Graphical modeling of causal factors associated with the postoperative survival of esophageal cancer subjects.

PURPOSE: To clarify the causal relationship between factors contributing to the postoperative survival of patients with esophageal cancer. METHODS: A cohort of 195 patients who underwent surgery for esophageal cancer between 2008 and 2021 was used in the study. All patients had preoperative chest computed tomography (CT) and positron emission tomography-CT (PET-CT) scans prior to receiving any treatment. From these images, high throughput and quantitative radiomic features, tumor features, and various body composition features were automatically extracted. Causal relationships among these image features, patient demographics, and other clinicopathological variables were analyzed and visualized using a novel score-based directed graph called "Grouped Greedy Equivalence Search" (GGES) while taking prior knowledge into consideration. After supplementing and screening the causal variables, the intervention do-calculus adjustment (IDA) scores were calculated to determine the degree of impact of each variable on survival. Based on this IDA score, a GGES prediction formula was generated. Ten-fold cross-validation was used to assess the performance of the models. The prediction results were evaluated using the R-Squared Score (R2 score). RESULTS: The final causal graphical model was formed by two PET-based image variables, ten body composition variables, four pathological variables, four demographic variables, two tumor variables, and one radiological variable (Percentile 10). Intramuscular fat mass was found to have the most impact on overall survival month. Percentile 10 and overall TNM (T: tumor, N: nodes, M: metastasis) stage were identified as direct causes of overall survival (month). The GGES casual model outperformed GES in regression prediction (R2  = 0.251) (p < 0.05) and was able to avoid unreasonable causality that may contradict common sense. CONCLUSION: The GGES causal model can provide a reliable and straightforward representation of the intricate causal relationships among the variables that impact the postoperative survival of patients with esophageal cancer.

A key gene of the small RNA pathway in the flounder, Paralichthys olivaceus: identification and functional characterization of dicer.

Dicer is critical for producing mature microRNAs (miRNAs) from precursor molecules and small interfering RNAs and plays an important role in controlling development and metabolism. In the present study, we cloned the flounder dicer gene, which is 6585 nucleotides (nt), including a 5'-untranslated region (UTR) of 231 nt, a 3'-UTR of 663 nt and an open reading frame of 5691 nt encoding a polypeptide of 1897 amino acids, and analyzed the conservation and expression pattern of dicer. The tissue distribution analysis indicated that dicer is abundantly expressed in the brain, heart, liver, spleen, stomach, kidney, gill, muscle, intestine and gonad of adult fish. Temporal expression analysis indicated that dicer mRNA is highly expressed during the embryonic and early larval stages, and exhibits low expression during the metamorphic stages. Treatment with thyroid hormone (TH) or thiourea indirectly or directly up-regulated dicer mRNA levels at 17 and 23 dph, whereas treatment with TH down-regulated dicer mRNA levels at 36 dph. The dicer-specific siRNA significantly down-regulated dicer mRNA and pol-let-7d levels, while pol-let-7d precursor levels were not differentially changed compared with the control (NC). These results demonstrated that dicer plays a key role in development and metabolism through the production of mature miRNAs, providing basic information for further studies concerning the role of dicer in Paralichthys olivaceus development.

cDNA clone and expression analysis of α-Tropomyosin during Japanese flounder (Paralichthys olivaceus) metamorphosis.

Tropomyosin (TM) plays a critical role in skeletal and cardiac muscle development and function. To assess the functional significance of α-TM in Japanese flounder (Paralichthys olivaceus) development and metamorphosis, cDNA from Japanese flounder was cloned and α-TM mRNA measured during development and metamorphosis. The full-length cDNA is 1 191 bp, including a 5'-untranslated region of 114 bp, a 3'-UTR of 222 bp, and an open reading frame of 855 bp encoding a polypeptide of 284 amino acids. Real-time quantitative PCR revealed that α-TM mRNA is initially expressed in unfertilized ovum, indicating the α-TM gene is maternal. Relatively low mRNA levels were observed in different embryonic stages. A higher level of α-TM mRNA was detected 3 days post hatching (dph), while the highest level was measured at 29 dph (metamorphic climax) after which it declined towards the end of metamorphosis. The expression of α-TM mRNA was up-regulated in thyroid hormone-treated larvae at 36 dph, but there was no marked difference at other stages when compared to control animals. After thiourea treatment, the expression of α-TM mRNA declined slightly. These data provide basic information that can be utilized in further studies into the role of α-TM in P. olivaceus development and metamorphosis.

