Integrative analysis of DNA replication origins and ORC-/MCM-binding sites in human cells reveals a lack of overlap.

Based on experimentally determined average inter-origin distances of ~100 kb, DNA replication initiates from ~50,000 origins on human chromosomes in each cell cycle. The origins are believed to be specified by binding of factors like the origin recognition complex (ORC) or CTCF or other features like G-quadruplexes. We have performed an integrative analysis of 113 genome-wide human origin profiles (from five different techniques) and five ORC-binding profiles to critically evaluate whether the most reproducible origins are specified by these features. Out of ~7.5 million union origins identified by all datasets, only 0.27% (20,250 shared origins) were reproducibly obtained in at least 20 independent SNS-seq datasets and contained in initiation zones identified by each of three other techniques, suggesting extensive variability in origin usage and identification. Also, 21% of the shared origins overlap with transcriptional promoters, posing a conundrum. Although the shared origins overlap more than union origins with constitutive CTCF-binding sites, G-quadruplex sites, and activating histone marks, these overlaps are comparable or less than that of known transcription start sites, so that these features could be enriched in origins because of the overlap of origins with epigenetically open, promoter-like sequences. Only 6.4% of the 20,250 shared origins were within 1 kb from any of the ~13,000 reproducible ORC-binding sites in human cancer cells, and only 4.5% were within 1 kb of the ~11,000 union MCM2-7-binding sites in contrast to the nearly 100% overlap in the two comparisons in the yeast, Saccharomyces cerevisiae. Thus, in human cancer cell lines, replication origins appear to be specified by highly variable stochastic events dependent on the high epigenetic accessibility around promoters, without extensive overlap between the most reproducible origins and currently known ORC- or MCM-binding sites.

The clinical characteristics of subcutaneous and mediastinal emphysema in anti-melanoma differentiation-associated 5 positive dermatomyositis associated with interstitial lung disease.

OBJECTIVES: To investigate the clinical characteristics of subcutaneous emphysema (SE) and mediastinal emphysema (ME) occurring in patients with anti-melanoma differentiation-associated gene 5 antibody-positive dermatomyositis associated with interstitial lung disease (anti-MDA5-positive DM-ILD). METHODS: In this retrospective study, a total of 117 anti-MDA5-positive DM-ILD patients were admitted to our hospital. All patients underwent an assessment of autoantibodies, serum ferritin levels, and lung high-resolution CT scans. RESULTS: In patients with anti-MDA5-positive DM-ILD, the incidence of SE/ME was found to be 11.1%, which was significantly higher compared to patients with anti-synthetase syndrome (p<0.01). The mortality rate among anti-MDA5-positive DM-ILD patients with SE/ME was significantly higher than those without SE/ME (p=0.0022). There was no statistically significant difference in the occurrence of SE/ME between patients with positive anti-Ro-52 antibodies and those with negative anti-Ro-52 antibodies (p=0.18). Patients with higher serum ferritin levels (1000 ng/ml ≤serum ferritin ≤1500 ng/ml) had a higher likelihood of developing SE/ME compared to patients with lower serum ferritin levels (serum ferritin <500 ng/ml) (p<0.01). Among 13 anti-MDA5-positive DM-ILD patients with SE/ME, six (46.2%) developed SE/ME within 1 month of being diagnosed and 53.8% of patients underwent positive pressure ventilation prior to the onset of SE/ME. CONCLUSIONS: We found that SE/ME is not uncommon in anti-MDA5-positive DM-ILD and is an important factor associated with poor patient prognosis. The occurrence of SE/ME is correlated with high levels of serum ferritin and is not related to anti-Ro-52 antibodies. Rheumatologists should pay close attention to SE/ME caused by positive pressure ventilation in anti-MDA5-positive DM-ILD patients.

Integrative analysis of DNA replication origins and ORC/MCM binding sites in human cells reveals a lack of overlap.

