Epigenetic silencing of HOPX is critically involved in aggressive phenotypes and patient prognosis in papillary thyroid cancer

Methyltransferase-like 3-mediated m6A modification of miR-1908-5p contributes to nasopharyngeal carcinoma progression by targeting homeodomain-only protein homeobox

BACKGROUND

N6-methyladenosine (m6A) modification interacting microRNAs (miRNAs) have been confirmed to participate in nasopharyngeal carcinoma (NPC) progression. This research investigated miR-1908-5p's function and regulatory mechanism in the tumorigenesis of NPC via m6A modification and targeting a key gene.

METHODS

The levels of miR-1908-5p, homeodomain-only protein homeobox (HOPX), and methyltransferase-like 3 (METTL3) expressions were detected via RT-qPCR. The correlation between miR-1908-5p and the HOPX/METTL3 axis, as well as their regulatory mechanism, was investigated by dual luciferase reporter, western blotting, and MeRIP assays. Moreover, the bio-functions of miR-1908-5p, HOPX, and METTL3 in NPC were explored through CCK8, transwell, caspase-3 activity, and xenograft tumor assays.

RESULTS

RT-qPCR results indicated a miR-1908-5p upregulation in NPC. Knocking down miR-1908-5p diminished the NPC cell viability and migration in vitro. In vivo, downregulating miR-1908-5p repressed NPC cell tumor growth. Moreover, HOPX was specifically targeted by miR-1908-5p, and HOPX downregulation led to reversal of the anti-tumor impact of the miR-1908-5p inhibitor against NPC cell malignancy. Also, METTL3 could mediate the m6A modification of miR-1908-5p to regulate its influence on NPC cells.

CONCLUSION

This study demonstrated that the METTL3-mediated m6A modification of miR-1908-5p enhanced the tumorigenesis of NPC by targeting HOPX. These findings propose new insights for NPC diagnosis and therapy.

HOPX is a tumor-suppressive biomarker that corresponds to T cell infiltration in skin cutaneous melanoma

BACKGROUND

Skin cutaneous melanoma (SKCM) is the most threatening type of skin cancer. Approximately 55,000 people lose their lives every year due to SKCM, illustrating that it seriously threatens human life and health. Homeodomain-only protein homeobox (HOPX) is the smallest member of the homeodomain family and is widely expressed in a variety of tissues. HOPX is involved in regulating the homeostasis of hematopoietic stem cells and is closely related to the development of tumors such as breast cancer, nasopharyngeal carcinoma, and head and neck squamous cell carcinoma. However, its function in SKCM is unclear, and further studies are needed.

METHODS

We used the R language to construct ROC (Receiver-Operating Characteristic) curves, KM (Kaplan‒Meier) curves and nomograms based on databases such as the TCGA and GEO to analyze the diagnostic and prognostic value of HOPX in SKCM patients. Enrichment analysis, immune scoring, GSVA (Gene Set Variation Analysis), and single-cell sequencing were used to verify the association between HOPX expression and immune infiltration. In vitro experiments were performed using A375 cells for phenotypic validation. Transcriptome sequencing was performed to further analyze HOPX gene-related genes and their signaling pathways.

RESULTS

Compared to normal cells, SKCM cells had low HOPX expression (p < 0.001). Patients with high HOPX expression had a better prognosis (p < 0.01), and the marker had good diagnostic efficacy (AUC = 0.744). GO/KEGG (Gene Ontology/ Kyoto Encyclopedia of Genes and Genomes) analysis, GSVA and single-cell sequencing analysis showed that HOPX expression is associated with immune processes and high enrichment of T cells and could serve as an immune checkpoint in SKCM. Furthermore, cellular assays verified that HOPX inhibits the proliferation, migration and invasion of A375 cells and promotes apoptosis and S-phase arrest. Interestingly, tumor drug sensitivity analysis revealed that HOPX also plays an important role in reducing clinical drug resistance.

CONCLUSION

These findings suggest that HOPX is a blocker of SKCM progression that inhibits the proliferation of SKCM cells and promotes apoptosis. Furthermore, it may be a new diagnostic and prognostic indicator and a novel target for immunotherapy in SKCM patients.

HOPX: A Unique Homeodomain Protein in Development and Tumor Suppression

Simple Summary

Homeobox (HOX) genes encode homeodomain proteins that regulate a wide range of molecular pathways. The homeodomain is highly conserved and binds to DNA. One exception is homeodomain-only protein (HOPX) that lacks DNA-binding capacity. HOPX plays a crucial role in development and its functional impairment is associated with a variety of diseases, including cancer. Loss of HOPX function occurs in a wide range of cancer types, where it functions as a tumor suppressor gene. Understanding the molecular mechanisms by which HOPX regulates carcinogenesis will likely lead to the development of new therapeutic approaches.

