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Microbiology Spectrum Sep 2023Pseudogenes, once considered "junk DNA" based on the incorrect assumption that the absence of full coding potential means a complete lack of functionality, have recently...
Pseudogenes, once considered "junk DNA" based on the incorrect assumption that the absence of full coding potential means a complete lack of functionality, have recently become a subject of significant interest in the scientific community. Concurrently, it is widely assumed that bacterial genomes are compact and have a high density of coding genes with little room for non-coding genes, including pseudogenes. A key aspect of genome annotation is the correct identification of genes and the distinction between coding genes and pseudogenes, as it directly impacts functional and comparative genomics studies. In this study, we analyzed the genomic data of 4,699 strains of the bacterium () as they exhibit high variability in the number of annotated pseudogenes. In particular, we looked for correlations between the number of pseudogenes and other genomic and meta-features of the strains. We identified clusters of orthologous genes and pseudogenes and compared cluster size distributions and length homogeneity within clusters. We then mapped and examined orthology relationships between genes and pseudogenes. Additionally, we generated a phylogenetic tree of the strains and found that phylogenetically related strains are more homogeneous in the number of pseudogenes and share a significant amount of pseudogenes. Finally, we delved into clusters of orthologous genes and pseudogenes and quantified their phylogenetic neighborhood, classifying pseudogenes into evolutionary preserved pseudogenes, mis-annotated pseudogenes, or pseudogenes formed by failed horizontal transfer events. This in-depth study provides important insights that can be incorporated into pseudogene annotation pipelines in the future. IMPORTANCE Accurate annotation of genes and pseudogenes is vital for comparative genomics analysis. Recent studies have shown that bacterial pseudogenes have an important role in regulatory processes and can provide insight into the evolutionary history of homologous genes or the genome as a whole. Due to pseudogenes' nature as non-functional genes, there is no commonly accepted definition of a pseudogene, which poses difficulties in verifying the annotation through experimental methods and resolving discrepancies among different annotation techniques. Our study introduces an in-depth analysis of annotated genes and pseudogenes and insights that can be incorporated into improved pseudogene annotation pipelines in the future.
PubMed: 37750703
DOI: 10.1128/spectrum.01704-23 -
Human Genetics Mar 2021Next-generation sequencing (NGS) is an incredibly useful tool for genetic disease diagnosis. However, the most commonly used bioinformatics methods for analyzing...
Next-generation sequencing (NGS) is an incredibly useful tool for genetic disease diagnosis. However, the most commonly used bioinformatics methods for analyzing sequence reads insufficiently discriminate genomic regions with extensive sequence identity, such as gene families and pseudogenes, complicating diagnostics. This problem has been recognized for specific genes, including many involved in human disease, and diagnostic labs must perform additional costly steps to guarantee accurate diagnosis in these cases. Here we report a new data analysis method based on the comparison of read depth between highly homologous regions to identify misalignment. Analyzing six clinically important genes-CYP21A2, GBA, HBA1/2, PMS2, and SMN1-each exhibiting misalignment issues related to homology, we show that our technique can correctly identify potential misalignment events and be used to make appropriate calls. Combined with long-range PCR and/or MLPA orthogonal testing, our clinical laboratory can improve variant calling with minimal additional cost. We propose an accurate and cost-efficient NGS testing procedure that will benefit disease diagnostics, carrier screening, and research-based population studies.
Topics: Algorithms; Genetic Diseases, Inborn; High-Throughput Nucleotide Sequencing; Humans; Polymerase Chain Reaction; Polymorphism, Single Nucleotide; Pseudogenes
PubMed: 32915251
DOI: 10.1007/s00439-020-02216-5 -
Digestive and Liver Disease : Official... Jul 2022Pseudogenes are dysfunctional copies of protein-coding genes that showed critical regulatory roles during carcinogenesis. Plasminogen like A (PLGLA) is a transcribed...
BACKGROUND
Pseudogenes are dysfunctional copies of protein-coding genes that showed critical regulatory roles during carcinogenesis. Plasminogen like A (PLGLA) is a transcribed unprocessed pseudogene and biasedly expressed in liver. But its function has not been studied in hepatocellular carcinoma (HCC).
