Construction of an immune predictive model and identification of TRIP6 as a prognostic marker and therapeutic target of CRC by integration of single-cell and bulk RNA-seq data.

BACKGROUND: Investigations elucidating the complex immunological mechanisms involved in colorectal cancer (CRC) and accurately predicting patient outcomes via bulk RNA-Seq analysis have been notably limited. This study aimed to identify the immune status of CRC patients, construct a prognostic model, and identify prognostic signatures via bulk RNA sequencing (RNA-seq) and single-cell RNA-seq (scRNA-seq). METHODS: The scRNA-seq data of CRC were downloaded from Gene Expression Omnibus (GEO). The UCSC Xena database was used to obtain bulk RNA-seq data. Differentially expressed gene (DEG), functional enrichment, and random forest analyses were conducted in order to identify core genes associated with colorectal cancer (CRC) that were relevant to prognosis. A molecular immune prediction model was developed using logistic regression after screening features using the least absolute shrinkage and selection operator (LASSO). The differences in immune cell infiltration, mutation, chemotherapeutic drug sensitivity, cellular senescence, and communication between patients who were at high and low risk of CRC according to the predictive model were investigated. The prognostic genes that were closely associated with CRC were identified by random survival forest (RSF) analysis. The expression levels and clinical significance of the hub genes were analyzed in vitro. The LoVo cell line was employed to ascertain the biological role of thyroid hormone receptor-interacting protein 6 (TRIP6). RESULTS: A total of seven main cell subtypes were identified by scRNA-seq analysis. A molecular immune predictive model was constructed based on the risk scores. The risk score was significantly associated with OS, stage, mutation burden, immune cell infiltration, response to immunotherapy, key pathways, and cell-cell communication. The functions of the six hub genes were determined and further utilized to establish a regulatory network. Our findings unequivocally confirmed that TRIP6 upregulation was verified in the CRC samples. After knocking down TRIP6, cell proliferation, migration, and invasion of LoVo cells were inhibited, and apoptosis was promoted. CONCLUSIONS: The molecular predictive model reliably distinguished the immune status of CRC patients. We further revealed that TRIP6 may act as an oncogene in CRC, making it a promising candidate for targeted therapy and as a prognostic marker for CRC.

Difference in calcium ion precipitation between free and immobilized Halovibrio mesolongii HMY2.

Biomineralization has become a research focus in wastewater treatment due to its much lower costs compared to traditional methods. However, the low sodium chloride (NaCl)-tolerance of bacteria limits applications to only water with low NaCl concentrations. Here, calcium ions in hypersaline wastewater (10% NaCl) were precipitated by free and immobilized Halovibrio mesolongii HMY2 bacteria and the differences between them were determined. The results show that calcium ions can be transformed into several types of calcium carbonate with a range of morphologies, abundant organic functional groups (C-H, C-O-C, C=O, etc), protein secondary structures (ß-sheet, α-helix, 310 helix, and ß-turn), P=O and S-H indicated by P2p and S2p, and more negative δ13CPDB (‰) values (-16.8‰ to -18.4‰). The optimal conditions for the immobilized bacteria were determined by doing experiments with six factors and five levels and using response surface method. Under the action of two groups of immobilized bacteria prepared under the optimal conditions, by the 10th day, Ca2+ ion precipitation ratios had increased to 79%-89% and 80%-88% with changes in magnesium ion cencentrations. Magnesium ions can significantly inhibit the calcium ion precipitation, and this inhibitory effect can be decreased under the action of immobilized bacteria. Minerals induced by immobilized bacteria always aggregated together, had higher contents of Mg, P, and S, lower stable carbon isotope values and less well-developed protein secondary structures. This study demonstrates an economic and eco-friendly method for recycling calcium ions in hypersaline wastewater, providing an easy step in the process of desalination.

Application of a treatment planning system-assisted large-aperture computed tomography simulator to percutaneous biopsy: initial experience of a radiation therapist.

OBJECTIVE: To evaluate the application of treatment planning system (TPS)-assisted large-aperture computed tomography (CT) simulator to percutaneous biopsy. METHODS: This retrospective study enrolled patients that underwent TPS-assisted large-aperture CT simulator-guided percutaneous biopsy from November 2018 to December 2019. Retrospective analyses of puncture accuracy were compared using paired t-test and a Wilcoxon rank sum test. The risk factors for puncture accuracy and complications were identified. RESULTS: A total of 38 patients were included in this study. There were no significant differences between the planned and actual puncture depth and angle. Pulmonary puncture was significantly associated with the accuracy of the puncture angle. The diagnostic rate of malignancy was 76% (29 of 38), of which 20 of 25 patients were in the group initially diagnosed with unconfirmed lesions and nine of 13 patients were in the group of treated patients that needed additional pathological analyses. For patients that underwent a pulmonary biopsy, 12 had minor pneumothorax and three suffered needle track bleeding. No other complications were observed. Regression analyses indicated a significant correlation between puncture angle and the incidence of pneumothorax. CONCLUSION: TPS-assisted large-aperture CT simulator may improve the percutaneous biopsy procedure by combining the advantages of radiotherapy specialties with computer targeting.

