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Objective: To investigate the expression of cutaneous T cell lymphoma associated antigen 15 (CTAGE15) and its association with clinical prognosis of esophageal squamous cell carcinoma (ESCC) patients, as well as its effect on the proliferation, migration, and invasion abilities of ESCC cells. Methods: Kaplan-Meier analysis was used to analyze the effect of CTAGE15 on the prognosis of ESCC patients in public database. The mRNA expression levels of CTAGE15 in esophageal epithelial cells and ESCC cells were measured by qRT⁃PCR. Furthermore, the expression of CTAGE15 was detected in cancer and adjacent normal tissues from 120 ESCC patients with a complete follow⁃up information. COX proportional survival risk model was enrolled to analyze the survival risk factors of ESCC patients, and multivariate correlation analysis was used for the analysis of the association between CTAGE15 expression and the clinicopathology of ESCC patients. Kaplan⁃Meier analysis was employed to analyze the effect of CTAGE15 on the prognosis of ESCC patients. The knockdown of CTAGE15 in ESCC cells was achieved by using small interfering RNA (siRNA), and the changes in cell proliferation, migration, and invasion abilities of ESCC cells were assessed. Results: The public database showed that the CTAGE15 expression was significantly associated with overall survival (P < 0.05) and disease⁃specific survival (P < 0.05) in ESCC patients, and a higher GTAGE15 expression was correlated with a better survival. The qRT-PCR results revealed significantly high expression of CTAGE15 in ESCC tissues and cells, compared with normal esophageal epithelial tissues and cells. In addition, the expression of CTAGE15 was significantly associated with T stage and N stage of ESCC patients, and a higher GTAGE15 expression was associated with an earlier T stage and N stage. Knockdown of CTAGE15 enhanced the proliferation, migration, and invasion abilities of ESCC cells (P < 0.05). Conclusion: CTAGE15 expression is positively associated with the prognosis of ESCC patients, and it inhibits the proliferation, migration and invasion abilities of ESCC cells. [ABSTRACT FROM AUTHOR]

BACKGROUND: Osteoarthritis is one of the most common joint diseases. With the increasing global incidence and prevalence of osteoarthritis, effective early diagnosis and treatment of osteoarthritis have become an urgent problem. OBJECTIVE: To elucidate the important biological functions of long non-coding RNAs, circular RNAs and pseudogenes and their regulatory roles as competing endogenous RNAs in osteoarthritis pathogenesis to gain a comprehensive, in-depth and new understanding of the involvement of competing endogenous RNAs in osteoarthritis progression and to provide new clues for early diagnosis and treatment of osteoarthritis. METHODS: CNKI, PubMed, VIP and WanFang databases were searched for articles published before 2022. The search terms were “osteoarthritis, competing endogenous RNA, circular RNA, long non-coding RNAs, pseudogenes” in Chinese and English. RESULTS AND CONCLUSION: Non-coding RNAs with the same microRNA response elements, including long non-coding RNAs, cyclic RNAs and pseudogenes, are involved in the construction of a regulatory network of competing endogenous RNAs centered on microRNAs. Non-coding RNAs, cyclic RNAs and pseudogenes can act as competing endogenous RNAs to adsorb microRNAs through “sponge” so as to regulate gene expression. Long non-coding RNAs, cyclic RNAs and pseudogenes can act as competing endogenous RNAs to regulate the proliferation, apoptosis and autophagy of osteoarthritic chondrocytes, the synthesis and degradation of extracellular matrix and the occurrence of inflammatory events. The practical application of the regulatory network of competing endogenous RNA to the clinical setting still faces many challenges and problems. The research on competing endogenous RNA as diagnostic markers or therapeutic targets for osteoarthritis is still at an early stage, and the current research on competing endogenous RNA regulatory network is still focused on the identification and validation of individual competing endogenous RNAs, and this regulatory network needs to be further supplemented and improved. However, with the development of advanced technologies, competing endogenous RNAs are expected to become early diagnostic markers and therapeutic targets for osteoarthritis diseases. [ABSTRACT FROM AUTHOR]

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Objective: To investigate the association between IL-1beta and DVWA gene and Kashin-Beck disease (KBD)., Methods: Peripheral genomic DNA were extracted from 105 patients with KBD and 98 healthy controls. PCR-RFLP were performed to detect SNP loci of IL-1beta gene and DVWA gene., Results: The patients with KBD had significantly higher frequency of rs16944 (IL-1beta) locus (chi2 = 24.28, P < 0.001) and single allele frequency of rs16944 (chi2 = 5.683, P = 0.0171) than the healthy controls. There were no significant differences in genotype frequencies,single allele frequencies and haplotypes in rs4685241 and rs1143627 between the patients with KBD and the healthy controls., Conclusion: rs16944 (IL-1beta) is associated with KBD.

