Identification of clinical prognosis features and significant DNA methylation regulation in pineoblastoma.

BACKGROUND: Pineoblastoma (PB) represents a great challenge for clinical management due to lack of a specific therapeutic regimen. This study aims to identify relevant prognostic factors and potential treatment targets by mining public databases. METHODS: The clinical characteristics and survival data of PB patients were obtained from the SEER database between 2000 and 2019 for Cox regression analysis and nomogram construction. The PB's DNA methylation data was acquired from two GEO datasets, GSE133801 and GSE215240, for bioinformatics analysis. RESULTS: Of 383 PB patients, Cox univariate analysis unveiled that male gender (p = 0.017), age younger than 3 years at diagnosis (p < 0.001) and absence of radiotherapy (p < 0.001) correlated with poorer overall survival (OS), the subsequent multivariate analysis confirmed sex (p = 0.036), age (p < 0.001) and radiotherapy (p = 0.005) as independent prognostic factors for OS. A nomogram showed robust predictive accuracy as evidenced by AUC values (1-year OS: 0.774, 3-year OS: 0.692, 5-year OS: 0.643). DNA methylation analysis observed tumor hypomethylation, notably in promoter regions. Later, the GO enrichment analysis of aberrantly methylated genes indicated associations with embryonic organ development, cellular membrane composition and DNA-binding transcription, while KEGG analysis revealed enrichment in tumor-associated MAPK, calcium and RAS signaling pathways. CONCLUSIONS: The prognosis of PB is closely associated with sex, age and receipt of radiotherapy, potentially linked to aberrations in the RAS and MAPK signaling pathways. The individual case suggests that dasatinib and trametinib are potential targeted therapies for improving PB prognosis.

High Biologically Effective Dose Radiotherapy for Brain Metastases May Improve Survival and Decrease Risk for Local Relapse Among Patients With Small-Cell Lung Cancer: A Propensity-Matching Analysis.

To evaluate whether high biologically effective dose (BED) radiotherapy improves local control and survival outcomes for patients with brain metastases (BMs) from small-cell lung cancer (SCLC) and to determine possible prognostic factors. From January 1998 to June 2018, 250 patients with BM from SCLC were retrospectively analyzed. The Cutoff Finder program was used to classify patients by BED. Overall survival (OS) and BM progression-free survival (BM-PFS) were analyzed using the Kaplan-Meier method and log-rank test. A Cox regression model was used to calculate the hazard ratio and 95% CI for prognostic factors for OS among the study population and propensity score (PS)-matched patients. A BED of 47.4 was taken as the optimal cutoff value. Both OS and BM-PFS were significantly improved in the high-BED (>47.4 Gy) than in the low-BED (≤47.4 Gy) group (median OS: 17.5 months vs 9.5 months, P < .001, median BM-PFS: 14.4 months vs 8.3 months, P < .001). Biologically effective dose (P < .001), Eastern Cooperative Oncology Group performance status (P = .047), smoking (P = .005), and pleural effusion (P = .004) were independent prognostic factors for OS. Propensity score matching with a ratio of 1:2 resulted in 57 patients in the high-BED group and 106 patients in the low-BED group. In the PS-matched cohort, OS and BM-PFS were significantly prolonged in the high-BED group compared with the low-BED group (P < .001). Biologically effective dose >47.4 Gy improves survival among patients with BM from SCLC. Eastern Cooperative Oncology Group score, smoking, and pleural effusion independently affect OS of SCLC patients with BM.

Identification of a ferroptosis-related gene signature for the prognosis of pediatric neuroblastoma.