AIMS
We aimed to explore the role of PLGLA in HCC.
METHODS
The expression of PLGLA and its association with pathological features in HCC patients was analyzed using The Cancer Genome Atlas (TCGA) datasets. Quantitative reverse transcription PCR (qRT-PCR) was used to validate PLGLA level in HCC tissue samples and cell lines. Gain-of-function experiments in vitro and in vivo were employed to assess the impact of PLGLA on HCC cell proliferation, migration and invasion. Luciferase reporter assay and RNA pull-down assay were conducted to confirm the interaction among PLGLA, miR-324-3p and GLYATL1.
RESULTS
PLGLA expression was significantly downregulated in HCC tissues and cell lines. Furthermore, low PLGLA expression was positively associated with tumor progression and poor prognosis. PLGLA restoration markedly suppressed cell proliferation, migration and invasion. Mechanistically, PLGLA could competitively bind to miR-324-3p and acted as a competitive endogenous RNA (ceRNA) to enhance GLYATL1 expression.
CONCLUSIONS
Our results established a novel tumor suppressive role of PLGLA in HCC pathogenesis and highlighted its potential as a therapeutic target for HCC treatment.
Topics: Carcinoma, Hepatocellular; Cell Line, Tumor; Cell Movement; Cell Proliferation; Gene Expression Regulation, Neoplastic; Humans; Liver Neoplasms; MicroRNAs; Plasminogen; Pseudogenes; RNA, Long Noncoding
PubMed: 34782279
DOI: 10.1016/j.dld.2021.10.003 -
BMC Cancer Apr 2021Nasopharyngeal carcinoma (NPC) is a malignant head and neck tumor, and more than 70% of new cases are in East and Southeast Asia. However, association between NPC and...
BACKGROUND
Nasopharyngeal carcinoma (NPC) is a malignant head and neck tumor, and more than 70% of new cases are in East and Southeast Asia. However, association between NPC and pseudogenes playing important roles in genesis of multiple tumor types is still not clear and needs to be investigated.
METHODS
Using RNA-Sequencing (RNA-seq) technology, we analyzed pseudogene expression in 13 primary NPC and 6 recurrent NPC samples as well as their paracancerous counterparts. Quantitative PCR was used to validate the differentially expressed pseudogenes.
RESULTS
We found 251 differentially expressed pseudogenes including 73 up-regulated and 178 down-regulated ones between primary NPC and paracancerous tissues. Enrichment analysis of gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were conducted to filter out the key pseudogenes. We reported that pseudogenes from cytochrome P450 (CYP) family, such as CYP2F2P, CYP2G1P, CYP4F24P, CYP2B7P and CYP2G2P were significantly down-regulated in NPC compared to paracancerous tissues, while IGHV1OR15-2, IGHV3-11, FCGR1CP and IGHV3-69-1 belonging to Fc gamma receptors were significantly up-regulated. CYP2B7P, CYP2F2P and CYP4F26P were enriched in arachidonic acid metabolism pathway. The qRT-PCR analysis validated the lower expression of pseudogenes CYP2F2P and CYP2B7P in NPC tissues and cell lines compared to paracancerous tissues and normal human nasopharyngeal epithelial cell line. CYP2B7P overexpression weakened migratory and invasive capacity of NPC cell line. Moreover, the expression pattern of those pseudogenes in recurrent NPC tissues was different from the primary NPC.
CONCLUSION
This study suggested the role of pseudogenes in tumorigenesis and progression, potentially functioning as therapeutic targets to NPC.
Topics: Adult; Aged; Arachidonic Acid; Cell Line, Tumor; Cell Movement; Cytochrome P-450 Enzyme System; Cytochrome P450 Family 2; Down-Regulation; Female; Gene Ontology; Humans; Male; Middle Aged; Nasopharyngeal Carcinoma; Nasopharyngeal Neoplasms; Neoplasm Invasiveness; Neoplasm Recurrence, Local; Pseudogenes; Real-Time Polymerase Chain Reaction; Receptors, IgG; Sequence Analysis, RNA; Transfection; Up-Regulation
PubMed: 33931030
DOI: 10.1186/s12885-021-08211-x -
Life Sciences Aug 2021Norcantharidin (NCTD) exhibits antitumor, anti-inflammatory, and anti-fibrosis properties, which makes NCTD an attractive candidate for the treatment of pathological...
