5501
[4]	Girgenti MJ, Wang JW, Ji DJ, et al. Transcriptomic organization of the human brain in post-traumatic stress disorder[J]. Nat Neurosci, 2021, 24(1): 24-33. doi：10.1038/s41593-020-00748-7
[5]	Zhang C, Lian H, Xie L, et al. LncRNA ELFN1-AS1 promotes esophageal cancer progression by up-regulating GFPT1 via sponging miR-183-3p[J]. Biol Chem, 2020, 401(9): 1053-61. doi：10.1515/hsz-2019-0430
[6]	Jie YK, Ye L, Chen H, et al. ELFN1-AS1 accelerates cell proliferation, invasion and migration via regulating miR-497-3p/CLDN4 axis in ovarian cancer[J]. Bioengineered, 2020, 11(1): 872-82. doi：10.1080/21655979.2020.1797281
[7]	Feng WG, Zhu RX, Ma JL, et al. LncRNA ELFN1-AS1 promotes retinoblastoma growth and invasion via regulating miR-4270/SBK1 axis[J]. Cancer Manag Res, 2021, 13: 1067-73. doi：10.2147/cmar.s281536
[8]	Ma G, Li GC, Gou AJ, et al. Long non-coding RNA ELFN1-AS1 in the pathogenesis of pancreatic cancer[J]. Ann Transl Med, 2021, 9(10): 877. doi：10.21037/atm-21-2376
[9]	Office FE. Retraction: Long non-coding RNA ELFN1-AS1 promoted colon cancer cell growth and migration via the miR-191-5p/special AT-rich sequence-binding protein 1 axis[J]. Front Oncol, 2023, 13: 1322464. doi：10.3389/fonc.2023.1322464
[10]	Lei R, Feng LC, Hong D. ELFN1-AS1 accelerates the proliferation and migration of colorectal cancer via regulation of miR-4644/TRIM44 axis[J]. Cancer Biomark, 2020, 27(4): 433-43. doi：10.3233/cbm-190559
[11]	Li YM, Gan YQ, Liu JX, et al. Downregulation of MEIS1 mediated by ELFN1-AS1/EZH2/DNMT3a axis promotes tumorigenesis and oxaliplatin resistance in colorectal cancer[J]. Signal Transduct Target Ther, 2022, 7(1): 87. doi：10.1038/s41392-022-00902-6
[12]	Dekker E, Tanis PJ, Vleugels JLA, et al. Colorectal cancer[J]. Lancet, 2019, 394(10207): 1467-80. doi：10.1016/s0140-6736(19)32319-0
[13]	Eng C, Jácome AA, Agarwal R, et al. A comprehensive framework for early-onset colorectal cancer research[J]. Lancet Oncol, 2022, 23(3): e116-28. doi：10.1016/s1470-2045(21)00588-x
[14]	Libé-Philippot B, Lejeune A, Wierda K, et al. LRRC37B is a human modifier of voltage-gated sodium channels and axon excitability in cortical neurons[J]. Cell, 2023, 186(26): 5766-83.e25. doi：10.1016/j.cell.2023.11.028
[15]	Huang JX, Yuan WW, Chen BB, et al. lncRNA ELFN1-AS1 upregulates TRIM29 by suppressing miR-211-3p to promote gastric cancer progression[J]. Acta Biochim Biophys Sin (Shanghai), 2023, 55(3): 484-97. doi：10.3724/abbs.2023023
[16]	Deng X, Kong FY, Li S, et al. A KLF4/PiHL/EZH2/HMGA2 regulatory axis and its function in promoting oxaliplatin-resistance of colorectal cancer[J]. Cell Death Dis, 2021, 12(5): 485. doi：10.1038/s41419-021-03753-1
[17]	Huang L, Xiao W, Wang Y, et al. Metabotropic glutamate receptors (mGluRs) in epileptogenesis: an update on abnormal mGluRs signaling and its therapeutic implications[J]. Neural Regen Res, 2024, 19(2): 360-8. doi：10.4103/1673-5374.379018
[18]	Becker JAJ, Pellissier LP, Corde Y, et al. Facilitating mGluR4 activity reverses the long-term deleterious consequences of chronic morphine exposure in male mice[J]. Neuropsychopharmacology, 2021, 46(7): 1373-85. doi：10.1038/s41386-020-00927-x
