Enhancing metastatic colorectal cancer prediction through advanced feature selection and machine learning techniques.

BACKGROUND AND AIMS: Colorectal cancer (CRC) is the third most prevalent cancer globally, posing a significant challenge due to its high rate of metastasis. Approximately 20% of patients with CRC present with distant metastases at diagnosis, and over 50% develop metastases within five years. Accurate prediction of metastasis is crucial for improving survival outcomes in patients with CRC. METHODS: This study introduces an innovative cost-sensitive fast correlation-based filter (CS-FCBF) algorithm for feature selection, integrated with machine learning techniques to predict metastatic CRC. The CS-FCBF algorithm effectively reduced the number of genomic features from 184 to 9 critical genes: CXCL9, C2CD4B, RGCC, GFI1, BEX2, CXCL3, FOXQ1, PBK, and PLAG1. The methodology combined in vitro, in vivo, and analysis of publicly available single-cell RNA-seq datasets to validate the findings. RESULTS: The application of the CS-FCBF algorithm led to a significant improvement in prediction model performance, with an average 21.16% increase in the area under the precision-recall curve. The nine identified genes hold potential as diagnostic biomarkers and therapeutic targets for metastatic CRC. CONCLUSIONS: This study highlights the critical role of advanced feature selection methods, combined with machine learning, in addressing the challenge of class imbalance in medical diagnosis, particularly for CRC. Early detection of metastasis is vital, and the identified genes underscore their importance in the metastatic process of CRC. The methodology applied here offers valuable insights and paves the way for future research in other cancers or diseases that face similar diagnostic challenges.

TULP3 silencing suppresses cell proliferation, migration and invasion in gastric cancer via the PTEN/Akt/Snail pathway.

BACKGROUND: Tubby-like protein 3 (TULP3) is a member of the tubby family, has been related to the development of nervous system by gene knockout researches. Nevertheless, the role of TULP3 in the gastric cancer is not clear. METHODS: Western blotting and real-time polymerase chain reaction (PCR) were employed for the quantitative detection of TULP3 expression in the gastric cancer and consecutive non-cancerous tissues, and gastric cancer cells. The roles of TULP3 in invasion, migration as well as proliferation of the gastric cancer cell in vivo and in vitro through utilizing colony formation, MTT, wound-healing, transwell and mouse xenograft model. Western blotting assay was implemented in order to clarify the potential molecular mechanisms. Furthermore, electron microscopy and western blot were evaluated TULP3 expression in gastric cancer patient extracted serum exosomes. RESULTS: TULP3 expression levels were remarkably upregulated in the gastric cancer tissues and cells. Subsequent functional assays demonstrated that TULP3 downregulation suppressed invasion, migration as well as the proliferation of the gastric cancer cell. Mechanism assays depicted that the PTEN/Akt/Snail signaling pathway can inhibit invasion, migration as well as the proliferation of the gastric cancer cell via TULP3 silencing. Finally, we found that the expression of TULP3 could be determined in the extracted serum exosomes. The expression of TULP3 in gastric cancer group was higher in comparison with normal group. CONCLUSIONS: Our results reveal that TULP3 might serve as a potential prognostic biomarker and therapeutic target for the treatment of gastric cancer.

Effect of sodium hypochlorite on biofilm of Klebsiella pneumoniae with different drug resistance.

BACKGROUND: Biofilm formation is a major factor in the resistance mechanism of Klebsiella pneumoniae. This study aimed to evaluate the effects of sodium hypochlorite on the biofilm of K. pneumoniae with different drug resistance. METHODS: We collected 3 different types of K. pneumoniae respectively. The growth trend of biofilms of different drug-resistant K. pneumoniae was quantified by measuring the OD590 for 7 consecutive days using crystal violet staining. Scanning confocal fluorescence microscopy was used to observe biofilm morphology. RESULTS: After adding sodium hypochlorite, there were significant differences between the OD590 value of the 200, 500, and 1,000 µg/mL groups and the positive control group (all P < .05) on the fifth day. Concentrations of 2,000 and 5,000 µg/mL sodium hypochlorite were added after the biofilm had matured. In the 5,000 µg/mL sodium hypochlorite group, the OD590 of K. pneumoniae biofilm in the 3 groups decreased significantly compared with the blank control group (all P < .05). CONCLUSIONS: Sodium hypochlorite inhibited and cleared the biofilm of K. pneumoniae with different drug resistance, and the effect was enhanced with the increase of concentration in the range of bacteriostatic and bactericidal concentration.