Background: Ferroptosis-related genes are correlated with the prognosis of patients with neuroblastoma (NB) remains unknown. This study aims to establish a prognostic ferroptosis-related gene model for predicting prognostic value in pediatric NB patients. Methods: The gene expression array and clinical characteristics of NB were downloaded from a public database. Correlations between ferroptosis-related genes and drug responses were analyzed by Childhood Cancer Therapeutics. The prognostic model was constructed by least absolute shrinkage and selection operator (LASSO) Cox regression and was validated in NB patients from the ICGC cohort. The survival analysis was performed by Cox regression analysis. single-sample gene set enrichment analysis (ssGSEA) was used to quantify the immune cell infiltration correlation. Results: Overall, 70 genes were identified as ferroptosis-related differentially expressed genes (DEGs) from 247 samples. Then, 13 ferroptosis-related genes were correlated with OS in the univariate Cox regression analysis. Five prognostic ferroptosis-related DEGs (pFR-DEGs) (STEAP3, MAP1LC3A, ULK2, MTOR and TUBE1), which were defined as the intersection of DEGs and prognostic ferroptosis-related genes, were identified and utilized to construct the prognostic signature. The correlation between five pFR-DEGs and drug responses was analyzed, and the box plots indicated that MTOR gene expression was highest, suggesting that MTOR expression is related to progressive NB disease. The receiver operating characteristic (ROC) curve showed that the model had moderate predictive power. The survival analysis indicated that the high-risk group had poor overall survival (OS) (P=2.087×10-06). Univariate and multivariate analyses identified the risk score as a significant prognostic risk factor [P=0.003, hazard ratio (HR) =1.933]. Immune cell infiltration correlation analysis showed that the high-risk group was related to more immune cells. Conclusions: The present study indicated a difference in ferroptosis-related gene expression between low- and high-risk NB patients. The ferroptosis-related signature could serve as a prognostic prediction tool. Additionally, immune infiltration might play an important role in different risk groups for NB patients.

sRNA chaperone Hfq controls bioluminescence and other phenotypes through Qrr1-dependent and -independent mechanisms in Vibrio fischeri.

Colonization of the squid Euprymna scolopes by the bacterium Vibrio fischeri depends on bacterial biofilm formation, motility, and bioluminescence. Previous work has demonstrated an inhibitory role for the small RNA (sRNA) Qrr1 in quorum-induced bioluminescence of V. fischeri, but the contribution of the corresponding sRNA chaperone, Hfq, was not examined. We thus hypothesized that V. fischeri Hfq similarly functions to inhibit bacterial bioluminescence as well as regulate other key steps of symbiosis, including bacterial biofilm formation and motility. Surprisingly, deletion of hfq increased luminescence of V. fischeri beyond what was observed for the loss of qrr1 sRNA. Epistasis experiments revealed that, while Hfq contributes to the Qrr1-dependent regulation of light production, it also functions independently of Qrr1 and its downstream target, LitR. This Hfq-dependent, Qrr1-independent regulation of bioluminescence is also independent of the major repressor of light production in V. fischeri, ArcA. We further determined that Hfq is required for full motility of V. fischeri in a mechanism that partially depends on the Qrr1/LitR regulators. Finally, Hfq also appears to function in the control of biofilm formation: loss of Hfq delayed the timing and diminished the extent of wrinkled colony development, but did not eliminate the production of SYP-polysaccharide-dependent cohesive colonies. Furthermore, loss of Hfq enhanced production of cellulose and resulted in increased Congo red binding. Together, these findings point to Hfq as an important regulator of multiple phenotypes relevant to symbiosis between V. fischeri and its squid host.

Prognostic nomogram based on the metastatic lymph node ratio for gastric neuroendocrine tumour: SEER database analysis.

OBJECTIVE: The prediction of survival of gastric neuroendocrine tumours (g-NETs) is controversial. Prognostic effects of the metastatic lymph node ratio (LNR) in patients with g-NET were explored, and a nomogram was plotted to predict the survival rates of patients. METHODS: A longitudinal study conducted on the basis of the Surveillance, Epidemiology, and End Results database. The association between LNR and survival were investigated by using Pearson correlation and Cox regression. Overall survival (OS) and cancer-specific survival (CSS) rates were predicted with the help of nomograms. RESULTS: A total of 315 patients with g-NET diagnosed from 2004 to 2015 were included in this study. LNR was discovered to have a negative correlation with OS and CSS (Pearson correlation coefficients: 0.343 (p<0.001) and 0.389 (p<0.001), respectively). The multivariate analyses indicated age, tumour site, differentiation, T staging, M staging, chemotherapy and LNR to be independent prognostic factors for both OS and CSS. Surgery was also a prognostic determinant for CSS (p=0.003). Concordance indices of the nomograms for OS and CSS were higher than those of the TNM classification (0.772 vs 0.730 and 0.807 vs 0.768, respectively). As per the area under the receiver operating characteristic curve, predictive ability of the nomograms for survival of 1, 3 and 5 years was all better than that of TNM classification. CONCLUSIONS: LNR is an independent predictor of g-NETs. The nomograms plotted in this study have a satisfying predictive ability of survival risks and are capable of guiding tailored treatment strategies for patients with g-NET.