AIMS
Norcantharidin (NCTD) exhibits antitumor, anti-inflammatory, and anti-fibrosis properties, which makes NCTD an attractive candidate for the treatment of pathological scars. This study was designed to investigate the potential effects of NCTD on fibroblast proliferation and explore the underlying mechanisms.
MATERIALS AND METHODS
First, cell viability and cell apoptosis were evaluated to determine the effects of NCTD on human skin fibroblasts, at 10, 50, and 100 μM. To explore the mechanism, bioinformatics analyses, chromatin immunoprecipitation, RNA immunoprecipitation, and RNA pulldown assays, and luciferase reporter assays were performed to verify the relationships among NCTD, signal transducer and activator of transcription 3 (STAT3), annexin A2 pseudogene 2 (ANXA2P2), and ubiquitin-associated protein 2-like (UBAP2L) mRNA in fibroblasts. Loss-of-function experiments were performed to investigate the roles played by STAT3, ANXA2P2, and UBAP2L in the proliferation and apoptosis of fibroblasts.
KEY FINDINGS
We found that NCTD administration induced fibroblast apoptosis and inhibited fibroblast proliferation in a dose-dependent manner. Mechanistically, NCTD inhibited ANXA2P2 transcription through the inhibition of STAT3 phosphorylation. Subsequently, ANXA2P2 was found to enhance the physical interaction between UBAP2L mRNA and lin-28 homolog B (LIN28B), which increased the stability and levels of UBAP2L mRNA. Loss-of-function assays demonstrated that ANXA2P2 and UBAP2L knockdown induced fibroblast apoptosis and suppressed fibroblast proliferation.
SIGNIFICANCE
In conclusion, we confirmed that NCTD inhibits fibroblast proliferation by inhibiting the STAT3/ANXA2P2/UBAP2L axis, which suggested that NCTD could represent a new candidate for the treatment of pathological scars.
Topics: Annexin A2; Antineoplastic Agents; Apoptosis; Bridged Bicyclo Compounds, Heterocyclic; Carrier Proteins; Cell Proliferation; Cells, Cultured; Fibroblasts; Gene Expression Regulation; Humans; Pseudogenes; RNA Stability; RNA-Binding Proteins
PubMed: 34043991
DOI: 10.1016/j.lfs.2021.119645 -
Hereditas Nov 2022Gastric cancer is one of the most common and deadly types of cancer. The molecular mechanism of gastric cancer progression remains unclear.
OBJECTIVE
Gastric cancer is one of the most common and deadly types of cancer. The molecular mechanism of gastric cancer progression remains unclear.
MATERIALS AND METHODS
Four hub genes were identified through GEO and TCGA database screening and analysis. Prognostic analysis revealed that COL5A2 was the most likely to affect the prognosis of gastric cancer among the four hub genes. The relationships between COL5A2 and clinical variables and immune cell infiltration were analyzed. Then, COL5A2 was analyzed for single-gene differences and related functional enrichment. Using the starBase database for prediction and analysis, miRNAs and pseudogenes/lncRNAs that might combine with COL5A2 were identified; thus, the ceRNA network was constructed. Finally, the network was verified by Cox analysis and qPCR, and a nomogram was constructed.
RESULTS
First, we found that COL5A2, COL12A1, BGN and THBS2 were highly expressed in gastric cancer. COL5A2 had statistical significance in overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) analysis. Immune infiltration analysis suggested that COL5A2 might influence the changes in the tumor immune microenvironment. The StarBase database was used to predict that 3 pseudogenes and 7 lncRNAs might inhibit the hsa-miR-200b-3p-COL5A2 axis in gastric cancer. The pseudogenes/lncRNA-hsa-miR-200b-3p-COL5A2 ceRNA network was identified and verified using Cox regression analysis and PCR. Finally, we constructed a nomogram.
