Integrating Multi-Omics Analysis Reveals the Regulatory Mechanisms of White-Violet Mutant Flowers in Grape Hyacinth (Muscari latifolium).

Grape hyacinth (Muscari spp.) is a famous bulbous blue flower; however, few bicolor varieties are available in the market. Therefore, the discovery of bicolor varieties and understanding of their mechanisms are crucial to the breeding of new varieties. In this study, we report a significant bicolor mutant with white upper and violet lower portions, with both parts belonging to a single raceme. Ionomics showed that pH and metal element contents were not responsible for the bicolor formation. Targeted metabolomics illustrated that the content of the 24 color-related compounds was significantly lower in the upper part than that in the lower part. Moreover, full-length transcriptomics combined with second-generation transcriptomics revealed 12,237 differentially expressed genes in which anthocyanin synthesis gene expression of the upper part was noted to be significantly lower than that of the lower part. Transcription factor differential expression analysis was used to describe the presence of a pair of MaMYB113a/b sequences, with low levels of expression in the upper part and high expression in the lower part. Furthermore, tobacco transformation confirmed that overexpression of MaMYB113a/b can promote anthocyanin accumulation in tobacco leaves. Accordingly, the differential expression of MaMYB113a/b contributes the formation of a bicolor mutant in Muscari latifolium.

The Prognostic Significance and Gene Expression Characteristics of Gastric Signet-Ring Cell Carcinoma: A Study Based on the SEER and TCGA Databases.

Purpose: This study is based on the Surveillance, Epidemiology, and End Results (SEER) program to explore the prognostic differences between signet-ring cell carcinoma (SRC) and intestinal-type gastric carcinoma (ITGC). This study is also based on gene sequencing data from The Cancer Genome Atlas (TCGA) to identify unique genetic contributions to the prognostic differences between the two subtypes of gastric cancer. Patients and Methods: The clinical data were based on the SEER database from 2004 to 2015. Kaplan-Meier (KM) curves were used to compare 5-year overall survival (OS), and Cox regression was used for univariate and multivariate analyses. Gene expression profiles were obtained from TCGA database, and differentially expressed genes (DEGs) were screened. Functional enrichment analysis, protein interaction and survival analysis will be further carried out. Genes of interest were verified by the Human Protein Atlas, immunohistochemistry, and encyclopedia of Cancer Cell Lines (CCLE). The relationship between genes of interest and immune cell infiltration was also analyzed by Tumor Immune Estimation Resource (TIMER). Results: Compared with ITGC patients, SRC patients were more likely to be female, tended to be younger, and have a greater tumor distribution in the middle and lower stomach (p < 0.01). SRCs showed a significantly better prognosis than ITGCs (p < 0.01) in early gastric cancer (EGC), while the prognosis of SRCs was significantly worse than ITGCs (p < 0.05) in advanced gastric cancer (AGC). A total of 256 DEGs were screened in SRCs compared to ITGCs, and the enrichment analysis and protein interactions revealed that differential genes were mainly related to extracellular matrix organization. Thrombospondin1 (THBS1) and serpin peptidase inhibitor, clade E, member 1 (SERPINE1) are significantly differentially expressed between SRC and ITGC, which has been preliminarily verified by immunohistochemistry and open-source databases. THBS1 and SERPINE1 are also associated with multiple immune cell infiltrates in gastric cancer. Conclusions: There were significant differences in the clinicopathological features and prognosis between SRC and ITGC. These results suggest that SRC and ITGC may be two distinct types of tumors with different pathogeneses. We found many codifferentially expressed genes and important pathways between SRC and ITGC. THBS1 and SERPINE1 were significantly differentially expressed in the two types of gastric cancer, and may have potentially important functions.

Long non-coding RNA profile study identifies a metabolism-related signature for colorectal cancer.

