Mapping of the human DNA primase 1 (PRIM1) to chromosome 12q13

Analysis of core genes for colorectal cancer prognosis based on immune and stromal scores

Background

Colorectal cancer (CRC) is one of the most common malignancies.An early diagnosis and an accurate prognosis are major focuses of CRC research. Tumor microenvironment cells and the extent of infiltrating immune and stromal cells contribute significantly to the tumor prognosis.

Methods

Immune and stromal scores were calculated based on the ESTIMATE algorithm using the sample expression profile of the The Cancer Genome Atlas (TCGA) database. GSE102479 was used as the validation database. Differentially expressed genes whose expression was significantly associated with the prognosis of CRC patients were identified based on the immune matrix score. Survival analysis was conducted on the union of the differentially expressed genes. A protein–protein interaction (PPI) network was constructed using the STRING database to identify the closely connected modules. To conduct functional enrichment analysis of the relevant genes, GO and KEGG pathway analyses were performed with Cluster Profiler. Pivot analysis of the ncRNAs and TFs was performed by using the RAID2.0 database and TRRUST v2 database. TF-mRNA regulatory relationships were analyzed in the TRRUST V2 database. Hubgene targeting relationships were screened in the TargetScan, miRTarBase and miRDB databases. The SNV data of the hub genes were analyzed by using the R maftools package. A ROC curve was drawn based on the TCGA database. The proportion of immune cells was estimated using CIBERSORT and the LM22 feature matrix.

Results

The results showed that the matrix score was significantly correlated with colorectal cancer stage T. A total of 789 differentially expressed genes and 121 survival-related prognostic genes were identified. The PPI network showed that 22 core genes were related to the CRC prognosis. Furthermore, four ncRNAs that regulated the core prognosis genes, 11 TFs with regulatory effects on the core prognosis genes, and two drugs, quercetin and pseudoephedrine, that have regulatory effects on colorectal cancer were also identified.

Conclusions

We obtained a list of tumor microenvironment-related genes for CRC patients. These genes could be useful for determining the prognosis of CRC patients. To confirm the function of these genes, additional experiments are necessary.

The linkage of cell cycle and DNA replication with growth difference in female Chinese tongue sole (Cynoglossus semilaevis): Analysis from transcriptomic study and WGCNA

In addition to the typical sexual size dimorphism, considerable size differences within the female population of the Chinese tongue sole (Cynoglossus semilaevis) have become a further bottleneck of the improvement of sole aquaculture. To identify the internal mechanism, transcriptomic analysis and weighted gene co-expression network analysis (WGCNA) were employed simultaneously. Transcriptomic analyses of brain, pituitary gland, liver, gonad, and muscle tissues from two female groups with size differences identified 109, 698, 1325, 2299, and 2141 differentially expressed genes (DEGs), respectively. The results of these enrichment analyses suggest that the up-regulation of neuroactive ligand-receptor interaction, cell cycle, DNA replication, and MAPK signaling pathway in the group with larger females may be involved in the regulation of the observed growth differences. WGCNA of DEGs showed that cell cycle and DNA replication might be crucial pathways for accelerating cell growth in the groups with larger females. Finally, a series of hub genes including 6-phosphofructokinase type C (pfkp), ribosome biogenesis protein (wdr12), bleomycin hydrolase (blmh), and semaphorin-3A (sema3a) were recognized by the illustrated network map of modules. The linkage of cell cycle, DNA replication, and hub genes in the growth regulation of C. semilaevis provides further information for a better understanding of growth differences in fish.

DNA Primase Subunit 1 Expression in Hepatocellular Carcinoma and Its Clinical Implication

DNA Primase Subunit 1 (PRIM1) is crucial for cancer development and progression. However, there remains a lack of comprehension concerning the clinical implication of PRIM1 in HCC. Here, aberrant expression of PRIM1 was identified in HCC according to available databases. The prognostic value of PRIM1 in patients presenting with HCC was further assessed based on TCGA data. Gene set enrichment analysis (GSEA) was subsequently conducted to investigate the potential function of PRIM1. Additionally, the correlations between tumor-infiltrating immune cells (TIICs) and PRIM1 expression were evaluated. The data from TCGA, GEO, ONCOMINE, and HCCDB databases illustrated that PRIM1 was overexpressed in HCC tissues, compared to normal liver tissues (all p < 0.05). Kaplan-Meier analysis revealed that high PRIM1 expression in HCC was closely correlated with worse overall survival (p < 0.05). The univariate and multivariate analyses illustrated that PRIM1 expression was an independent novel prognostic indicator in HCC. Additionally, the area under the receiver operating characteristic (AUROC) curve for PRIM1 reached 0.8651, indicating the diagnostic significance of PRIM1 in patients with HCC. GSEA showed that PRIM1 overexpression was significantly enriched in several tumor-related signaling pathways. Besides, TIIC analysis clarified the association between PRIM1 expression and TIICs in HCC. The findings disclose that PRIM1 profoundly implicated in promoting tumorigenesis might work as a desirable biomarker for HCC.