Correlation analysis of 18F-FDG PET/CT for the staging and treatment effect assessment of breast cancer.

OBJECTIVE: Since cancer treatment and outcome differ among the patients diagnosed with breast cancer at different stages, this study aims to elucidate the factors associated with PET/CT staging, treatment effect, and maximal standardized uptake value (SUVmax) in breast cancer patients. METHODS: Twenty-eight patients who underwent two PET/CT examinations with the complete pathological and immunohistochemical data were retrospectively reviewed. Pearson and Spearman correlation analyses were performed to investigate the relationships of patient PET/CT staging (first round PET/CT), treatment effect (comparison between the results of two rounds of PET/CT), and tumor SUVmax, with respect to patient age, tumor location, tumor long diameter, short diameter, time of first round PET/CT examination, histological type and grade, axillary lymph node metastasis rate, interval between the two PET/CT examinations, treatment method, and the expression of the estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), P53, and Ki67. RESULTS: PET/CT staging (first round PET/CT) relates to HER2 and Ki67 expression with the correlation coefficients of 0.432 and 0.552, and P-values of 0.022 and 0.002, respectively. The treatment effect (comparison between the results of two rounds of PET/CT) associates with tumor site and P53 expression in which the correlation coefficients are - 0.412 and 0.845, and P-values are 0.029 and 0.000, respectively. The measured SUVmax correlates well with the tumor long diameter, short diameter, and treatment effect in which the correlation coefficients are 0.943, 0.886, and 0.878, and P-values are 0.005, 0.019, and 0.02, respectively. CONCLUSIONS: Study results indicate that PET/CT staging and treatment effect associate well with SUVmax and immunohistochemical results of tumor, while SUVmax of tumor associates well with tumor size.

Application of automated bronchial 3D-CT measurement in pulmonary contusion complicated with acute respiratory distress syndrome.

BACKGROUNDQuantitative measurement of bronchial morphological changes in pulmonary contusion with acute respiratory distress syndrome (ARDS) has important clinical implications.OBJECTIVETo investigate the morphological changes in bronchus before and after treatment in patients with pulmonary contusion combined with ARDS using an automated bronchial three-dimensional computed tomography (3D-CT) measurement method.METHODSThe study involves a dataset of CT images of 62 patients diagnosed with pulmonary contusion combined with ARDS. The volume of pulmonary contusion lesions was calculated as a percentage of the total lung volume using the automated 3D-CT method. The bronchial luminal cross-sectional area, wall cross-sectional area, the maximum and average wall thickness, the maximum and average luminal densities, intraluminal and extraluminal diameters, and circumferences of generations 2-4 bronchi before and after treatment were measured. Furthermore, the corresponding differences were analyzed statistically.RESULTSThe luminal cross-sectional area, wall cross-sectional area, intraluminal and extraluminal diameters, and circumferences of generations 2-4 bronchi were all significantly lower before treatment than after treatment (P < 0.05). However, the maximum and average wall thicknesses were both significantly higher before treatment than after treatment (P < 0.05). No significant difference was found in the maximum and average luminal densities before and after treatment (P > 0.05). The percentage of the pulmonary contusion lesion volume to the total lung volume correlated positively with the thoracic trauma severity score (r = 0.74, P < 0.01).CONCLUSIONSQuantitative bronchial CT image analysis enables to detect and assess bronchial morphological changes in patients diagnosed with pulmonary contusion combined with ARDS.

Morphological analysis of blood vessels near lung tumors using 3-D quantitative CT.