Based on experimentally determined average inter-origin distances of ∼100 kb, DNA replication initiates from ∼50,000 origins on human chromosomes in each cell cycle. The origins are believed to be specified by binding of factors like the Origin Recognition Complex (ORC) or CTCF or other features like G-quadruplexes. We have performed an integrative analysis of 113 genome-wide human origin profiles (from five different techniques) and 5 ORC-binding profiles to critically evaluate whether the most reproducible origins are specified by these features. Out of ∼7.5 million union origins identified by all datasets, only 0.27% were reproducibly obtained in at least 20 independent SNS-seq datasets and contained in initiation zones identified by each of three other techniques (20,250 shared origins), suggesting extensive variability in origin usage and identification. 21% of the shared origins overlap with transcriptional promoters, posing a conundrum. Although the shared origins overlap more than union origins with constitutive CTCF binding sites, G-quadruplex sites and activating histone marks, these overlaps are comparable or less than that of known Transcription Start Sites, so that these features could be enriched in origins because of the overlap of origins with epigenetically open, promoter-like sequences. Only 6.4% of the 20,250 shared origins were within 1 kb from any of the ∼13,000 reproducible ORC binding sites in human cancer cells, and only 4.5% were within 1 kb of the ∼11,000 union MCM2-7 binding sites in contrast to the nearly 100% overlap in the two comparisons in the yeast, S. cerevisiae . Thus, in human cancer cell lines, replication origins appear to be specified by highly variable stochastic events dependent on the high epigenetic accessibility around promoters, without extensive overlap between the most reproducible origins and currently known ORC- or MCM-binding sites.

Evaluating the value of superoxide dismutase in anti-MDA5-positive dermatomyositis associated with interstitial lung disease.

OBJECTIVE: This study aimed to investigate the relationship between serum superoxide dismutase (SOD) and interstitial lung disease (ILD) among patients with anti-melanoma differentiation-associated gene 5 antibody (MDA5)-positive DM. METHOD: In this retrospective study, serum SOD of 90 health check-ups were tested in our hospital. A total of 94 hospitalized patients with anti-MDA5-positive DM had ILD. Their serum SOD, serum ferritin and autoantibody levels were determined and lung high-resolution CT was performed. RESULTS: The serum SOD level was significantly lower in the anti-MDA5-positive DM group compared with the control group. The SOD level was significantly lower in patients positive for both anti-MDA5 antibodies and anti-Ro-52 antibodies than in those positive for only anti-MDA5 antibodies before treatment. The SOD level was significantly lower in the higher serum ferritin group compared with the lower serum ferritin group before treatment. After treatment, the serum SOD level decreased in patients with exacerbation of ILD, while it increased in those with alleviated ILD. The SOD level was significantly lower in the death group than in the survival group before treatment. CONCLUSIONS: In patients with anti-MDA5-positive DM, the low SOD level before treatment indicated the presence of oxidative stress in the disease; the serum SOD level was affected by anti-Ro-52 antibodies and ferritin; there is a close relationship between serum SOD level and ILD among patients with anti-MDA5-positive DM, suggesting that SOD might serve as an effective indicator to evaluate the changes in ILD in these patients; and the low SOD level is an important indicator of poor prognosis in these patients, which deserves attention from rheumatologists.

Analysis of Risk Factors and the Establishment of a Predictive Model for Thrombosis in Patients with Antineutrophil Cytoplasmic Antibody-Associated Vasculitis.