Identification and expression analysis of IGFBP-1 gene from Japanese flounder (Paralichthys olivaceus).

Insulin-like growth factor binding protein-1 (IGFBP-1) plays an important role in IGF regulating vertebrate growth and development. In this study, we cloned IGFBP-1 cDNA from Japanese flounder (Paralichthys olivaceus) liver. The full-length cDNA is 1070 bp, including a 5'-untranslated region (UTR) of 69 bp, a 3'-UTR of 272 bp, and an open reading frame (ORF) of 729 bp encoding a polypeptide of 242 amino acids. Real-time quantitative PCR revealed that IGFBP-1 mRNA is mainly expressed in the liver, and a small amount of mRNAs was also found in other adult tissues. There are maternal transcripts of IGFBP-1 gene, and relatively low mRNA levels were observed in different embryonic stages. A higher level of IGFBP-1 mRNA was detected at 3 days post hatching (dph), and it got to the highest level at 29 dph (metamorphic climax), and finally brought back to a lower level at the end of metamorphosis. The expression of IGFBP-1 mRNA was greatly up-regulated in thyroid hormone (TH)-treated larvae, and declined after thiourea (TU) treatment. These results provide basic information for further studies on the role of IGF system in the P. olivaceus development and metamorphosis.

[Prokaryotic expression and polyclonal antibody preparation of TRalphaA in Japanese flounder Paralichthys olivaceus].

To study the role of the thyroid hormone receptor TRalphaA involved in the process of the metamorphic development of Japanese flounder, we firstly cloned the TRalphaA gene, then ligated into the fusion expression vector pET30a and expressed in Escherichia coli DE3 (BL21) host cells. After induced for 4 h with 1 mmol/L Isopropyl beta-D-Thiogalactoside, the target fusion protein was successfully expressed and identified in inclusion bodies by SDS-PAGE and Western blotting. The recombinant protein was denatured and purified by His-Bind resin, then renatured through gradient washing on His-bind resin column. After that, polyclonal antibody was prepared by immunizing New Zealand rabbits with purified protein. Dot blotting analysis showed the antibody with the titer of 1:200 000 reacted specifically to the expressed recombinant protein. Furthermore, a chromatin immunoprecipitation assay was performed to identify the specific binding between the antibody and TRalphaA in living cells of Japanese flounder. The result showed that thyroid hormone was involved in the alkaline phosphatase (ALP) gene transcriptional regulation through TRalphaA in vivo.

Sequence Analysis of the Full-length cDNA and Protein Structure Homology Modeling of FABP2 from Paralichthys Olivaceus.

Using zebrafish intestinal fatty acid-binding protein 2 (FABP2) mRNA sequence as the initial query probe, four highly homologous Paralichthys olivaceus EST sequences were retrieved from Genbank database. The assembled full-length cDNA contains the open reading frame of P. olivaceus FABP2 gene, which was validated by subsequent RT-PCR cloning. In the coding region, the average GC content is 56%, but it would reach 76.8% if only counting for the third base of the codons. The deduced P. olivaceus FABP2 polypeptide contains 132 amino acids (aa), with a predicted molecular size of 15.3 kD and pI at 6.74. This protein multiple-alignment has shown that this peptide is 75.7% identical to the corresponding homologous protein in Danio rerio. Among the 7 aa that are essential for FABP2 function, 3 were found to be conserved among P. olivaceus, Danio rerio, Tetraodon nigroviridi, Rattus norvegicus, and Homo sapiens. The study provides essential information on molecular evolution and function of FABP family.