Analysis of risk factors for the progression and prognosis of connective tissue disease-associated interstitial lung disease.

Objectives: This study aimed to investigate the risk factors of lung progression in patients with connective tissue disease-associated interstitial lung disease (ILD). Patients and methods: A total of 91 ILD patients (28 males, 63 females; mean age: 54.9±11.3 years; range, 30 to 77 years) were included in the prospective follow-up study conducted throughout 2020. They were divided into progressors (n=27) and nonprogressors (n=64) according to whether the pulmonary disease progressed during a six-month follow-up period. The clinical data of the two groups were analyzed, and a logistic regression model was constructed to analyze the risk factors of the progression of ILD in all patients. Results: Univariate analysis revealed significant differences (p<0.05) between the two groups in smoking history, serum ferritin, FVC% (the percentage of forced vital capacity), DLCO% (the percentage of diffusion capacity for carbon monoxide), and computed tomography involvement range. Further application of a logistic regression model revealed that increased serum ferritin level was an independent risk factor for ILD progression (odds ratio=1.002, 95% confidence interval: 1.000-1.003, p=0.004). The optimal critical value of serum ferritin was 303.25 ng/mL, the sensitivity and specificity were 81.5% and 54.7%, respectively, and the area under the curve was 0.747. Conclusion: The level of serum ferritin may be an independent predictor for ILD progression.

HiCmapTools: a tool to access HiC contact maps.

BACKGROUND: With the development of HiC technology, more and more HiC sequencing data have been produced. Although there are dozens of packages that can turn sequencing data into contact maps, there is no appropriate tool to query contact maps in order to extract biological information from HiC datasets. RESULTS: We present HiCmapTools, a tool for biologists to efficiently calculate and analyze HiC maps. The complete program provides multi-query modes and analysis tools. We have validated its utility on two real biological questions: TAD loop and TAD intra-density. CONCLUSIONS: HiCmapTools supports seven access options so that biologists can quantify contact frequency of the interest sites. The tool has been implemented in C++ and R and is freely available at https://github.com/changlabtw/hicmaptools and documented at https://hicmaptools.readthedocs.io/ .

Pattern of Nailfold Capillaroscopy in Patients With Systemic Lupus Erythematosus.

OBJECTIVES: This study aims to assess the nailfold capillary changes in patients with systemic lupus erythematosus (SLE), particularly among those with Raynaud's phenomenon (RP), and the correlation between nailfold capillary changes and autoantibodies and disease activity. PATIENTS AND METHODS: A total of 85 patients (9 males, 76 females; median age 31 years; range, 15 to 58 years) with newly diagnosed SLE were selected between July 2016 and July 2018 from our hospital. Disease activity was scored by the SLE Disease Activity Index. Nailfold capillaroscopy (NFC) was performed in all patients. RESULTS: Normal pattern, non-specific pattern, and scleroderma pattern were found in 13 (15.3%), 64 (75.3%), and eight (9.4%) patients, respectively. There was no significant difference between anti-double stranded deoxyribonucleic acid, anti-Smith antibodies, and low complements (all p>0.05), while significant differences of NFC pattern were found between low disease activity and high disease activity (p=0.002). RP was present in 31.7% of SLE patients, and the NFC findings in SLE patients with and without RP were significantly different in dilatation (81.5% vs. 14.0%). CONCLUSION: The results of our study showed that capillary changes were very common in patients with SLE, which seem to associate with disease activity and RP condition.

Beyond Blackboards: Engaging Underserved Middle School Students in Engineering.

Beyond Blackboards is an inquiry-centered, after-school program designed to enhance middle school students' engagement with engineering through design-based experiences focused on the 21st Century Engineering Challenges. Set within a predominantly low-income, majority-minority community, our study aims to investigate the impact of Beyond Blackboards on students' interest in and understanding of engineering, as well as their ability to align their educational and career plans. We compare participants' and nonparticipants' questionnaire responses before the implementation and at the end of the program's first academic year. Statistically significant findings indicate a school-wide increase in students' interest in engineering careers, supporting a shift in school culture. However, only program participants showed increased enjoyment of design-based strategies, understanding of what engineers do, and awareness of the steps for preparing for an engineering career. These quantitative findings are supported by qualitative evidence from participant focus groups highlighting the importance of mentors in shaping students' awareness of opportunities within engineering.

[Inhibitory effect of VPA on multiple myeloma U266 cell proliferation and regulation of histone acetylation].