Purpose: To explore the risk factors for thrombi occurring in patients with antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) and establish a risk prediction model to better predict the risk of thrombosis in patients with AAV. Patients and Methods: We retrospectively analyzed 117 AAV patients who had been hospitalized in The Second Affiliated Hospital of Chongqing Medical University between October 2010 and December 2021. For all patients, we recorded demographic characteristics and clinical data, analyzed the risk factors for thrombosis in AAV patients and then developed a risk prediction model. Results: Stepwise logistic regression analysis indicated that a high complement C3 level, a high BVAS score and a high Padua score were independent risk factors for thrombosis in AAV patients. According to multivariate analysis, a predictive model for thrombus risk was successfully established; the area under the ROC curve(AUC) was 0.803 (95% CI: 0.716-0.890) and the maximum Youden index, sensitivity and specificity were 0.487, 59.0% and 89.7%, respectively. Conclusion: A high complement C3 level, high BVAS score, and a high Padua score were shown to be independent risk factors for thrombosis in AAV patients. We developed a risk prediction model based on these three risk factors that could predict the risk of thrombosis in AAV patients to some extent.

The ACE2-Ang-(1­7)-Mas Axis Modulates M1/M2 Macrophage Polarization to Relieve CLP-Induced Inflammation via TLR4-Mediated NF-кb and MAPK Pathways.

PURPOSE: Angiotensin 1-7 [Ang-(1-7)] has been identified as an important anti-inflammatory and anti-fibrotic factor. This study determined how the ACE2-Ang-(1-7)-Mas axis affected M1/M2 macrophage polarization and thus contributed to anti-inflammatory processes in the cecal ligation and puncture (CLP)-induced inflammation model. MATERIALS AND METHODS: ELISA, western blotting, and qRT-PCR were used to verify that Ang-(1-7) decreased the expression of pro-inflammatory cytokines and increased anti-inflammatory cytokines. The differentiation of M1/M2 macrophages was assessed by flow cytometry for assessing the cell-surface markers, CD86 and CD206. The related key receptors and pathways were analyzed by Western blotting, qRT-PCR, and immunofluorescence. CLP-induced inflammatory mice models were used for in vivo studies. Hematoxylin and eosin and immunohistochemical and immunofluorescence staining protocols were used to analyze histological changes in the spleen, and the related key pathway proteins were analyzed by western blotting. RESULTS: Ang-(1-7) decreased the expressions of the TNF-α and IL-6 pro-inflammatory cytokines and increased the expressions of the IL-4 and IL-10 anti-inflammatory cytokines. INOS and TNF-α, which represented M1 macrophage polarization, were decreased by Ang-(1-7). ARG1 and CD163, which represented M2 macrophage polarization, were increased by Ang-(1-7). Both Mas receptor and ACE2 are expressed on macrophages. Furthermore, the ACE2-Ang-(1-7)-MAS axis modulated macrophage polarization by ameliorating TLR4 expression and regulating the NF-кB and MAPK pathways. In addition, splenomegaly and macrophage infiltration were observed in the spleen of the CLP-induced mouse models and macrophages in the spleen suspension of CLP models were shifted to M1 phenotype and were effectively inhibited by Ang-(1-7) via the TLR4-mediated NF-кB and MAPK pathways, which could be partially rescued by A-779. CONCLUSION: Ang-(1-7) inhibited inflammatory responses in vivo and in vitro, and repressed macrophage polarization toward the M1 phenotype and promoted it toward the M2 phenotype, which provided new evidence for the anti-inflammation activity of the ACE2-Ang-(1-7)-MAS axis.

Fetal growth restriction mice are more likely to exhibit depression-like behaviors due to stress-induced loss of dopaminergic neurons in the VTA.

Fetal growth restriction (FGR) is a severe perinatal complication that can increase risk for mental illness. To investigate the mechanism by which FGR mice develop mental illness in adulthood, we established the FGR mouse model and the FGR mice did not display obvious depression-like behaviors, but after environmental stress exposure, FGR mice were more likely to exhibit depression-like behaviors than control mice. Moreover, FGR mice had significantly fewer dopaminergic neurons in the ventral tegmental area but no difference in serotoninergic neurons in the dorsal raphe. RNA-seq analysis showed that the downregulated genes in the midbrain of FGR mice were associated with many mental diseases and were especially involved in the regulation of NMDA-selective glutamate receptor (NMDAR) activity. Furthermore, the NMDAR antagonist memantine can relieve the stress-induced depression-like behaviors of FGR mice. In summary, our findings provide a theoretical basis for future research and treatment of FGR-related depression.

