Nomenclature for human homeobox genes

HOXC6-mediated transcriptional activation of ENO2 promotes oral squamous cell carcinoma progression through the Warburg effect

Oral squamous cell carcinoma (OSCC) requires an in-depth exploration of its molecular mechanisms. The Warburg effect, along with the oncogenes enolase 2 (ENO2) and homeobox C6 (HOXC6), plays a central role in cancer. However, the specific interaction between ENO2 and HOXC6 in driving the Warburg effect and OSCC progression remains poorly understood. Through differential gene expression analysis in head and neck squamous cell carcinomas using Gene Expression Profiling Interactive Analysis, we identified upregulated ENO2 in OSCC. Silencing ENO2 in OSCC cells revealed its involvement in migration, invasion, and aerobic glycolysis of OSCC cells. Further exploration of ENO2's regulatory network identified HOXC6 as a potential transcriptional regulator. Subsequently, HOXC6 was silenced in OSCC cells, and expressions of ENO2 were assessed to validate its relationship with ENO2. Chromatin Immunoprecipitation and luciferase assays were utilized to investigate the direct transcriptional activation of ENO2 by HOXC6. A rescue assay co-overexpressing ENO2 and silencing HOXC6 in OSCC cells affirmed HOXC6's role in ENO2-associated glycolysis. High ENO2 expression in OSCC was validated through quantitative real-time polymerase chain reaction, Western blot, and immunohistochemistry analyses, which correlated with poor patient survival. Functional assays demonstrated that ENO2 silencing inhibited glycolysis and attenuated the aggressiveness of OSCC cells. In vivo studies confirmed the oncogenic role of ENO2 in OSCC growth. Notably, HOXC6 exhibited a positive correlation with ENO2 expression in clinical samples. Mechanistically, HOXC6 was identified as a direct transcriptional activator of ENO2, orchestrating the Warburg effect in OSCC cells. This study reveals the intricate link between HOXC6-mediated ENO2 transcriptional activation and the Warburg effect in OSCC, offering a potential therapeutic target for treating OSCC patients.

Cell Cycle-Related Gene SPC24: A Novel Potential Diagnostic and Prognostic Biomarker for Laryngeal Squamous Cell Cancer

Laryngeal squamous cell cancer (LSCC) is a common malignant tumor with a high degree of malignancy, and its etiology remains unclear. Therefore, screening potential biomarkers is necessary to facilitate the treatment and diagnosis of LSCC. Robust rank aggregation (RRA) analysis was used to integrate two gene expression datasets of LSCC patients from the Gene Expression Omnibus (GEO) database and identify differentially expressed genes (DEGs) between LSCC and nonneoplastic tissues. A gene coexpression network was constructed using weighted gene correlation network analysis (WGCNA) to explore potential associations between the module genes and clinical features of LSCC. Combining differential gene expression analysis and survival analysis, we screened potential hub genes, including CDK1, SPC24, HOXB7, and SELENBP1. Subsequently, western blotting and immunohistochemistry were used to test the protein levels in clinical specimens to verify our findings. Finally, four candidate diagnostic and prognostic biomarkers (CDK1, SPC24, HOXB7, and SELENBP1) were identified. We propose, for the first time, that SPC24 is a gene that may associate with LSCC malignancy and is a novel therapeutic target. These findings may provide important mechanistic insight of LSCC.

HOXC6 Overexpression Is Associated With Ki-67 Expression and Poor Survival in NPC Patients

BACKGROUND: Homeobox (HOX) genes are expressed in adult cells and regulate expression of genes involved in cell proliferation as well as cell-cell and cell-extracellular matrix interactions. Dysregulation of HOX gene expression plays important roles in carcinogenesis in a variety of organs. Through data mining on a published transcriptome dataset, this study first identified Homeobox protein Hox-C6 (HOXC6) gene as one of the differentially upregulated genes in nasopharyngeal carcinoma (NPC). We aimed to evaluate HOXC6 expression and its prognostic effect in a large cohort of NPC patients.

METHODS: We retrospectively examined the HOXC6 expression and Ki-67 index by immunohistochemistry in biopsy specimens from 124 patients with non-metastasized NPC. The results were correlated with the clinicopathological variables including disease-specific survival (DSS), metastasis-free survival (MeFS), and local recurrence-free survival (LRFS).

