C1D family proteins in coordinating RNA processing, chromosome condensation and DNA damage response

A combined biomarker panel shows improved sensitivity and specificity for detection of ovarian cancer

Background

Combined biomarkers can improve the sensitivity and specificity of ovarian cancer (OC) diagnosis and effectively predict patient prognosis. This study explored the diagnostic and prognostic values of serum CCL18 and CXCL1 antigens combined with C1D, FXR1, ZNF573, and TM4SF1 autoantibodies in OC.

Methods

CCL18 and CXCL1 monoclonal antibodies and C1D, FXR1, ZNF573, and TM4SF1 antigens were coated with microspheres. Logistic regression was used to construct a serum antigen‐antibody combined detection model; receiver‐operating characteristic curve (ROC) was used to evaluate the diagnostic efficacy of the model; and the Kaplan‐Meier method and Cox regression models were used for survival analysis to evaluate the prognosis of OC. Data from The Cancer Genome Atlas (TCGA) and Genotype‐Tissue Expression (GTEx) projects and online survival analysis tools were used to evaluate prognostic genes for OC. The CIBERSORT immune score was used to explore the factors influencing prognosis and their relationship with tumor‐infiltrating immune cells.

Results

The levels of each index in the blood samples of patients with OC were higher than those of the other groups. The combined detection model has higher specificity and sensitivity in the diagnosis of OC, and its diagnostic efficiency is better than that of CA125 alone and diagnosing other malignant tumors. CCL18 and TM4SF1 may be factors affecting the prognosis of OC, and CCL18 may be related to immune‐infiltrating cells.

Conclusions

The serum antigen‐antibody combined detection model established in this study has high sensitivity and specificity for the diagnosis of OC.

Expression of genes involved in apoptosis is dysregulated in mucopolysaccharidoses as revealed by pilot transcriptomic analyses

Mucopolysaccharidoses (MPS), a group of lysosomal storage diseases (LSD), are inherited disorders caused by mutations in genes coding for enzymes involved in the degradation of glycosaminoglycans (GAGs). Therefore, accumulated GAGs in lysosomes lead to severe symptoms in patients and significantly shortened life span. Although GAG accumulation in cells is the primary cellular defect in MPS, recent reports indicated that severe changes in cellular processes occur there as secondary or tertiary effects, which may contribute significantly to the disease pathomechanism. Apoptosis is one of such process, while mechanisms leading to dysregulation of this process in MPS remain largely unknown. To learn about these mechanisms, we have performed transcriptomic studies using cultures of fibroblasts derived from patients suffering from all types and subtypes of MPS, and assessed genes related to apoptosis. We found that there are significant changes in expression levels of many such genes relative to control fibroblasts (Human Dermal Fibroblasts-adult cell line), and the number of down- or up-regulated transcripts was between 19 and 73 in different MPS types. We have identified apoptosis-related genes, which were considerably dysregulated in many MPS types, as well as those in which expression was significantly changed in specific MPS types. BNIP3, C1D, CLU, GPER1, KREMEN1, and PRKCD genes displayed the most changed expression profiles in most MPS types relative to control cells. Caspase 3/7 activity was increased in MPS IVA and IX. These results indicate that changes in apoptosis, observed in MPS, may arise, at least partially, from dysregulation of genes coding for proteins involved in this process.

EXOSC10 is required for RPA assembly and controlled DNA end resection at DNA double-strand breaks

The exosome is a ribonucleolytic complex that plays important roles in RNA metabolism. Here we show that the exosome is necessary for the repair of DNA double-strand breaks (DSBs) in human cells and that RNA clearance is an essential step in homologous recombination. Transcription of DSB-flanking sequences results in the production of damage-induced long non-coding RNAs (dilncRNAs) that engage in DNA-RNA hybrid formation. Depletion of EXOSC10, an exosome catalytic subunit, leads to increased dilncRNA and DNA-RNA hybrid levels. Moreover, the targeting of the ssDNA-binding protein RPA to sites of DNA damage is impaired whereas DNA end resection is hyper-stimulated in EXOSC10-depleted cells. The DNA end resection deregulation is abolished by transcription inhibitors, and RNase H1 overexpression restores the RPA recruitment defect caused by EXOSC10 depletion, which suggests that RNA clearance of newly synthesized dilncRNAs is required for RPA recruitment, controlled DNA end resection and assembly of the homologous recombination machinery.

C1D is not directly involved in the repair of UV-damaged DNA but protects cells from oxidative stress by regulating gene expressions in human cell lines

A small nuclear protein, C1D, has roles in various cellular processes, transcription regulation, genome stability surveillance, DNA repair and RNA processing, all of which are required to maintain the host life cycles. In the previous report, C1D directly interacts with XPB, a component of the nucleotide excision repair complex, and C1D knockdown reduced cell survival of 27-1 cells, CHO derivative cells, after UV irradiation. To find out the role of C1D in UV-damaged cells, we used human cell lines with siRNA or shRNA to knockdown C1D. C1D knockdown reduced cell survival rates of LU99 and 786-O after UV irradiation, although C1D knockdown did not affect the efficiency of the nucleotide excision repair. Immunostaining data support that C1D is not directly involved in the DNA repair process in UV-damaged cells. However, H2O2 treatment reduced cell viability in LU99 and 786-O cells. We also found that C1D knockdown upregulated DDIT3 expression in LU99 cells and downregulated APEX1 in 786-O cells, suggesting that C1D functions as a co-repressor/activator. The data accounts for the reduction of cell survival rates upon UV irradiation.

Identification of six serum antigens and autoantibodies for the detection of early stage epithelial ovarian carcinoma by bioinformatics analysis and liquid chip analysis

The early detection of ovarian cancer is critical for improving the prognosis of patients, but there are currently insufficient tumor biomarkers for early detection owing to their low diagnostic sensitivity and specificity. The aim of the present study was to investigate the use of the serum antigens C-C motif chemokine ligand 18 and C-X-C motif chemokine ligand 1, and autoantibodies C1D, transmembrane 4 L six family member 1, zinc finger protein 675 and fragile X mental retardation 1 autosomal homolog 1, for the early screening of epithelial ovarian cancer (EOC). The expression of these sex genes/proteins in ovarian cancer and normal ovarian tissue was examined, and the potential functions of the six genes/proteins in ovarian cancer were analyzed by bioinformatics. Finally, these data were verified in clinical samples, and the multi-analyte suspension array method was compared with the ELISA method. Taken together, these data indicated that these six genes/proteins may serve as potential biomarkers for the early detection of EOC.

Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors

In this review, Zinder and Lima highlight recent advances that have illuminated roles for the RNA exosome and its cofactors in specific biological pathways, alongside studies that attempted to dissect these activities through structural and biochemical characterization of nuclear and cytoplasmic RNA exosome complexes.

The eukaryotic RNA exosome is an essential and conserved protein complex that can degrade or process RNA substrates in the 3′-to-5′ direction. Since its discovery nearly two decades ago, studies have focused on determining how the exosome, along with associated cofactors, achieves the demanding task of targeting particular RNAs for degradation and/or processing in both the nucleus and cytoplasm. In this review, we highlight recent advances that have illuminated roles for the RNA exosome and its cofactors in specific biological pathways, alongside studies that attempted to dissect these activities through structural and biochemical characterization of nuclear and cytoplasmic RNA exosome complexes.