Reference Intervals of Cytokeratin-19 Fragment (CYFRA 21-1) in Healthy Adults in China.

BACKGROUND: The reference intervals for serum cytokeratin-19 fragment (CYFRA 21-1) have not been established in Chinese population. This study aimed to measure serum CYFRA 21-1 levels in healthy Chinese subjects. METHODS: This cross-sectional, four-center study in two Chinese provinces enrolled participants (aged 18 - 85 years) with normal liver/kidney function and normal results for routine blood tests/urinalysis. Serum CYFRA 211 level was measured by ARCHITECT immunoassay (Abbott Diagnostics). RESULTS: The study included 3,366 participants. The median (interquartile range) value for serum CYFRA 21-1 level was 1.38 (1.00 - 1.89) ng/mL and tended to increase with age. The upper limit of the 97.5th percentile was 3.55 ng/mL and tended to increase with age. Serum CYFRA 21-1 median level varied between the four centers from 1.22 (0.89, 1.71) to 1.55 (1.12, 2.18) ng/mL, while the 97.5th percentile varied from 3.24 to 4.09 ng/mL. CYFRA 21-1 level correlated weakly with age and creatinine level. CONCLUSIONS: These new data can help to establish the 'normal range' of serum CYFRA 21-1 in people in China.

[Differential invasion and metastasis capacities of methotrexate enantiomer-resistant A549 cell lines].

OBJECTIVE: To study the differential in vitro motor and invasion capacities of methotrexate (MTX) enantiomer-resistant tumor cells. METHODS: The incremental concentrations and successive low-dose induction were employed to acquire the cell series resistant to 15 µmol/L MTX enantiomer, namely L-(+)-MTX/A549 and D-(-)-MTX/A549. Their drug-resistant indices were determined by MTT assay and their migration capacities by wound healing assay. Double soft-agar clone formation was used to detect the colony efficiency and size. And Transwell was employed to detect the in vitro movement and invasion capacity of three cell types. RESULTS: The resistance indices of L-(+)-MTX/A549 and D-(-)-MTX/A549 were (6.1 ± 1.0) and (20.3 ± 1.8) respectively. At 72 hours after wound healing assay, the number of L-(+)-MTX/A549 entering scratch zone was fewer than that of D-(-)-MTX/A549; The numbers of colony formation in D-(-)-MTX/A549, L-(+)-MTX/A549 and parental cells were (50 ± 7), (44 ± 6), (52 ± 7) and the rates of colony formation (1.68% ± 0.23%), (1.49% ± 0.18%), (1.73% ± 0.23%) respectively. And there was no significant significance among three groups (P > 0.05). But the size of D-(-)-MTX/A549 was larger than that of L-(+)-MTX/A549. Transwell detected infiltration and invasion through artificial basement membrane Matrigel. The numbers of D-(-)-MTX/A549, L-(+)-MTX/A549 and parent cells were (267 ± 30), (106 ± 16) and (134 ± 16) respectively. The data were significant between D-(-)-MTX/A549 cells and L-(+)-MTX/A549 or parent cells (P < 0.05) but not significant between L-(+)-MTX/A549 and parent cells (P > 0.05). CONCLUSION: The D-(-)-MTX-induced NSCLC A549 cells have greater motor and invasion capacities than those of L-(+)-MTX-induced ones. It suggests that MTX enantiomer has different capacities of tumor invasion and metastasis after acquiring resistance.