CONCLUSIONS
We elucidated the regulatory role of the pseudogenes/lncRNA-hsa-miR-200b-3p-COL5A2 network in gastric cancer progression and constructed a nomogram. These studies may provide effective treatments and potential prognostic biomarkers for gastric cancer.
Topics: Humans; RNA, Long Noncoding; Pseudogenes; Stomach Neoplasms; Prognosis; MicroRNAs; Biomarkers; Tumor Microenvironment
PubMed: 36447214
DOI: 10.1186/s41065-022-00257-6 -
Journal of Immunology (Baltimore, Md. :... Jan 2022The biological relevance of genes initially categorized as "pseudogenes" is slowly emerging, notably in innate immunity. In the HLA region on chromosome 6, is one such...
The biological relevance of genes initially categorized as "pseudogenes" is slowly emerging, notably in innate immunity. In the HLA region on chromosome 6, is one such pseudogene; yet, it is transcribed, and its variation is associated with immune properties. Furthermore, two alleles, * and *, putatively encode a complete, membrane-bound HLA protein. Here we thus hypothesized that HLA-H contributes to immune homeostasis similarly to tolerogenic molecules HLA-G, -E, and -F. We tested if * encodes a membrane-bound protein that can inhibit the cytotoxicity of effector cells. We used an HLA-null human erythroblast cell line transduced with * cDNA to demonstrate that HLA-H*02:07 encodes a membrane-bound protein. Additionally, using a cytotoxicity assay, our results support that K562 * inhibits human effector IL-2-activated PBMCs and human IL-2-independent NK92-MI cell line activity. Finally, through in silico genotyping of the Denisovan genome and haplotypic association with Denisovan-derived *, we also show that * is of archaic origin. Hence, admixture with archaic humans brought a functional allele into modern European and Asian populations.
Topics: Alleles; Asian People; Cell Membrane; Cytotoxicity, Immunologic; Evolution, Molecular; Gene Frequency; Genotype; HLA-A11 Antigen; Haplotypes; Hemochromatosis Protein; Homeostasis; Humans; Immune Tolerance; K562 Cells; Killer Cells, Natural; Lymphocyte Activation; Pseudogenes; White People
PubMed: 34872977
DOI: 10.4049/jimmunol.2100358 -
Molecular and Cellular Biochemistry Jan 2021As a momentous post-transcriptional regulator, microRNAs (miRNAs) are attracting more and more attention. The classical miRNAs regulated mechanism shows it binds to the... (Review)
Review
As a momentous post-transcriptional regulator, microRNAs (miRNAs) are attracting more and more attention. The classical miRNAs regulated mechanism shows it binds to the targets' 3'UTR thus play the role in post-transcription. Meanwhile, single miRNA can target multiple genes, so those should compete to bind that miRNA. Vice versa, single gene can sponge mass of miRNAs as well. Thus the competitive endogenous RNAs (ceRNAs) hypothesis was put forward in 2011. The ceRNA hypothesis has made huge achievements, in particular in non-coding genes, which including long non-coding RNAs (lncRNAs), circle RNAs (circRNAs) and pseudogenes, even viral transcripts. It also contributed greatly to epigenetics development. However, an increasing number of controversies have occurred with applause. Based on this situation, this review introduces something in detail about the ceRNAs hypothesis achieved in lncRNAs, circRNAs, pseudogenes and viral transcripts, respectively. Meanwhile, it also covers controversy of the ceRNAs hypothesis.
Topics: 3' Untranslated Regions; Animals; Apoptosis; Caenorhabditis elegans; Epigenesis, Genetic; Gene Expression Regulation, Neoplastic; Gene Regulatory Networks; Humans; Mice; Models, Genetic; Neoplasms; Pseudogenes; RNA; RNA, Circular; RNA, Long Noncoding; Species Specificity; Transcriptome
PubMed: 32975695
DOI: 10.1007/s11010-020-03889-2 -
Scientific Reports Dec 2022Pseudogene-derived transcripts, especially those barely transcribed in normal tissues, have been regarded as a kind of non-coding RNAs, and present potential functions...
