AP-64, Encoded by C5orf46, Exhibits Antimicrobial Activity against Gram-Negative Bacteria

Uncharacterized Proteins CxORFx: Subinteractome Analysis and Prognostic Significance in Cancers

Functions of about 10% of all the proteins and their associations with diseases are poorly annotated or not annotated at all. Among these proteins, there is a group of uncharacterized chromosome-specific open-reading frame genes (CxORFx) from the 'Tdark' category. The aim of the work was to reveal associations of CxORFx gene expression and ORF proteins' subinteractomes with cancer-driven cellular processes and molecular pathways. We performed systems biology and bioinformatic analysis of 219 differentially expressed CxORFx genes in cancers, an estimation of prognostic significance of novel transcriptomic signatures and analysis of subinteractome composition using several web servers (GEPIA2, KMplotter, ROC-plotter, TIMER, cBioPortal, DepMap, EnrichR, PepPSy, cProSite, WebGestalt, CancerGeneNet, PathwAX II and FunCoup). The subinteractome of each ORF protein was revealed using ten different data sources on physical protein-protein interactions (PPIs) to obtain representative datasets for the exploration of possible cellular functions of ORF proteins through a spectrum of neighboring annotated protein partners. A total of 42 out of 219 presumably cancer-associated ORF proteins and 30 cancer-dependent binary PPIs were found. Additionally, a bibliometric analysis of 204 publications allowed us to retrieve biomedical terms related to ORF genes. In spite of recent progress in functional studies of ORF genes, the current investigations aim at finding out the prognostic value of CxORFx expression patterns in cancers. The results obtained expand the understanding of the possible functions of the poorly annotated CxORFx in the cancer context.

Detecting the Mechanism of Action of Antimicrobial Peptides by Using Microscopic Detection Techniques

Increasing antibiotic resistance has shifted researchers’ focus to antimicrobial peptides (AMPs) as alternatives to antibiotics. AMPs are small, positively charged, amphipathic peptides with secondary helical structures. They have the ability to disrupt the bacterial membrane and create wedges due to electrostatic differences. Water molecules enter the pathogens through those wedges and disrupt their normal cellular functioning, eventually causing the death of the pathogens. Keeping in mind the importance of AMPs, this review compiles recent data and is divided into three parts. The first part explains the AMP structure and properties, the second part comprises the spectroscopy techniques currently used for evaluating the AMP-bacterial targeting mechanism as well as its structure and safety; and the third part describes the production of AMPs from an animal source (whey protein). Most of the peptides that were used in recent studies have been either the precursors of a natural peptide or synthetic peptides with some modifications, but data on the exploitation of dairy protein are scarce. Among the little-studied milk proteins and peptides, in the last three years, whey protein has been studied the least based on the reported data. Because whey protein is a leftover part of cheese making that often drains out as cheese waste, causing soil and environmental pollution, today, the need of the hour is to produce safe AMPs from whey protein. The use of whey protein that is based on hydrolyzing lactic acid bacteria with some structural modifications can increase AMPs’ potency, stability, and safety, and it can also help to avoid soil and environmental pollution as a result of whey drainage.

A systematic analysis of C5ORF46 in gastrointestinal tumors as a potential prognostic and immunological biomarker

Background: Chromosome 5 open reading frame 46 (C5ORF46), also known as antimicrobial peptide with 64 amino acid residues (AP-64) and skin and saliva-secreted protein 1 (SSSP1), belongs to the family of open reading frame genes and encodes a small exosomal protein. C5ORF46 has been implicated in antibacterial activity and associated with patient prognosis in pancreatic cancer, colorectal cancer, and stomach cancer. These findings highlight the importance of C5ORF46 in gastrointestinal (GI) tumor inception and development. However, the prognostic and immunological value of C5ORF46 in human GI tumors remains largely unknown. In this study, we sought to explore the potential value of C5ORF46 in GI tumor prognosis and immunology.

Method: RNA sequencing (RNA-seq) was performed on the tumor and tumor-adjacent normal samples we collected to identify potential target genes for GI tumors. Apart from our RNA-seq data, all original data were downloaded from The Cancer Genome Atlas (TCGA) database and integrated via Strawberry Perl (v 5.32.0) and R (v 4.1.1). The differential expression of C5ORF46 was examined with Oncomine, Tumor Immune Estimation Resource (TIMER), Gene Expression Profiling Interactive Analysis (GEPIA), Cancer Cell Line Encyclopedia (CCLE), the Human Protein Atlas (HPA) and TCGA databases. The c-BioPortal database was used to investigate the genomic alterations of C5ORF46. The effect of C5ORF46 on prognosis and clinical phenotypes was explored via bioinformatics analyses on the TCGA and GEPIA databases. We used the bioinformatics analyses based on the TCGA database to analyze tumor mutational burden (TMB), microsatellite instability (MSI), tumor immune cell infiltration, and the correlations between C5ORF46 expression and several immune-related genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was carried out via the DAVID website and presented as bubble charts using ShengXinRen online tools. Gene set enrichment analysis (GSEA) was performed using R scripts based on data downloaded from the GSEA website. Immunohistochemistry (IHC) was used to validate the expression of C5ORF46 in GI tumors.

Results: The results of our RNA-seq data indicated a critical role for C5ORF46 in colon carcinogenesis. Consistently, we demonstrated that C5ORF46 was highly expressed in tumor tissues compared to normal tissues in human GI tumors. Moreover, a strong correlation was observed between C5ORF46 expression levels and patient prognosis, staging, TMB, MSI, and immune cell infiltration. Further, C5ORF46 presented as an important regulator in the tumor microenvironment (TME) and was active in the regulation of cancer immune functions. C5ORF46 is significantly correlated with genes regulating inflammation and immune responses.

Conclusion:C5ORF46 may serve as a biomarker for GI tumor prognosis and immunology. C5ORF46 could be a novel target for GI tumor immunotherapy.

Preliminary study on the role of the C5orf46 gene in renal cancer

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The C5orf46 gene was first studied in tumors.

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C5orf46 gene is involved in tumor immunity.

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C5orf46 gene as a possible target for immunotherapy in renal cancer

Background

C5orf46 has been found to have antibacterial and anti-inflammatory effects via sequencing and microarray technologies, but its effects on cancer are unclear.

Methods

C5orf46 expression in renal cancer patients and cell lines was measured by quantitative polymerase chain reaction (qPCR). RNA sequencing data and clinicopathological information from renal cancer patients extracted from The Tumor Genome Atlas (TCGA) were analyzed to evaluate the prognostic value of C5orf46. The role of C5orf46 in vitro was verified by migration, proliferation and apoptosis experiments in renal cancer cell lines. Furthermore, the transcriptome of renal cancer cell lines with C5orf46 knocked down was sequenced to analyze potential signaling network pathways. Finally, the possible mechanisms of C5orf46 involvement in renal cancer development were analyzed by evaluating the immune microenvironment, mutation status and methylation levels.

Results

C5orf46 was highly expressed in renal cancer and was an independent prognostic factor. In vitro cell experiments showed that inhibition of C5orf46 expression could reduce renal cancer cell proliferation and migration and increase apoptosis. Transcriptomic sequencing after knockdown of C5orf46 in renal cancer cells revealed that it is involved in the malignant phenotype and immune microenvironment regulation of renal cancer. Finally, public databases suggest that C5orf46-related immune cell infiltration, mutational potential, and low methylation levels may contribute to poor prognosis in renal cancer.

Conclusion

These findings suggest that C5orf46 is associated with renal cancer progression and could be a potential target for improving renal cancer prognosis.