This study was aimed to investigate the effects of sodium valproate (VPA) on the proliferation and regulation of histone acetylation of multiple myeloma cell line U266. U266 cells were treated with VPA. Cell proliferation was determined by CCK-8 assay, and cell cycle were analyzed by flow cytometry (FCM). The expression level of HDAC1 mRNA was detected by RT-PCR, and the protein levels of HDAC1 and histone H3, H4 acetylation was detected by Western blot. The results showed that the VPA inhibited the proliferation of U266 cells in concentration-and time-dependent manners.After exposure to different concentrations of VPA for 48 hours, the proportion of G(0)/G(1) cells increased, while the proportion of S phase cells decreased. The cell cycle was arrested obviously in G(0)/G(1) phase (p < 0.05). The expression of HDAC1 mRNA was inhibited, and the protein level of HDAC1 was down-regulated, while the histone H3/H4 acetylation was up-regulated in U266 cells. It is concluded that the VPA can inhibit cell proliferation of U266 and induce G(0)/G(1) phase arrest. The increase of histone H3/H4 acetylation resulting from inhibiting HDAC1 by VPA might be considered as a possible mechanism.

[Investigation on the mechanisms of p15INK4B gene demethylation by valproate in Molt-4 cells].

OBJECTIVE: To study the antitumour effects of sodium valproate (VPA) on the proliferation, differentiation and cell cycle of Molt-4 cell and to investigate its demethylation mechanisms. METHODS: After Molt-4 cells trated with VPA at different concentrations, cell viability and growth curve were assessed by MTT assay. Cell cycle changes were analyzed by flow cytometry. The expression level of p15, DNA methyltransferase 1 (DNMT-1), DNMT3A and 3B mRNA were detected by RT-PCR and the methylation level was detected by hn-MSPCR. RESULTS: VPA significantly inhibited the proliferation of Molt-4 cells. After 48 h culture with 5.0 mmol/L VPA, the percentages of Molt-4 cells in G(0)/G(1) phase was (66.87 ± 3.31)% and in S phase was (8.47 ± 2.56)%, while in control group, the cells in G(0)/G(1) phase increased and in S phase decreased significantly. The p15 gene in Molt-4 cells failed to express due to its hypermethylation. The expression level of p15 gene mRNA increased significantly after exposure to VPA for 48 h. As compared with control group, the expression of DNMT-1 was down-regulated in a dose-dependent manner. The expression level of DNMT3B decreased at 10.0 mmol/L concentration. CONCLUSION: VPA has a demethylation effect on p15 INK4B gene by inhibiting the DNMT-1 and DNMT3B gene activities to recover p15 gene activity, which arrests Molt-4 cell in G(0)/G(1) phase.

[Synergistic effects of VPA and As2O3 on Molt-4 cells in vitro and its possible mechanisms].

This study was purposed to investigate the synergistic effects of sodium valproate (VPA) and As2O3 on the proliferation of Molt-4 cells in vitro and its possible mechanisms. Cell viability and growth curve were assessed by the MTT assay. The synergistic activity in combination of 2 drugs was determined by the Q format. The expression levels of p15, DNA methyltransferase 1 (DNMT-1), DNMT3A and DNMT 3B mRNA were detected by RT-PCR and the methylation level was detected by hn-MSPCR. The results indicated that the VPA and As2O3 both inhibited proliferation of Molt-4 cells. The combination of two drugs showed an additive effect (values of Q were>or=0.85). The inhibitory rate in combination of 5 mmol/L of VPA with 10 micromol/L of As2O3 was (70.31+/-2.54)%. The p15 gene in Molt-4 cell line failed to express due to its hypermethylation. The level of p15 gene mRNA expression increased significantly after exposure to VPA in combination with As2O3 for 48 h. As compared with control group, the expression of DNMT-1 was down-regulated in a dose-dependent manner, whereas DNMT3A had no significant differences from the control. The level of expression of DNMT3B seemed to decrease at 10 mmol/L concentration. There were significant differences between the combination of the two drugs and the control group. The gray value of methylated bands decreased after the treatment of VPA alone and in combination with As2O3 in a dose-dependent manner. It is concluded that VPA induces demethylation of p15 INK4B gene by inhibiting the DNMT-1 and DNMT3B gene activities, which up-regulates the p15 gene, recovers its activity. The combination of VPA with As2O3 has the synergistic additive effect on the inhibition of cell viability, so that VPA can reduce the side effect of As2O3 on liver function, which would be verified in the clinical practice.

[Demethylation and transcription of p16 gene in malignant lymphoma cell line CA46 induced by EGCG].