RESULTS: HOXC6 high expression was positively correlated with increased Ki-67 labeling index, and significantly associated with increment of tumor stage (p=0.024), advanced nodal status (p<0.001) and American Joint Committee on Cancer (AJCC) stage (p=0.002). Its expression also correlated with worse prognosis in terms of DSS (p=0.008), MeFS (p=0.0047) univariately. In multivariate analyses, HOXC6 expression still remained prognostically independent to portend worse DSS (p=0.015, hazard ratio=1.988) and MeFS (p=0.036, hazard ratio=1.899), together with stage III-IV (p=0.024, DSS; p=0.043, MeFS).

CONCLUSION: In summary, our results suggest HOXC6 may play a critical role in NPC progression and may serve as a potential prognostic biomarker in NPC patients.

The use of Gene Ontology terms and KEGG pathways for analysis and prediction of oncogenes

BACKGROUND

Oncogenes are a type of genes that have the potential to cause cancer. Most normal cells undergo programmed cell death, namely apoptosis, but activated oncogenes can help cells avoid apoptosis and survive. Thus, studying oncogenes is helpful for obtaining a good understanding of the formation and development of various types of cancers.

METHODS

In this study, we proposed a computational method, called OPM, for investigating oncogenes from the view of Gene Ontology (GO) and biological pathways. All investigated genes, including validated oncogenes retrieved from some public databases and other genes that have not been reported to be oncogenes thus far, were encoded into numeric vectors according to the enrichment theory of GO terms and KEGG pathways. Some popular feature selection methods, minimum redundancy maximum relevance and incremental feature selection, and an advanced machine learning algorithm, random forest, were adopted to analyze the numeric vectors to extract key GO terms and KEGG pathways.

RESULTS

Along with the oncogenes, GO terms and KEGG pathways were discussed in terms of their relevance in this study. Some important GO terms and KEGG pathways were extracted using feature selection methods and were confirmed to be highly related to oncogenes. Additionally, the importance of these terms and pathways in predicting oncogenes was further demonstrated by finding new putative oncogenes based on them.

CONCLUSIONS

This study investigated oncogenes based on GO terms and KEGG pathways. Some important GO terms and KEGG pathways were confirmed to be highly related to oncogenes. We hope that these GO terms and KEGG pathways can provide new insight for the study of oncogenes, particularly for building more effective prediction models to identify novel oncogenes. The program is available upon request.

GENERAL SIGNIFICANCE

We hope that the new findings listed in this study may provide a new insight for the investigation of oncogenes. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.

Ectopic expression of Hoxb4a in hemangioblasts promotes hematopoietic development in early embryogenesis of zebrafish

Hemangioblast, including primitive hematopoietic progenitor cells, play an important role in hematopoietic development, however, the underlying mechanism for the propagation of hematopoietic progenitor cells remains elusive. A variety of regulatory molecules activated in early embryonic development play a critical role in the maintenance of function of hematopoietic progenitor cells. Homeobox transcription factors are an important class of early embryonic developmental regulators determining hematopoietic development. However, the effect of homeobox protein Hox-B4 (HOXB4) ectopic expression on the development of hemangioblasts has not been fully addressed. This study aimed to investigate the role of Hoxb4a, an ortholog gene of HOXB4 in zebrafish, in the hematopoietic development in zebrafish. A transgenic zebrafish line was established with Cre-loxP system that stably overexpressed enhanced green fluorescent protein (EGFP)-tagged Hoxb4a protein under the control of hemangioblast-specific lmo2 promoter. Overexpression of Hoxb4a in the development of hemangioblasts resulted in a considerable increase in the number of stem cell leukemia (scl) and lmo2-positive primitive hematopoietic progenitor cells occurring in the posterior intermediate cell mass (ICM). Interestingly, Hoxb4a overexpression also disrupted the development of myelomonocytes in the anterior yolk sac and the posterior ICM, without affecting erythropoiesis in the posterior ICM. Taken together, these results indicate that Hoxb4a favours the development of hematopoietic progenitor cells originated from hemangioblasts in vivo.