BACKGROUND: Heterogeneity in colorectal cancer (CRC) patients provides novel strategies in clinical decision-making. Identifying distinctive subgroups in patients can improve the screening of CRC and reduce the cost of tests. Metabolism-related long non-coding RNA (lncRNA) can help detection of tumorigenesis and development for CRC patients. METHODS: RNA sequencing and clinical data of CRC patients which extracted and integrated from public databases including The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were set as training cohort and validation cohort. Metabolism-related genes were acquired from Kyoto Encyclopedia of Genes and Genomes (KEGG) and the metabolism-related lncRNAs were filtered using correlation analysis. The risk score was calculated based on lncRNAs with prognostic value and verified through survival curve, receiver operating characteristic (ROC) curve and risk curve. Prognostic factors of CRC patients were also analyzed. Nomogram was constructed based on the results of cox regression analyses. The different immune status was observed in the single sample Gene Set Enrichment Analysis (ssGSEA). RESULTS: The training cohort and the validation cohort enrolled 432 and 547 CRC patients respectively. A total of 23 metabolism-related lncRNAs with prognostic value were screened out and 10 of which were significantly differentially expressed between tumour and normal tissues. Finally, 8 lncRNAs were used to establish a risk score (DICER1-AS1, PCAT6, GAS5, PRR7-AS1, MCM3AP-AS1, GAS6-AS1, LINC01082 and ADIRF-AS1). Patients were divided into high-risk and low-risk groups according to the median of risk scores in training cohort and the survival curves indicated that the survival prognosis was significantly different. The area under curve (AUC) of the ROC curve in two cohorts were both greater than 0.6. The age, tumour stage and risk score were selected as independent factors and used to construct a nomogram to predict CRC patients' survival rate with the c-index of 0.806. The ssGSEA indicated that the risk score was associated with immune cells and functions. CONCLUSIONS: Our systematic study established a metabolism-related lncRNA signature to predict outcomes of CRC patients which may contribute to individual prevention and treatment.

Role of osteopontin in diet-induced brown gallstone formation in rats.

BACKGROUND: Although osteopontin (OPN) is expressed in the liver and pigment gallstones of patients with hepatolithiasis, its role in pigment gallstone formation remains unclear. This study aimed to explore the function of OPN in pigment gallstone formation. METHODS: Rats were fed a chow diet (CD) or lithogenic diet (LD) for 10 consecutive weeks; blocking tests were then performed using an OPN antibody (OPN-Ab). Incidence of gallstones and levels of several bile components, OPN, tumor necrosis factor alpha (TNF-α), and cholesterol 7 alpha-hydroxylase (CYP7A1) were analyzed. To determine TNF-α expression in hepatic macrophages and both CYP7A1 and bile acid (BA) expression in liver cells, recombinant rat OPN and recombinant rat TNF-α were used to treat rat hepatic macrophages and rat liver cells, respectively. Chi-square or Fisher exact tests were used to analyze qualitative data, Student t-test or one-way analysis of variance were used to analyze qualitative data. RESULTS: Incidence of gallstones was higher in LD-fed rats than in CD-fed rats (80% vs. 10%, P < 0.05). BA content significantly decreased in bile (t = -36.08, P < 0.01) and liver tissue (t = -16.16, P < 0.01) of LD-fed rats. Both hepatic OPN protein expression (t = 9.78, P < 0.01) and TNF-α level (t = 8.83, P < 0.01) distinctly increased in the LD group; what's more, CYP7A1 mRNA and protein levels (t = -12.35, P < 0.01) were markedly down-regulated in the LD group. Following OPN-Ab pretreatment, gallstone formation decreased (85% vs. 25%, χ2 = 14.55, P < 0.01), liver TNF-α expression (F = 20.36, P < 0.01) was down-regulated in the LD group, and CYP7A1 expression (F = 17.51, P < 0.01) was up-regulated. Through CD44 and integrin receptors, OPN promoted TNF-α production in macrophage (F = 1041, P < 0.01), which suppressed CYP7A1 expression (F = 48.08, P < 0.01) and reduced liver BA synthesis (F = 119.4, P < 0.01). CONCLUSIONS: We provide novel evidence of OPN involvement in pigmented gallstone pathogenesis in rats.