[Chiral selectivity in differentiation of lung cancer A549 cell to vascular endothelial cells after drug resistance induced by D-or L-methotrexate enantiomers].

OBJECTIVE: To study the chiral selectivity in vascular endothelial differentiation in drug resistant lung cancer cells induced by high-dose L- or D-methotrexate (MTX) enantiomer. METHODS: Human lung cancer cells of the line A549 were co-cultured with high-dose (15 micromol/L) L- or D-MTX enantiomer so as to develop cancer cells resistant to MTX. MTT method was used to detect the drug resistant index. Flow cytometry was used to detect the expression of CD44, a transmembrane glycoprotein reflecting the migration ability of cells, CD31, a marker of vascular endothelium, and P-170 protein. Fifteen BALB/c nude mice were inoculated with the parent A549 cells, L-MTX-resistant A549 cells induced by L-MTX enantiomer, and D-MTX-resistant A549 cells induced by D-MTX enantiomer. Four weeks later the mice were killed to take out the tumor masses. Immunohistochemistry with CD34 staining was used to detect the microvascular density (MVD). RESULTS: The drug resistant index of the D-MTX induced drug resistant A549 cells was 20.1 +/- 2.3, significantly higher than that of the L-MTX-induced cells (12.4 +/- 1.2, P = 0.000). The CD44 positive rate of the D-MTX induced A549 cells was 97.0% +/- 0.9%, not significantly different from that of the L-MTX-induced A549 cells (96.7% +/- 1.4%, P = 0.544). The CD31 positive rate of the D-MTX induced A549 cells was 91.9% +/- 3.2%, significantly higher than that of the L-MTX-induced A549 cells (32.9% +/- 8.0%, P = 0.000). The P-170 protein positive rate of the parent cells was 85.5% +/- 4.6%, and the P-170 protein positive rate of the D-MTX-induced A549 cells was 87.0% +/- 8.9%, significantly higher than that of the L-MTX-induced cells (71.5% +/- 8.2%, P = 0.002). The MVD of the D-MTX-induced cells was 55.9 +/- 11.9, significantly higher than that of the L-MTX-induced cells (7.2 +/- 1.7, P = 0.000). MVD was significantly positively correlated with the CD31 level (r = 0.462, P = 0.007), and not correlated with P-170 protein and CD34 levels. CONCLUSION: The MTX enantiomers have different chiral selectivity on human lung cancer cell, D-MTX resistant cells shows a potential of differentiation from cancer cells to vascular endothelial cells. D-MTX is not be regarded just as a pollutant in the drug MTX, MTX with single enantiomer (L-MTX) should be selected clinically so as to decrease the side effects of D-MTX.

High-performance capillary electrophoretic method for the quantification of global DNA methylation: application to methotrexate-resistant cells.

Global DNA hypomethylation in tumor tissue is a common characteristic in a variety of malignancies such as breast, colon, oral, lung, and blood cancers. A rapid and sensitive method has been developed for the determination of global DNA methylation in cells. Five substances--2'-deoxycytidine (dC), 5-methyl 2'-deoxycytidine (mdC), 2'-deoxyadenosine (dA), 2'-deoxythymidine (dT), and 2'-deoxyguanosine (dG)--were completely separated by high-performance capillary electrophoresis in 10 min. Intraday coefficient of variation was less than 1%, and interday coefficient of variation was less than 2%. The minimal detection limit was 1 microM. Acquired drug resistance to methotrexate (MTX) is one of the most serious problems in cancer chemotherapy. Under optimal conditions, we analyzed global DNA methylation levels in A549 and A549/MTX cells, and only 10(5) cells are needed to obtain reliable results. The percentage of 5-methyl-2'-deoxycytidine (5-mC) was 4.80+/-0.52% in A549 cells, and this decreased to 4.20+/-0.44% in A549/MTX cells. It was considered as statistically significant. This demonstrated that the mechanisms of acquired drug resistance to MTX might be concerned with DNA methylation.