[19]	Qin X, Cardoso Rodriguez F, Sufi J, et al. An oncogenic phenoscape of colonic stem cell polarization[J]. Cell, 2023, 186(25): 5554-68.e18. doi：10.1016/j.cell.2023.11.004
[20]	Chen CK, Ng CS, Wu SM, et al. Regulatory differences in natal down development between altricial Zebra finch and precocial chicken[J]. Mol Biol Evol, 2016, 33(8): 2030-43. doi：10.1093/molbev/msw085
[21]	Taylor KR, Barron T, Hui A, et al. Glioma synapses recruit mechanisms of adaptive plasticity[J]. Nature, 2023, 623(7986): 366-74. doi：10.1038/s41586-023-06678-1
[22]	Iijima N, Sato K, Kuranaga E, et al. Differential cell adhesion implemented by Drosophila Toll corrects local distortions of the anterior-posterior compartment boundary[J]. Nat Commun, 2020, 11(1): 6320. doi：10.1038/s41467-020-20118-y
[23]	Valle JW, Lamarca A, Goyal L, et al. New horizons for precision medicine in biliary tract cancers[J]. Cancer Discov, 2017, 7(9): 943-62. doi：10.1158/2159-8290.cd-17-0245
[24]	Dai J, Su YZ, Zhong SY, et al. Exosomes: key players in cancer and potential therapeutic strategy[J]. Signal Transduct Target Ther, 2020, 5(1): 145. doi：10.1038/s41392-020-00261-0
[25]	Dunn HA, Dhaliwal SK, Chang CT, et al. Distinct autoregulatory roles of ELFN1 intracellular and extracellular domains on membrane trafficking, synaptic localization, and dimerization[J]. J Biol Chem, 2025, 301(1): 108073. doi：10.1016/j.jbc.2024.108073
[26]	Ayhan S, Dursun A. ELFN1 is a new extracellular matrix (ECM)-associated protein[J]. Life Sci, 2024, 352: 122900. doi：10.1016/j.lfs.2024.122900
[27]	Wishart AL, Conner SJ, Guarin JR, et al. Decellularized extracellular matrix scaffolds identify full-length collagen VI as a driver of breast cancer cell invasion in obesity and metastasis[J]. Sci Adv, 2020, 6(43): eabc3175. doi：10.1126/sciadv.abc3175
[28]	Dunn HA, Orlandi C, Martemyanov KA. Beyond the ligand: extracellular and transcellular G protein-coupled receptor complexes in physiology and pharmacology[J]. Pharmacol Rev, 2019, 71(4): 503-19. doi：10.1124/pr.119.018044
[29]	Kumar US, Natarajan A, Massoud TF, et al. FN₃ linked nanobubbles as a targeted contrast agent for US imaging of cancer-associated human PD-L1[J]. J Control Release, 2022, 346: 317-27. doi：10.1016/j.jconrel.2022.04.030
[30]	Winkler J, Abisoye-Ogunniyan A, Metcalf KJ, et al. Concepts of extracellular matrix remodelling in tumour progression and metastasis[J]. Nat Commun, 2020, 11(1): 5120. doi：10.1038/s41467-020-18794-x
[31]	Glaviano A, Foo ASC, Lam HY, et al. PI3K/AKT/mTOR signaling transduction pathway and targeted therapies in cancer[J]. Mol Cancer, 2023, 22(1): 138. doi：10.1186/s12943-023-01827-6
[32]	Deng ZQ, Fan T, Xiao C, et al. TGF-β signaling in health, disease and therapeutics[J]. Sig Transduct Target Ther, 2024, 9: 61. doi：10.1038/s41392-024-01764-w
[33]	Rigillo G, Belluti S, Campani V, et al. The NF-Y splicing signature controls hybrid EMT and ECM-related pathways to promote aggressiveness of colon cancer[J]. Cancer Lett, 2023, 567: 216262. doi：10.1016/j.canlet.2023.216262
[34]	Strating E, Verhagen MP, Wensink E, et al. Co-cultures of colon cancer cells and cancer-associated fibroblasts recapitulate the aggressive features of mesenchymal-like colon cancer[J]. Front Immunol, 2023, 14: 1053920. doi：10.3389/fimmu.2023.1053920