Structural Basis for Inhibition of Human Primase by Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine

Nucleoside analogues are widely used in clinical practice as chemotherapy drugs. Arabinose nucleoside derivatives such as fludarabine are effective in the treatment of patients with acute and chronic leukemias and non-Hodgkin's lymphomas. Although nucleoside analogues are generally known to function by inhibiting DNA synthesis in rapidly proliferating cells, the identity of their in vivo targets and mechanism of action are often not known in molecular detail. Here we provide a structural basis for arabinose nucleotide-mediated inhibition of human primase, the DNA-dependent RNA polymerase responsible for initiation of DNA synthesis in DNA replication. Our data suggest ways in which the chemical structure of fludarabine could be modified to improve its specificity and affinity toward primase, possibly leading to less toxic and more effective therapeutic agents.

Variation analysis of PRIM1 gene in Chinese patients with primary ovarian insufficiency

Insights into common genetic susceptibility between primary ovarian insufficiency (POI) and natural or early menopause have delivered an innovative way of assessing the genetic mechanisms involved in POI. PRIM1 plays a crucial role in DNA replication by synthesizing RNA primers for Okazaki fragments. It is closely associated with age at natural menopause, early menopause and POI in European women. In this study, we aimed to investigate whether mutations in PRIM1 contribute to POI in Chinese women. All exons and exon-intron boundaries of PRIM1 gene were sequenced in 192 Han Chinese women with non-syndromic POI. No plausible mutations were identified. The results suggest that the perturbations in PRIM1 gene are not a common explanation for POI in Chinese women.

Structures to complement the archaeo-eukaryotic primases catalytic cycle description: What's next?

DNA replication is a crucial stage in the transfer of genetic information from parent to daughter cells. This mechanism involves multiple proteins with one key player being the primase. Primases are single-stranded DNA dependent RNA polymerases. On the leading strand, they synthesize the primer once allowing DNA elongation while on the lagging strand primers are generated repeatedly (Okazaki fragments). Primases have the unique ability to create the first phosphodiester bond yielding a dinucleotide which is initially elongated by primases and then by DNA polymerases.

Primase activity has been studied in the last decades but the detailed molecular steps explaining some unique features remain unclear. High-resolution structures of free and bound primases domains have brought significant insights in the understanding of the primase reaction cycle. Here, we give a short review of the structural work conducted in the field of archaeo-eukaryotic primases and we underline the missing “pictures” of the active forms of the enzyme which are of major interest. We organized our analysis with respect to the progression through the catalytic pathway.

Kinetic analysis of human PrimPol DNA polymerase activity reveals a generally error-prone enzyme capable of accurately bypassing 7,8-dihydro-8-oxo-2'-deoxyguanosine

Recent studies have identified human PrimPol as a new RNA/DNA primase and translesion DNA synthesis polymerase (TLS pol) that contributes to nuclear and mitochondrial DNA replication. We investigated the mechanism of PrimPol polymerase activity on both undamaged and damaged DNA substrates. With Mg²⁺ as a cofactor, PrimPol binds primer-template DNA with low affinity K(d,DNA) values (∼200-1200 nM). DNA binding is enhanced 34-fold by Mn²⁺ (K(d,DNA) = 27 nM). The pol activity of PrimPol is increased 400-1000-fold by Mn²⁺ compared to Mg²⁺ based on steady-state kinetic parameters. PrimPol makes a mistake copying undamaged DNA once every ∼100-2500 insertions events, which is comparable to other TLS pols, and the fidelity of PrimPol is ∼1.7-fold more accurate when Mg²⁺ is the cofactor compared to Mn²⁺. PrimPol inserts dCMP opposite 8-oxo-dG with 2- (Mn²⁺) to 6-fold (Mg²⁺) greater efficiency than dAMP misinsertion. PrimPol-catalyzed dCMP insertion opposite 8-oxo-dG proceeds at ∼25% efficiency relative to unmodified template dG, and PrimPol readily extends from dC:8-oxo-dG base pairs (bps) with ∼2-fold greater efficiency than dA:8-oxo-dG bps. A tetrahydrofuran (THF) abasic-site mimic decreases PrimPol activity to ∼0.04%. In summary, PrimPol exhibits the fidelity typical of other TLS pols, is rather unusual in the degree of activation afforded by Mn²⁺, and accurately bypasses 8-oxo-dG, a DNA lesion of special relevance to mitochondrial DNA replication and transcription.