Preoperative Fibrinogen-Albumin Ratio Index (FARI) is a Reliable Prognosis and Chemoradiotherapy Sensitivity Predictor in Locally Advanced Rectal Cancer Patients Undergoing Radical Surgery Following Neoadjuvant Chemoradiotherapy.

BACKGROUND: Inflammatory response and nutritional status are associated with cancer development and progression. The purpose of this study was to explore whether the preoperative fibrinogen-albumin ratio index (FARI) is related to prognosis and chemoradiotherapy outcome of radical surgery after neoadjuvant chemoradiotherapy (NCRT) in patients with locally advanced rectal cancer (LARC). METHODS: In total, 123 patients with LARC who underwent radical surgery after NCRT between June 2012 and December 2018 were collected in this study. Time-dependent receiver operating characteristic (ROC) curve analysis was made to evaluate the ability of the markers for forecasting prognosis. The correlation between FARI and clinicopathological parameters was analyzed. The Kaplan-Meier survival analysis, univariate and multivariate analysis based on Cox proportional hazards models, and subgroup analysis were performed to evaluate overall survival (OS) and disease-free survival (DFS). A nomogram was constructed to evaluate the predictive role of FARI in DFS. RESULTS: The ROC curve analysis showed that the ability of FARI on DFS prediction was superior to those of other inflammatory markers and carcinoembryonic antigen (CEA) (P<0.05). Based on the Youden's index, the optimal cut-off value of FARI was 8.8%. High FARI patients (>8.8%) showed a poor response to NCRT and a decreased DFS rate (P<0.05). In addition, multivariate analysis revealed that FARI (HR=3.098, P=0.033), neutrophil-to-lymphocyte ratio (NLR), and postoperative T stage were independent prognostic factors for DFS in TNM stage III LARC patients. However, FARI failed to distinguish patients with poor OS. Harrell's concordance index (C-index) of the nomogram containing FARI (0.807) was obviously higher than that without it (0.732) among LARC patients who underwent radical surgery after NCRT. Moreover, multivariate analysis revealed FARI (OR=3.044, P=0.012) as an independent predictor for response to NCRT. CONCLUSION: Among LARC patients who underwent radical surgery after NCRT, preoperative FARI is an independent prognostic factor for DFS and an independent predictor for response to NCRT.

Loss of survival advantage for deficient mismatch repair in patients with advanced colorectal cancer may be caused by changes in prognostic value of CD8+T cell.

BACKGROUND: Patients with stage II deficient mismatch repair (dMMR) show a better prognosis than patients with colorectal cancer (CRC) with proficient mismatch repair (pMMR). However, this beneficial effect is decreased in advanced stages of the disease. This study was conducted to investigate the prognostic value of dMMR in different stage and alterations in the tumor microenvironment. METHODS: This was a matched retrospective cohort study. Thirty-two patients with stage III&IV dMMR matched with 32 patients with stage I&II dMMR and 64 patients with pMMR were evaluated. Immunohistochemistry analysis was performed for the 64 patients with dMMR to explore the expression and prognostic effect of CD3, CD4, CD8, and PD-L1. RESULTS: Patients with stage III-IV dMMR showed no advantage in overall survival (OS) and disease-free survival (DFS) compared to patients with pMMR (P = 0.244, P = 0.667). No expression differences in CD3, CD4, CD8, and PD-L1 at the center of the tumor (CT) or invasive margin (IM) were found between patients with stage I&II and stage III&IV dMMR. High CD3 expression at the CT and high CD3 an CD4 expression at the IM improved both OS and DFS. High CD8 expression showed opposite prognostic value in patients with stage I&II and III&IV dMMR. A similar tendency was observed for PD-L1 expression. CONCLUSION: Patients with stage III-IV dMMR showed no prognostic advantage over patients with pMMR. Expression of CD3, CD4, CD8, and PD-L1 was similar between stage I&II and III&IV dMMR CRC. High CD3 expression at the CT and high CD3 and CD4 expression at the IM can significantly improve patient prognosis. The opposite prognostic tendency of CD8 and PD-L1 for patients with stage I&II and III&IV dMMR may be relevant to CD8+T cell exhaustion and functional changes at inhibitory immune checkpoints.