Abstract

Homeobox genes are master regulators of morphogenesis and differentiation by acting at the top of genetic hierarchies and their deregulation is associated with a variety of human diseases. They usually contain a highly conserved sequence that codes for the homeodomain of the protein, a specialized motif with three α helices and an N-terminal arm that aids in DNA binding. However, one homeodomain protein, HOPX, is unique among its family members in that it lacks the capacity to bind DNA and instead functions by interacting with transcriptional regulators. HOPX plays crucial roles in organogenesis and is expressed in both embryonic and adult stem cells. Loss of HOPX expression is common in cancer, where it functions primarily as a tumor suppressor gene. In this review, we describe the function of HOPX in development and discuss its role in carcinogenesis.

Integrated Bioinformatics Analysis of DNA Methylation Biomarkers in Thyroid Cancer Based on TCGA Database

Previous studies have reported a cluster of aberrant promoter methylation changes associated with silencing of tumor suppressor genes in thyroid cancer (TC), but these results of individual genes are far from enough. In this work, we aimed to investigate the onset and pattern of methylation changes during the progression of TC by informatics analysis. We downloaded the DNA methylation and RNA sequencing datasets from The Cancer Genome Atlas focusing on TC. Abnormally methylated differentially expressed genes (DEGs) were sorted and pathways were analyzed. The KEGG and GO were then used to perform enrichment and functional analysis of identified pathways and genes. Gene-drug interaction network and human protein atlas were applied to obtain feature DNA methylation biomarkers. In total, we identified 2170 methylation-driven DEGs, including 1054 hypermethylatedlow-expression DEGs and 1116 hypomethylated-high-expression DEGs at the screening step. Further analysis screened total of eight feature DNA methylation biomarkers (RXRG, MET, PDGFRA, FCGR3A, VEGFA, CSF1R, FCGR1A and C1QA). Pathway analysis showed that aberrantly methylated DEGs mainly associated with transcriptional misregulation in cancer, MAPK signaling, and intrinsic apoptotic signaling in TC. Taken together, we have identified novel aberrantly methylated genes and pathways linked to TC, which might serve as novel biomarkers for precision diagnosis and disease treatment.

The role of HOPX in normal tissues and tumor progression

The homeodomain-only protein homeobox (HOPX) as the smallest homeodomain protein, lacks certain conserved residues required for DNA binding. Through our literature search, we reviewed the current understandings of HOPX in normal tissues and tumor progression. HOPX was initially identified as a critical transcription factor in various normal tissues, which interacted with serum response factor (SRF) or other substance to regulate normal physiological function. However, HOPX is at a low expression or methylation level in tumors. These data indicated that HOPX may play a very important role in regulating differentiation phenotype and tumor suppressive function. We predicted the prognosis of HOPX in tumors from TCGA database and discussed the downstream genes of HOPX. To understand how HOPX is involved in the mechanisms between physical and pathological conditions could lead to novel therapeutic strategies for treatment.

HOPX Is an Epigenetically Inactivated Tumor Suppressor and Overexpression of HOPX Induce Apoptosis and Cell Cycle Arrest in Breast Cancer

Background

Evidence has been shown that abnormal DNA methylation plays a vital role in the progression of breast cancer via silencing of gene expression. The results of bisulfite sequencing showed that the methylation status of HOPX in breast cancer tissues was higher than that in normal breast cancer tissues, but little known about the biological functions of HOPX in breast cancer.

Methods

A total of 13 paired breast cancer and adjacent noncancerous tissues were subjected to bisulfite sequencing. Meanwhile, the methylation levels of cg218995965 and cg24862548 in breast cancer cells were detected by methylation-specific PCR (MSP). Flow cytometry, wound healing and transwell invasion assays were used to detect the apoptosis, migration and invasion in breast cancer cells. In addition, the expressions of HOPX, p21, cyclin D1 and CDK4 in cells were detected with Western blot assay.

Results

Bisulfite sequencing indicated that the CpG sites (cg218995965 and cg24862548) in the HOPX promoter region showed significantly higher methylation in breast cancer tissues. In addition, methylation-specific PCR revealed that HOPX was significantly hypermethylated in breast cancer cell lines MDA-MB-468 and MCF-7. Furthermore, overexpression of HOPX significantly inhibited the proliferation of MDA-MB-468 and MCF-7 cells via inducing the apoptosis. Moreover, upregulation of HOPX markedly inhibited the migration and invasion abilities of MDA-MB-468 cells. Meanwhile, overexpression of HOPX obviously induced cell cycle arrest in MDA-MB-468 cells via upregulation of p21, and downregulation of cyclin D1 and CDK4. Additionally, overexpression of HOPX suppressed tumor growth of breast cancer in vivo.

Conclusion

Our data showed that HOPX, a tumor suppressor, is epigenetically silenced in breast cancer. Overexpression of HOPX could suppress the progression of breast cancer, and thus indicating that it might serve as a potential target for the treatment of patients with breast cancer.