Tissue factor enhances protease-activated receptor-2-mediated factor VIIa cell proliferative properties

In addition to its hemostatic functions, factor (F)VIIa exhibits cell proliferative properties as seen in angiogenesis and tumor growth. A role for tissue factor (TF) and protease-activated receptors (PAR)-1 and -2 in cell proliferation remain to be clarified. We tested the hypothesis that FVIIa induces cell proliferation by a mechanism involving TF and PAR-2. Human recombinant FVIIa induced cell proliferation of human BOSC23 cells transfected with plasmid containing human TF DNA sequence. Because DNA primase 1 (PRIM1) plays an essential role in cell proliferation, we used the cloned PRIM1 promoter upstream of the reporter gene chloramphenicol acetyl transferase (CAT) to elucidate the mode of action of FVIIa. FVIIa evoked a dose-dependent increase in cell proliferation and PRIM1 induction, which were markedly potentiated (4-5-fold) by the presence of TF and abrogated by TF antisense oligonucleotide. PRIM1 induction by FVIIa was also abolished by PAR-2 but not by PAR-1 antisense. In contrast, thrombin induced a small increase in CAT activity which was unaffected by TF, but was prevented only by PAR-1 antisense as well as the thrombin inhibitor hirudin. Proliferative properties of FVIIa were associated with a TF-dependent increase in intracellular calcium and were mediated by a concordant phosphorylation of p44/42 MAP kinase. In conclusion, data reveal that FVIIa induces PRIM1 and ensuing cellular proliferation via a TF- and of the PARs entirely PAR-2-dependent pathway, in distinction to that of thrombin which is PAR-1-dependent and TF-independent. We speculate that FVIIa-TF-PAR-2 inhibitors may be effective in suppressing cell proliferation.

Inhibition of DNA primase and induction of apoptosis by 3,3’-diethyl-9-methylthia-carbocyanine iodide in hepatocellular carcinoma BEL-7402 cells

AIM: To evaluate the effects of 3,3’-diethyl-9-methylthia-carbocyanine iodide (DMTCCI) on DNA primase activity and on apoptosis of human hepatocellular carcinoma BEL-7402 cells.

METHODS: DNA primase assay was used to investigate DNA primase activity. MTT assay was applied to determine cell proliferation. Flow cytometric analysis, transmission electron microscopy, DNA fragmentation assay were performed to detect DMTCCI-induced apoptosis. Expression levels of p53, Bcl-2, Bcl-xL, Bad, Bax, survivin, Caspase-3 and poly (ADP-ribose) polymerase (PARP) were evaluated by immunoblot analysis. Caspase-3 activity was assessed with ApoAlert Caspase-3 colorimetric assay kit.

RESULTS: DMTCCI had inhibitory effects on eukaryotic DNA primase activity with IC₅₀ value of 162.2 nmol/L. It also inhibited proliferation of human hepatocellular carcinoma BEL-7402 cells with IC₅₀ value of 2.09 μmol/L. Furthermore, DMTCCI-induced BEL-7402 cell apoptosis was confirmed by DNA fragmentation (DNA ladders and sub-G1 formation) and transmission electron microscopy (apoptotic bodies formation). During the induction of apoptosis, expression of Bcl-2, Bcl-xL and survivin was decreased, and that of p53, Bad and Bax was increased. Caspase-3 was activated and poly (ADP-ribose) polymerase (PARP) was cleaved in BEL-7402 cells treated with DMTCCI.

CONCLUSION: The present data suggest that DMTCCI has inhibitory effects on eukaryotic DNA primase and can induce apoptosis of BEL-7402 cells. The modulation of expression of p53 and Bcl-2 family proteins, and activation of Caspase-3 might be involved in the induction of apoptosis.

DNA primases

DNA primases are enzymes whose continual activity is required at the DNA replication fork. They catalyze the synthesis of short RNA molecules used as primers for DNA polymerases. Primers are synthesized from ribonucleoside triphosphates and are four to fifteen nucleotides long. Most DNA primases can be divided into two classes. The first class contains bacterial and bacteriophage enzymes found associated with replicative DNA helicases. These prokaryotic primases contain three distinct domains: an amino terminal domain with a zinc ribbon motif involved in binding template DNA, a middle RNA polymerase domain, and a carboxyl-terminal region that either is itself a DNA helicase or interacts with a DNA helicase. The second major primase class comprises heterodimeric eukaryotic primases that form a complex with DNA polymerase alpha and its accessory B subunit. The small eukaryotic primase subunit contains the active site for RNA synthesis, and its activity correlates with DNA replication during the cell cycle.

Amplifications of DNA primase 1 (PRIM1) in human osteosarcoma

We studied the involvement of PRIM1 in osteosarcoma by differential display, Northern and Southern hybridization, as well as fluorescence in situ hybridization (FISH) on interphase nuclei. In total, 22 pediatric oncology specimens were tested. PRIM1 was found to be amplified in 41% of the samples. PRIM1 is coamplified with the core 12q13 amplicon genes CDK4, SAS, and OS9, and was physically mapped very close to them. PRIM1 is therefore a new candidate for the role of a major target gene of 12q13 amplifications in human cancers. Genes Chromosomes Cancer 26:62-69, 1999.