Comparison of Clinical Outcomes and Pathological Characteristics of Self-Expandable Stent Bridge to Surgery and Emergency Surgery in Obstructive Colon Cancer.

AIM: Obstructive colon cancer can be treated by self-expanding metal stents (SEMS) prior to definitive surgery. However, the oncological outcome remains controversial, especially regarding whether stent placement or obstruction results in more perineural invasion (PNI) or lymphovascular invasion (LVI). This study aimed to compare clinical outcomes of emergency surgery (ES) and stent as bridge to surgery (SBTS) in patients with obstructive colon cancer. The pathological characteristics were also compared between obstructive and nonobstructive cancer. METHODS: This study included 880 patients (including 47 ES and 45 SBTS) admitted to Peking University Third Hospital from January 2010 to December 2018. Short-term and long-term outcomes were compared. The pathological differences between an equal number of obstructive and nonobstructive patients matched using propensity scores were investigated. RESULTS: SBTS patients had less intraoperative blood loss (P < 0.001), shorter ICU stay time (P = 0.007), lower incidence of colostomy (P < 0.001), and higher laparoscopic achievement (P < 0.001) than did ES patients. No pathological difference was found between the two groups. SBTS patients showed better overall survival (86.7% vs 68.1%, P = 0.029), but not disease-free survival (68.9% vs 59.6%, P = 0.211) than did ES patients. PNI was significantly higher in obstructive cancer than in nonobstructive cancer (29.3% vs 16.3%, P = 0.035). CONCLUSION: SBTS had a lower incidence of short-term complications and did not affect long-term prognosis compared with that of ES, indicating that SBTS is a safe and effective treatment. Further, PNI may be associated with obstruction, but not with stent insertion.

Cloning and Functional Characterization of Dihydroflavonol 4-Reductase Gene Involved in Anthocyanidin Biosynthesis of Grape Hyacinth.

Grape hyacinth (Muscari spp.) is a popular ornamental plant with bulbous flowers noted for their rich blue color. Muscari species have been thought to accumulate delphinidin and cyanidin rather than pelargonidin-type anthocyanins because their dihydroflavonol 4-reductase (DFR) does not efficiently reduce dihydrokaempferol. In our study, we clone a novel DFR gene from blue flowers of Muscari. aucheri. Quantitative real-time PCR (qRT-PCR) and anthocyanin analysis showed that the expression pattern of MaDFR had strong correlations with the accumulation of delphinidin, relatively weak correlations with cyanidin, and no correations with pelargonidin. However, in vitro enzymatic analysis revealed that the MaDFR enzyme can reduce all the three types of dihydroflavonols (dihydrokaempferol, dihydroquercetin, and dihydromyricetin), although it most preferred dihydromyricetin as a substrate to produce leucodelphinidin, the precursor of blue-hued delphinidin. This indicated that there may be other functional genes responsible for the loss of red pelargonidin-based pigments in Muscari. To further verify the substrate-specific selection domains of MaDFR, an assay of amino acid substitutions was conducted. The activity of MaDFR was not affected whenever the N135 or E146 site was mutated. However, when both of them were mutated, the catalytic activity of MaDFR was lost completely. The results suggest that both the N135 and E146 sites are essential for the activity of MaDFR. Additionally, the heterologous expression of MaDFR in tobacco (Nicotiana tabacum) resulted in increasing anthocyanin accumulation, leading to a darker flower color, which suggested that MaDFR was involved in color development in flowers. In summary, MaDFR has a high preference for dihydromyricetin, and it could be a powerful candidate gene for genetic engineering for blue flower colour modification. Our results also make a valuable contribution to understanding the basis of color variation in the genus Muscari.