Patterns of supraclavicular area failure after mastectomy in breast cancer patients: implications for target volume delineation.

PURPOSE: To characterize the pattern of post-mastectomy supraclavicular lymph node (LN) metastases in patients with breast cancer (BC) and to provide insights for individualized clinical target volume delineation for radiotherapy. METHODS: We retrospectively analyzed 88 patients with BC who developed post-mastectomy regional LN metastases. The affected regional LNs were categorized as the ipsilateral medial supraclavicular LN area (IMSC-LN), ipsilateral lateral supraclavicular LN area (ILSC-LN), ipsilateral infraclavicular LN area (IIC-LN), and ≥2 groups in the ipsilateral clavicular LN area (MMIC-LN). Clinical characteristics were included in a multivariate analysis to identify risk factors for clavicular LN metastases. RESULTS: The ILSC-LNs (68.2%) were the most common metastatic site. IMSC-LN metastases showed a significant association with estrogen-receptor (ER) negative status, left-sided BC, and positive axillary LNs. Tumor size ≥2.4 cm and Her2 type were predictors of ILSC-LN metastases. Additionally, tumor size ≥2.4 cm, and level I ipsilateral axillary metastases were associated with MMIC-LN metastasis. CONCLUSION: ILSC-LN was the most frequently affected group of supraclavicular lymph nodes. ER-negative status, left-sided BC, tumor size, and positive ipsilateral axillary LNs are potentially associated with the pattern of supraclavicular LN metastatic involvement.

Cloning, expression and characterization of recombinant elastase from Pseudomonas aeruginosa in Picha pastoris.

The gene lasB from Pseudomonas aeruginosa, which encoded elastase, was cloned and firstly successfully expressed in Pichia pastoris stain KM71 under the control of AOX promoter. The effects on the recombinant elastase activities of different pH, different temperatures and different metal ions were assayed. The full-length gene (1497 bp) encodes a preproenzyme including an N-terminal signal peptide (23 aa), a propeptide (197 aa) and mature elastase (301 aa). The recombinant elastase was secreted into culture supernatants using signal sequence from lasB and showed a single band at about 34 kDa by SDS-PAGE. The recombinant elastase expression hit the highest level of approximately 450 mg/L and the specific elastolytic activity of the recombinant elastase was 130 U/ml, which was approximately 26-fold higher than that of elastase obtained from P. aeruginosa. The optimal temperature and pH of the recombinant elastase was 28 degrees C and 7.4, respectively. The enzyme possessed high resistance to heat, and can be activated by Ca(2+). These enzyme properties suggested that it could be produced in an industrial scale and has the potential to be a commercial enzyme.

Association of markers of systemic and local inflammation with prognosis of patients with rectal cancer who received neoadjuvant radiotherapy.