Pseudogene-derived transcripts, especially those barely transcribed in normal tissues, have been regarded as a kind of non-coding RNAs, and present potential functions in tumorigenicity and tumor development in human beings. However, their exact effects on hepatocellular carcinoma (HCC) remain largely unknown. On basis of our previous research and the constructed online database for the non-coding RNAs related to HCC, a series of pseudogene transcripts have been discovered, and SNRPFP1, the homologous pseudogene of SNRPF, was found to produce an anomalously high expression long non-coding RNA in HCC. In this study, we validated the expression of the SNRPFP1 transcript in both HCC tissues and cell lines. The adverse correlation between SNRPFP1 expression and patients' outcomes was observed. And depletion of SNRPF1 in HCC cells significantly suppressed cell proliferation and apoptosis resistance. Meanwhile, the motility of HCC cells was potently impaired. Interestingly, miR-126-5p, one of the tumor-suppressive genes commonly decreased in HCC, was found negatively expressed and correlated with SNRPF1, and a specific region of SNRPF1 transcript is directly binding to miR-126-5p in a molecular sponge way. The rescue experiment by knock-out miR-126-5p significantly reversed the cell growth suppression and a higher ratio of cell apoptosis induced by SNRPF1 depletion. Lastly, we concluded that SNRPF1 is a pseudogene active in HCC, and its abnormally over-expressed transcript is a strong promoter of HCC cell progress in vitro by sponging miR-126-5p. We believe that the findings in this study provide new strategies for HCC prevention and therapeutic treatment.
Topics: Humans; Carcinoma, Hepatocellular; Liver Neoplasms; RNA, Long Noncoding; MicroRNAs; Pseudogenes; Cell Line, Tumor; Cell Proliferation; Gene Expression Regulation, Neoplastic; Cell Movement
PubMed: 36535956
DOI: 10.1038/s41598-022-24597-5 -
Cell Biology International Jan 2023Among malignant tumors, lung adenocarcinoma (LUAD) is the leading cause of death worldwide. This study explored the diagnostic, prognostic value, and preliminary...
Among malignant tumors, lung adenocarcinoma (LUAD) is the leading cause of death worldwide. This study explored the diagnostic, prognostic value, and preliminary functional verification of sialic acid binding Ig like lectin 17, pseudogene (SIGLEC17P) in LUAD. Prognostic lncRNAs for LUAD were identified by The Cancer Genome Atlas and quantitative real-time PCR (qRT-PCR) was used to detect the expression of SIGLEC17P in LUAD and paracarcinoma tissues. Subsequently, lentiviral vectors were used to overexpress SIGLEC17P in A549 and H1299 cells. The effects of SIGLEC17P overexpression on the proliferation, migration, and invasiveness of LUAD cells (A549 and H1299) were evaluated by Cell Counting Kit-8, wound healing, and transwell migration assays, respectively. Bioinformatics analyses were performed to reveal the potential pathways in which SIGLEC17P is involved in LUAD. qRT-PCR results revealed low SIGLEC17P expression in LUAD tissues and a significant association with the N stage, T stage, and tumor node metastasis stage. Furthermore, the receiver operating characteristic curve demonstrated a reliable diagnostic value. The proliferation, migration, and invasion of LUAD cells were inhibited by overexpression of SIGLEC17P. Bioinformatics analyses suggested that SIGLEC17P might exert antioncogenic effects in LUAD through the mir-20-3p/ADH1B or mir-4476-5p/DPYSL axis. In summary, our results revealed that SIGLEC17P acts as a prognostic biomarker, independent prognostic factor, and potential therapeutic target for patients with LUAD.
Topics: Humans; Adenocarcinoma; Cell Line, Tumor; Cell Movement; Cell Proliferation; Gene Expression Regulation, Neoplastic; Lung Neoplasms; MicroRNAs; Prognosis; Pseudogenes
PubMed: 36183365
DOI: 10.1002/cbin.11919