Comparative analysis of connective tissue disease-associated interstitial lung disease and interstitial pneumonia with autoimmune features.

OBJECTIVE: This retrospective clinical study aimed to examine the similarities and differences between connective tissue disease-associated interstitial lung disease (CTD-ILD) and interstitial pneumonia with autoimmune features (IPAF) and to identify the influencing factors of CTD-ILD, with a goal of early detection and active treatment of the disease. METHODS: We conducted a retrospective study of 480 patients: 412 with CTD-ILD and 68 with IPAF. Demographic features, clinical characteristics, laboratory indicators, and chest high-resolution computed tomography (HRCT) imaging data were analyzed. RESULTS: Compared with the IPAF group, the CTD-ILD group contained more women, and the incidences of joint pain, dry mouth/dry eyes, and Raynaud's phenomenon were higher; erythrocyte sedimentation rate (ESR) and D-dimer levels were higher; red blood cell (RBC) and hemoglobin (Hb) levels were lower; a high rheumatoid factor (RF) titer (> 2 times the normal upper limit) was observed, and anti-cyclic citrullinated peptide antibody (anti-CCP), anti-keratin antibody (AKA), antinuclear antibody (ANA), and anti-melanoma differentiation-associated gene 5 antibody (anti-MDA5) levels were higher. Compared with CTD-ILD patients, IPAF patients were more likely to present initially with respiratory symptoms, with higher rates of fever, cough and expectoration, dyspnea, and Velcro crackles; anti-Ro52 titers were higher; incidences of honeycombing opacity, reticulate opacity, patchy opacity, and pleural thickening were greater. Female sex, a high RF titer (> 2 times the normal upper limit), anti-CCP positivity, ANA positivity, and anti-MDA5 positivity were risk factors for CTD-ILD when the odds ratios were adjusted. CONCLUSION: CTD-ILD and IPAF patients differed in demographic features, clinical characteristics, laboratory indicators, and chest HRCT imaging data. Female sex, a high RF titer (> 2 times the normal upper limit), anti-CCP positivity, ANA positivity, and anti-MDA5 positivity were risk factors for CTD-ILD.Key Points• This retrospective clinical study comprehensively compared the demographic features, clinical characteristics, laboratory indicators, and chest HRCT imaging data of CTD-ILD and IPAF patients.• The evidence suggested that female sex, a high RF titer, anti-CCP positivity, ANA positivity, and anti-MDA5 positivity were risk factors for CTD-ILD.

Dynamic placement of the linker histone H1 associated with nucleosome arrangement and gene transcription in early Drosophila embryonic development.

The linker histone H1 is critical to maintenance of higher-order chromatin structures and to gene expression regulation. However, H1 dynamics and its functions in embryonic development remain unresolved. Here, we profiled gene expression, nucleosome positions, and H1 locations in early Drosophila embryos. The results show that H1 binding is positively correlated with the stability of beads-on-a-string nucleosome organization likely through stabilizing nucleosome positioning and maintaining nucleosome spacing. Strikingly, nucleosomes with H1 placement deviating to the left or the right relative to the dyad shift to the left or the right, respectively, during early Drosophila embryonic development. H1 occupancy on genic nucleosomes is inversely correlated with nucleosome distance to the transcription start sites. This inverse correlation reduces as gene transcription levels decrease. Additionally, H1 occupancy is lower at the 5' border of genic nucleosomes than that at the 3' border. This asymmetrical pattern of H1 occupancy on genic nucleosomes diminishes as gene transcription levels decrease. These findings shed new lights into how H1 placement dynamics correlates with nucleosome positioning and gene transcription during early Drosophila embryonic development.