PURPOSE: The inflammatory status of patients with cancer appears to affect cancer progression and patient prognosis. We examined the characteristics of cancer-associated systemic and local inflammation and its impact on the overall survival (OS) of patients with locally advanced rectal cancer (LARC) who received neoadjuvant radiotherapy (nRT). PATIENTS AND METHODS: Seventy-six consecutive LARC patients who received nRT from February 2012 to September 2015 were retrospectively analyzed. The peripheral neutrophil-to-lymphocyte ratio (NLR) was determined at diagnosis, and the CD8+ T-cell count was determined from surgical specimens. Factors associated with OS were identified by univariate and multivariate Cox regression. RESULTS: The median follow-up time was 23.0 months (range: 2-59), and the overall 5-year OS rate was 68.6% (95% CI =46.06-91.14). Patients with a high NLR (≥2.0) and a low CD8+ T-cell count (<9%) had a significantly worse 5-year OS than those with a low NLR and a high CD8+ T-cell count (P=0.005). NLR was also associated with lymphovascular invasion (P=0.014) and T stage (P=0.047), and the CD8+ T-cell count was associated with mucinous adenocarcinoma (P=0.005) and T stage (P=0.049). An NLR <2.0 was associated with pathological complete regression after nRT (P=0.039). Multivariate Cox regression indicated that NLR (P=0.025), CD8+ T-cell count (P=0.018), age (P=0.020), lymphovascular invasion (P=0.038), and T stage (P=0.011) were independently associated with OS. CONCLUSION: A high NLR and a low CD8+ T-cell count were significantly associated with poor survival in our population of patients with LARC. Measurement of markers of systemic and local inflammation might help to predict the prognosis of patients with LARC after nRT.

Role of postoperative radiotherapy in pT3N0 rectal cancer: A risk-stratification system based on population analyses.

The impact of adjuvant radiotherapy in pT3N0 rectal cancer is controversial. We aimed to determine the risk factors for cancer-specific survival (CSS) among these patients and to develop a risk-stratification system to identify which of these patients would benefit from adjuvant radiotherapy. In this review of the Surveillance, Epidemiology, and End Results database (2010-2014), we analyzed the data of pT3N0 rectal cancer patients who had not undergone neoadjuvant radiotherapy. Prognostic factors were identified using the Cox proportional hazards model, and risk scores were derived according to the ß regression coefficient. A total of 1021 patients were identified from the database search. The overall 5-year CSS was 86.31%. Multivariate analysis showed that age (P < 0.001), tumor differentiation (P = 0.044), number of nodes resected (P = 0.032), marital status (P = 0.005), and radiotherapy (P = 0.006) were independent prognostic factors for CSS. A risk-stratification system composed of age, tumor differentiation, and number of nodes resected was generated. Low-risk patients had better CSS than high-risk patients (92.13% vs 72.55%, P < 0.001). The addition of radiotherapy to surgery doubled the CSS among the high-risk patients (42.06% vs 91.26%, P = 0.001) but produced no survival benefit among the low-risk patients (93.36% vs 96.38%, P = 0.182). Our risk-stratification model based on age, tumor differentiation, and number of nodes resected predicted the outcomes of pT3N0 rectal cancer patients. This model could help identify patients who may benefit from adjuvant radiotherapy.

Molecular cloning and characterization of ETHYLENE OVERPRODUCER 1-LIKE 1 gene, LeEOL1, from tomato (Lycopersicon esculentum Mill.) fruit.

Recently, ETHYLENE OVERPRODUCER 1 (ETO1) had been cloned and identified as a negative post-transcriptional regulator in the ethylene biosynthesis in Arabidopsis. However, little was known about the role of ETO1 in other species, especially in tomato, which was an ideal model for studying the biosynthesis of ethylene during tomato fruit ripening. In this study, a tomato ETHYLENE OVERPRODUCER 1-LIKE 1 (LeEOL1) was cloned. The LeEOL1 cDNA was 3,515 bp long and carried an ORF that putatively encoded a polypeptide of 886 amino acids with a predicted molecular mass of 95 kDa. It shared 74% identity in amino acid sequence with Arabidopsis EOL1 and had one BTB (Broad-complex, Tramtrack, Bric-à-brac) domain and two TPR (tetratricopeptide repeat) domains, which were also conserved domains in AtEOL1. RT-PCR analysis of the temporal expression of LeEOL1 showed that its transcript decreased companied with increase of ethylene production in tomato ripening. The level of LeEOL1 transcripts in wild type tomato fruit at mature green stage did not distinctively change when treated with exogenous ethylene.