The study was purposed to investigate the possible mechanism of epigallocatechin-3-gallate (EGCG) induced p16 gene demethylation and transcription regulation in the malignant lymphoma cell line-CA46. The induced growth inhibition of CA46 cells was assayed by growth curve and MTT; the DNA content of CA46 cells was analyzed by flow cytometry after being exposed to EGCG; the methylation status of the p16 gene in CA46 cell line before and after treatment with EGCG was detected by the nested-methylation specific PCR and DNA sequencing; the mRNA of p16 and DNA methyltransferases (DNMT3A and DNMT3B) gene were determined by RT-PCR. The results showed that in comparison with the control, all the 3 different concentration of EGCG were able to inhibit the growth of malignancy cell lines and increase the cell number in G(0)/G(1) phase. After treatment with EGCG for 48 hours, the methylation level was apparently attenuated in a concentration-dependent manner. Expression of p16 gene in untreated group was mild while in the treated groups it had been greatly strengthened, as compared with untreated group, the gray scale ratio of p16 to beta-actin 1 treated with EGCG (6, 12, 24) microg/ml was increased from (0.05 +/- 0. 01) to (0.19 +/- 0.03), (0.39 +/- 0.10), (0.85 +/- 0.09) respectively, exhibiting a significant difference (p < 0.05); as compared with the untreated group, after treatment with EGCG for 48 hours, the expressions of DNMT3A and DNMT3B were obviously down-regulated. It is concluded that EGCG can activate and up-regulate the expression of p16 gene mRNA which inhibits the proliferation of CA46 cell through inducing the G(0)/G(1) arrest by demethylation and/or by inhibiting DNMT3A and DNMT3B gene.

[Detection of p16 gene methylation status in adult patients with acute leukemia by using n-MSP].

The study was aimed to explore the relationship between patterns of methylation or deletion and the development of acute leukemia, and further to clarify the possible mechanism in the development of adult acute leukemia. Nested methylation-specific polymerase chain reaction (n-MSP) was adopted to analyze p16 gene methylation or deletion patterns in 82 adult acute leukemia patients with different subtypes and stages. The results indicated that rate of p16 gene methylation was 39.0% in 82 adult acute leukemia patients, among them, 41.4% in acute myelogenous leukemia (AML) and 33.3% in acute lymphoblastic leukemia (ALL). It were found that 36.6% of de novo AL patients and 54.5% of relapsed AL patients developed the hypermethylation of p16 gene. Out of the 82 patients, 6 seemed to have deletion of p16 gene, including 1 AML (1.7%) and 5 ALL (20.8%). There were no hypermethylation or deletion of p16 gene in the 16 controls. It is concluded that methylation of p16 gene may play a more important role than homozygous deletion of p16 gene in the leukemogenesis and progression of adult acute leukemia.

[Detection of p15 gene methylation or deletion status in different malignant cell lines by using hemi-nested methylation specific polymerase chain reaction].

This study was aimed to investigate the methylation or deletion status of p15 gene in different malignant cell lines, and further to clarify their roles in the development and progression of malignant tumors. Hemi-nested methylation specific polymerase chain reaction (hn-MSP) was adopted to analyze p15 gene methylation or deletion status in 20 malignant tumor cell lines and mononuclear cells or normal cell lines in healthy people, as well as to evaluate its sensitivity and specificity. The results showed that among all of the cell lines, Molt-4, KG1, NCE, Raji, SMMC-7221, CA46, SW480 and NCI-H446 were partial methylated with CDKN2B gene, and its sensitivity of detection of p15 gene methylation was up to 1.0 x 10(-5), also it had great specificity. Peripheral blood mononuclear cell (MNCs) from healthy volunteer, HL-60, HepG2, 293, HeLa, SGC7901, U266 and CEM were unmethylated; and K562, NB4, GMC, Jurkat seemed to have deletion or mutation of p15 gene. It is concluded that the incidence of p15 gene methylation or deletion in many tumours, especially malignant hematopathy, is frequent, they correlate with disease progression and prognosis. Hn-MSP is highly sensitive and specific in analyzing p15 gene methylation, deserving in clinical application.

[Detection of promoter methylation of p16 gene in hematological malignant cell lines by nested methylation specific polymerase chain reaction].

This study was aimed to investigate the efficiency of modified methylation-specific polymerase chain reaction i.e. nested methylation-specific polymerase chain reaction, used to detect the promoter methylation of p16 gene in six hematological malignant cell lines, and to explore the application in selection of hematological malignant cell lines with promoter hypermethylation, and make them to be an idel cell models for studying the relationship between gene methylation and expression. DNAs were denatured by NaOH and then were subjected to bisulfite modification and a nested-MSP was used to amplify the promoter region, nested MSP product of p16 gene promoter was analyzed and sequenced. The results showed that the hypermethylation of p16 gene was detected in CA46 and U266, however, Molt4, K562, HL-60 and Jurkat cell lines were unmethylated. In conclusion, p16 gene methylation in hematological malignant cell lines can be perfectly detected by nested-MSP method, which is simple, sensitive and specific for screening all kinds of hematological malignant cell lines with p16 gene methylated.