BACKGROUND: Improved visualization of lung cancer-associated vessels is vital. OBJECTIVE: To evaluate the efficacy of 3-D quantitative CT in lung cancer-associated pulmonary vessel assessment. METHODS: Vascular CT changes were assessed visually and using FACT-Digital lung TM software (n = 162 patients, 178 controls). The total number of pulmonary vessels (TNV) and mean lumen area of pulmonary vessels (MAV) vertical to cross-sections of fifth/sixth-generation bronchioles were measured. RESULTS: Visual investigation revealed fewer ipsilateral pulmonary vascular abnormalities in lung cancer (151/162) than did quantitative CT (162/162), and required more time (3.2±1.5 vs. 2.5±1.3 min) (P < 0.05). CT measurements revealed that the TNV vertical to the fifth-generation bronchial cross-section of the ipsilateral, contralateral, and control groups was 14.58±4.75, 9.58±3.74, and 10.22±4.07 and the MAV in these groups was 99.70±26.20, 58.76±29.29, and 57.76±18.32, respectively. The TNV vertical to the sixth-generation bronchial cross-section of the ipsilateral, contralateral, and control groups was 16.64±5.14, 11.59±4.06, and 11.75±4.16 and the MAV was 110.22±31.47, 67.62±30.41, and 60.24±16.18, respectively. The TNV and MAV in ipsilateral lung cancer tissues exceeded those in the contralateral side and control group tissues (P < 0.001). CONCLUSIONS: Automated 3-D quantitative CT could successfully characterize pulmonary vessels and their lung cancer-associated changes.

The pulmonary damage caused by smoking: A longitudinal study.

BACKGROUND: Smoking for a long period is known to cause several harms to the human body, chiefly associated with serious pulmonary damage. OBJECTIVE: The purpose of this study was to evaluate the difference in the pulmonary damage between current smokers and ex-smokers, through measuring the bronchial parameters and the extent of emphysema, in order to further illustrate the harm of smoking and the need to stop smoking. METHODS: Using the FACT-Digital lung TM software quantitatively analysis of CT images, including the WT, WA%, LD, LV, PD, and %LAA-950 was performed. The percentage of low attenuation areas less than -950 Hounsfield units (%LAA-950) was defined as the extent of emphysema. The longitudinal data in the two consecutive years of these current smoker group and ex-smoker group were compared by paired t-test. RESULTS: The LV, %LAA-950, WT and WA% of current smokers increased more rapidly each year than that of ex-smokers. The PD and LD of current smokers declined more rapidly each year than that of ex-smokers. CONCLUSIONS: This study shows that pulmonary damage caused by smoking related to the smoking status, can be measured. Smoking cessation has a positive role in alleviating the progress of pulmonary damage.

Sex-related differences in bronchial parameters and pulmonary function test results in patients with chronic obstructive pulmonary disease based on three-dimensional quantitative computed tomography.

Objective This study was performed to evaluate the effect of sex on bronchial parameters and the predicted forced expiratory volume in 1 s expressed as a percentage of the forced vital capacity (FEV1% pred) on pulmonary function testing. Methods The data of 359 patients with chronic obstructive pulmonary disease (COPD) with available FEV1% pred and computed tomography (CT) images were retrospectively reviewed. FACT-Digital lung TM software (DeXin, Xi'an, China) was used to perform fully automated three-dimensional CT quantitative measurements of the bronchi. Generation 5 to 7 bronchi were measured, and the parameters analyzed were the lumen diameter (LD), wall thickness (WT), lumen area (LA), and WA% [WA / (WA + LA) × 100%]. Results In the smoking, smoking cessation, and nonsmoking groups, women had a significantly larger WA% and smaller LD, WT, and LA than men. The FEV1% pred was significantly lower in women than men in the smoking and smoking cessation groups. The FEV1% pred was significantly higher in women than men in the nonsmoking group. Conclusion Sex-related differences may partially explain why smoking women experience more severe pulmonary function impairment than men among patients with COPD.

Computer-aided detection for the automated evaluation of pulmonary embolism.

BACKGROUND: There are few quantitative studies that directly evaluate methods of determining pulmonary embolism (PE). New computer-aided detection (CAD) methods for measuring PE may help in defining the relationship of PE to right heart failure (RHF). OBJECTIVES: We used CAD to investigate the severity of PE and explored whether the severity of PE was associated with RHF. METHODS: A fully automatic calculation conducted by CAD was made of the embolism area/lumen area, which was used to evaluate the severity of the PE. The vascular obstruction index (VOI) was also used to evaluate PE, using the Mastora and Qanadli scores. Paired t tests were used to compare the severity of PE evaluated by Mastora or Qanadli score, to the severity determined by CAD. Correlation between the severity of the PE and RHF was also evaluated by Spearman's rank correlation analysis. RESULTS: There was no significant difference between the PE evaluated by Mastora compared with the measurement by CAD (P= 0.720), and also no difference between evaluation by Qanadli and automatic measurement by CAD (P= 0.617). The severity of PE evaluated by Mastora, Qanadli, and CAD had significant positive correlation with RHF (R= 0.75 P= 0.01, R= 0.69 P= 0.02, R= 0.80 P= 0.00). CONCLUSION: We found strong correlation between RHF and the severity of PE evaluated by CAD, and the method was found to be simple and reliable.