Identification of prognostic immune-related signature predicting the overall survival for colorectal cancer

OBJECTIVE

The morbidity and mortality of patients with colorectal cancer, one of the most common malignant tumors worldwide, is steadily increasing. The aim of this study was to investigate the association between prognostic immune-related gene profile and the outcome of colorectal cancer in patients by analyzing datasets from The Cancer Genome Atlas (TCGA).

MATERIALS AND METHODS

Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) further demonstrated that these genes were enriched in many immune-related biological processes. Univariate Cox regression analysis was applied to examine the association of immune-related genes with the prognosis in patients with colorectal cancer. The least absolute shrinkage and selection operation (LASSO) Cox regression model was then used to establish the immune-related signature for the prognostic evaluation of colorectal cancer in patients. Survival differences were assessed by the Kaplan-Meier method along with the log-rank test.

RESULTS

A total of 133 prognostic immune-related signatures were identified by using the univariate Cox proportional hazards regression analysis. A 14-gene signature-based risk score was constructed using the LASSO Cox regression. According to the cut-off of the risk-score, patients were assigned to the low-risk and high-risk groups. The log-rank test suggested that the survival time of the low-risk group was significantly higher than that of the high-risk group. In the time-dependent ROC curve analysis, the AUC for 1-year, 3-year, and 5-year overall survival (OS) were 0.781, 0.742, and 0.791, respectively. GO and KEGG analysis further revealed that the gene sets were actively involved in immune and inflammatory response, as well as the cytokine-cytokine receptor interaction pathway.

CONCLUSIONS

To summarize, we identified a novel 14-gene immune-related signature that may potentially serve as a prognostic predictor for colorectal cancer, thereby contributing to patient personalized treatment decisions. Further research needs to be conducted to validate the prognostic value of the selected genes.

Synthesis and degradation of a 28-kDa pod storage protein in french bean (Phaseolus vulgaris) plants

Pod storage protein (PSP) accumulated in developing pods of French bean (Phaseolus vulgaris L.) plants, and increasing the PSP mRNA level by pod removal resulted in the enhancement of PSP accumulation in pods that formed later. Pod storage protein was detected in flowers, young leaves and young stem internodes in addition to pods. Accumulation of PSP and its mRNA was induced by sink-removal in an organ-specific manner. In addition, wounding induced PSP accumulation systemically in leaves. Methyl jasmonate did not induce PSP synthesis but enhanced the synthesis that was induced by wounding. In senescing pods, PSP was degraded, and degradation products with molecular masses of 20 and 17 kDa were detected in the pods. The amount of 20-kDa degradation product was greater than that of the 17 kDa product.

A 28-kilodalton pod storage protein of French bean plants. Purification, characterization, and primary structure

When French bean (Phaseolus vulgaris) plants were depodded in the early stages of fruit development, relative levels of a specific protein with a relative molecular weight of 28,000 were enhanced in the young pods that formed later. The protein, designated pod storage protein (PSP), was purified from extracts of newly formed pods from plants that had been previously depodded four times at intervals of 2 weeks. Two-dimensional polyacrylamide gel electrophoresis showed the presence of three forms (designated A, B, and C) of PSP with identical electrophoretic mobilities but different charges. The molecular mass of native PSP was estimated by gel filtration to be 67 kD; therefore, the protein was most likely present as a dimer. The antisera raised against forms A and C were crossreactive with each other. Form B lacked the N-terminal alanine of forms A and C. An expression library from French bean pods was screened using the antiserum against form A, and a full-length cDNA clone was isolated. The cDNA insert included 765 bp potentially encoding a polypeptide with 255 amino acid residues (and a calculated molecular mass of 28,854 D). The amino acid sequence deduced from the PSP cDNA had 65 to 71% identity with soybean (Glycine max) vegetative storage protein sequences (P.E. Staswick [1988] Plant Physiol 87: 250-254; and Correction [1989] Plant Physiol 89: 717). Genomic Southern blot analysis suggested that PSP is derived from a single-copy gene.

Cofractionation of the 17-kD PK 14105 binding site protein with solubilized peripheral-type benzodiazepine binding sites

To examine the relationship between PKBS, a 17-kD protein covalently photolabeled by [3H]PK 14105, and its association with peripheral-type benzodiazepine binding sites, rat adrenal mitochondrial fractions were photolabeled with [3H]PK 14105, solubilized in digitonin, and subjected to anion-exchange chromatography over Q-Sepharose. The chromatographic behavior of PKBS was evident as principally two major fractions, signified as Q-I and Q-II. Specific binding sites for [3H]Ro5-4864 and [3H]PK 11195 were also assayed and found to cofractionate with each other and in a manner which coincided with the photolabeled PKBS profile. The Q-I and Q-II fractions were further distinguished based on their different molecular sizes observed by gel filtration, yet both fractions were characterized as containing peripheral-type benzodiazepine recognition sites according to the following criteria. Scatchard analysis of both subpopulations revealed a single class of binding sites for [3H]Ro5-4864 with an apparent KD of 14 nM for Q-I and 22 nM for Q-II; these affinities were slightly lower than those found in mitochondrial membrane preparations used as the starting material for solubilization. The rank order of potency to inhibit [3H]Ro5-4864 binding in both subpopulations was PK 11195 greater than Ro5-4864 greater than diazepam greater than clonazepam, in connection with the pharmacological specificity of membrane-associated peripheral-type benzodiazepine binding sites. These studies provide direct biochemical evidence that the recognition sites for benzodiazepines and isoquinoline carboxamides cofractionate in unison with the 17-kD PKBS protein, demonstrating an intimate relationship between this protein and the binding domains for peripheral-type benzodiazepine ligands.