Nuclear mitochondrial pseudogenes (Numts), widely existing in nuclear genomes of many organisms, are those nuclear DNA sequences which have high similarity with mtDNAs. In this study, we identified 14 different multiple nuclear pseudogenes of mitochondrial cytochrome oxidase I gene from an individual Scylla paramamosain (Decapoda: Portunidae). Of these sequences, ninety-six variable sites were detected, accounting for 15.7%. Nucleotide diversity (Pi) index and Haplo-type diversity (Hd) index were 0.05682 and 0.8800, respectively. Among the 14 pseudogenes, the copies of sequence one were the most, occupying 30.8% of total copies, and sequence two run the second one (occupying 19.2%). These sequences were divided into two groups compared with their homologues. In Group 1, there were no insertion or deletion sites, while 8 deletion and 5 insertion sites were detected in Group 2, resulting in frame-shift mutations. It was proved that these two groups of pseudogenes were evolved from at least two independent mtDNA integrations into S. paramamosain nuclear genomes through Chi-square and homogeneity tests.

In recent years, geneticists have been exploring the less visible parts of genome more thoroughly. They are coming to realize that these much more layers of genomic information, distinct from the protein-coding genes, connect in surprisingly deep and potent ways to growth and development in the high eukaryotes. This article reviews a number of startling observations about the extent of non-protein-coding RNA transcriptions, DNA methylation and covalent histone modifications in the complex organisms.

Objective: To determine the genome structure of human telomeric repeat binding factor 1 (TERF1) and its pseudogenes., Methods: Sequences were obtained from GenBank and analyzed using the BLAST program and other relevant biology program (Sequencher, DNA Strider and Autoassembler, etc) to determine the genome and pseudogenome structure of TERF1. PCR and sequencing were performed to verify the results., Result: TERF1 gene which mapped to 8q13 was divided into 10 exons. It had four processed pseudogenes located on chromosome 13, 18, 21 and X respectively (Psi TERF1-13 Psi TERF1-18 Psi TERF1-21 and Psi TERF1-X ). They were entire intronless TERF1 genes which lacked some exons. Three homologous fragments of at least 60 kb on the flanking region of Psi TERF1-13, Psi TERF1-18 and Psi TERF1-21, respectively were noted., Conclusion: TERF1 gene has 10 exons. It has four processed pseudogenes which are located on chromosome 13, 18, 21, and X, respectively. Large homologous fragments that belong to the recently duplicated segments are transchromosomal duplications.

Objective: To investigate the status of the augmenter of liver regeneration (ALR) in rat's genome., Methods: Polymerase chain reaction (PCR) was used to amplify the genomic DNA of rat, with a set of specific primers designed according to the cDNA sequence of ALR. The products were ligated into pGEM Teasy vector. Two positive clones were sequenced separately., Results: Two products were amplified from the rat's genome by PCR. After sequencing, one pseudogene was identified. The homology of the amino acid sequence between the ALR and its pseudogene was 88.8%., Conclusions: ALR pseudogene is found in rat's genome, implying that there is an ALR multigene family. This finding lays a foundation for further study of ALR molecular evolution mode.

Objective: This study aimed to set up an effective method to find the interference of processed pseudogene and overcome it in RT-PCR., Methods: Using RT-PCR methods, the authors amplified the cytokeratin 19 cDNA or DNA sequence in human lung squamous cell carcinoma samples., Results: They could find the influence of pseudogene through performing genomic DNA and nonreversed transcribed RNA controls. By digesting the extracted RNA sample with RNase-free DNase or regulating the annealing temperature based on mismatched primers, they could effectively eliminate the interference., Conclusion: The presence of processed pseudogene usually interferes in the experimental protocol in RT-PCR. This problem can be resolved with the method aforementioned.