Modulation of HOX2 gene expression following differentiation of neuronal cell lines

The expression of the genes in the human HOX2 locus has been studied during differentiation of two human neuroblastoma (SH-SY5Y and Kelly), a human glioblastoma (251-MG), and the murine F9 embryonal carcinoma cell lines. Cells were differentiated with retinoic acid (RA), or with RA together with dibutyral cyclic AMP (db-cAMP) and nerve growth factor (NGF) in order to assess the changes in the expression patterns of these homeobox genes during neuronal differentiation. We show that the genes of the HOX2 locus are expressed in a complex transcription pattern that varies with cell type. The two uninduced neuroblastoma cell lines show a similar pattern of expression for a number of HOX2 genes although the levels of expression are different for individual cell lines. The embryonal carcinoma cell line F9 expresses low levels of several HOX2 genes which is restricted to the 5' region of the HOX2 cluster. The glioblastoma cell line, 251-MG expresses almost all of the genes of the HOX2 locus. Differentiation of these cells modulates the expression of the HOX2 genes in a manner that is dependent upon the cell type as well as the differentiation factor. Differentiation affects both the level of HOX2 gene expression and the distribution of transcript sizes. In conclusion, our analysis reveals a complex pattern of expression for the genes of the HOX2 locus in neuronal and glial cells and suggests that the cell-specific expression of these genes may be correlated with the phenotypic differences that are observed between different neuronal and glial cell populations within the nervous system.

The Antennapedia-type homeobox genes have evolved from three precursors separated early in metazoan evolution

The developmental control genes containing an Antennapedia-type homeobox are clustered in insects and vertebrates. The evolution of these genes was studied by the construction of evolutionary trees and by statistical geometry in sequence space. The comparative analysis of the homeobox sequences reveals the subdivision of the Antennapedia-type homeobox genes into three classes early in metazoan evolution. This observation suggests an important function of these genes even in the most primitive metazoans. Subsequent duplication events generated a cluster of at least five homeobox genes in the last common ancestor of insects and vertebrates. These genes later independently gave rise to the 13 groups of paralogous genes in vertebrates and to the 11 Antennapedia-type genes in the Drosophila complexes.

Identification of 10 murine homeobox genes

In Drosophila a number of genes important in establishing segmentation patterns and in determining segment identities have been shown to carry the homeobox sequence. Over 30 murine homeobox genes have been cloned, many on the basis of sequence homology to Drosophila prototypes. Here we report the cloning and sequencing of 10 new and 6 previously known homeobox genes by screening a murine genomic library with a 768-fold degenerate oligonucleotide corresponding to the most conserved 8-amino acid motif in the recognition helix of the homeodomain. Eight of these new homeobox genes have been chromosomally mapped. Four genes do not belong to any of the known homeobox gene clusters but instead map to new locations on chromosome 1 (single gene) and chromosome 5 (three genes). Sequence comparisons indicate that two of these are very closely related and represent a distinct new category of homeobox genes. The remaining four mapped genes reside in previously established murine homeobox gene clusters. Specifically, two map to the cluster HOX-1 on chromosome 6 and one each to HOX-3 and HOX-4 on chromosome 15 and 2, respectively. The ratio of newly identified homeobox genes to the previously characterized murine homeobox genes suggests that there remain several uncharacterized homeobox genes in the murine genome.

Molecular cloning, chromosomal assignment, and nucleotide sequence of the feline homeobox HOX3A

The feline homolog to the mammalian homeobox locus, HOX3A, was isolated by screening a domestic cat genomic library with the murine Hox-3.1 probe. The nucleotide sequence similarity of the feline homeobox was 96% to human HOX3A, 94% to mouse Hox-3.1, and 94% to rat R4. The deduced amino acid sequence (homeodomain) of this feline homeobox was identical to all homeodomains of these cognate genes. Using a panel of feline x rodent somatic cell hybrids, the HOX3A locus was assigned to feline chromosome B4. Human HOX3A and mouse Hox-3.1 have been mapped previously to human chromosome 12 and mouse chromosome 15, respectively, both of which share syntenic homology to feline chromosome B4. These data demonstrate evolutionary conservation of both HOX3A gene sequences and chromosomal location during mammalian evolution.

Sequence analysis of the homeobox-containing exon of the murine Hox-4.3 homeogene

A homeobox-containing gene * was detected by Southern analysis of a cosmid spanning a region of the murine HOX-4 complex between Hox-4.4 (Hox-5.2) and Hox-4.2 (Hox-5.1) with a probe derived from the Hox-4.2 homeobox. The sequence of a cross-hybridizing region revealed an open reading frame encoding an Antennapedia (Antp) class homeodomain highly homologous to the products of human HOX4C (Hox-5.4/HOX4E), mouse Hox-3.1 and Hox-2.4. This, together with strong conservation of sequences 3' to the homoebox, indicates that we have cloned the murine Hox-4.3 gene. No other homeobox sequences were detected in this screen suggesting that the HOX-4 complex lacks paralogous genes represented in the equivalent regions of other HOX loci.