Integrated Transcriptome and Metabolome Analyses Reveal Bamboo Culm Color Formation Mechanisms Involved in Anthocyanin Biosynthetic in Phyllostachys nigra

Phyllostachys nigra has green young culms (S1) and purple black mature culms (S4). Anthocyanins are the principal pigment responsible for color presentation in ornamental plants. We employ a multi-omics approach to investigate the regulatory mechanisms of anthocyanins in Ph. nigra. Firstly, we found that the pigments of the culm of Ph. nigra accumulated only in one to four layers of cells below the epidermis. The levels of total anthocyanins and total flavonoids gradually increased during the process of bamboo culm color formation. Metabolomics analysis indicated that the predominant pigment metabolites observed were petunidin 3-O-glucoside and malvidin O-hexoside, exhibiting a significant increase of up to 9.36-fold and 13.23-fold, respectively, during pigmentation of Ph. nigra culm. Transcriptomics sequencing has revealed that genes involved in flavonoid biosynthesis, phenylpropanoid biosynthesis, and starch and sucrose metabolism pathways were significantly enriched, leading to color formation. A total of 62 differentially expressed structural genes associated with anthocyanin synthesis were identified. Notably, PnANS2, PnUFGT2, PnCHI2, and PnCHS1 showed significant correlations with anthocyanin metabolites. Additionally, certain transcription factors such as PnMYB6 and PnMYB1 showed significant positive or negative correlations with anthocyanins. With the accumulation of sucrose, the expression of PnMYB6 is enhanced, which in turn triggers the expression of anthocyanin biosynthesis genes. Based on these findings, we propose that these key genes primarily regulate the anthocyanin synthesis pathway in the culm and contribute to the accumulation of anthocyanin, ultimately resulting in the purple-black coloration of Ph. nigra.

LOXL1-AS1 Drives the Progression of Gastric Cancer via Regulating miR-142-5p/PIK3CA Axis [Retraction]

[This retracts the article DOI: 10.2147/OTT.S223702.].

Network of miR396-mRNA in Tissue Differentiation in Moso Bamboo (Phyllostachys edulis)

MiR396 plays an essential role in various developmental processes. However, the miR396-mRNA molecular network in bamboo vascular tissue differentiation during primary thickening has not been elucidated. Here, we revealed that three of the five members from the miR396 family were overexpressed in the underground thickening shoots collected from Moso bamboo. Furthermore, the predicted target genes were up/down-regulated in the early (S2), middle (S3) and late (S4) developmental samples. Mechanistically, we found that several of the genes encoding protein kinases (PKs), growth-regulating factors (GRF), transcription factors (TFs), and transcription regulators (TRs) were the potential targets of miR396 members. Moreover, we identified QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys) d omains in five PeGRF homologs and a Lipase_3 domain and a K_trans domain in another two potential targets, where the cleavage targets were identified via degradome sequencing (p < 0.05). The sequence alignment indicated many mutations in the precursor sequence of miR396d between Moso bamboo and rice. Our dual-luciferase assay revealed that ped-miR396d-5p binds to a PeGRF6 homolog. Thus, the miR396-GRF module was associated with Moso bamboo shoot development. Fluorescence in situ hybridization localized miR396 in the vascular tissues of the leaves, stems, and roots of pot Moso bamboo seedlings at the age of two months. Collectively, these experiments revealed that miR396 functions as a regulator of vascular tissue differentiation in Moso bamboo. Additionally, we propose that miR396 members are targets for bamboo improvement and breeding.

Paeonol inhibits the malignancy of Apatinib-resistant gastric cancer cells via LINC00665/miR-665/MAPK1 axis

BACKGROUND

Paeonol is the extractive of Paeonia suffruticosa Andr and is reported to reverse the chemotherapy resistance of cancer cells. The present study explores the role of paeonol in inhibiting the malignant biological behaviors of Apatinib-resistant gastric cancer (GC) cells.

METHODS

The Traditional Chinese Medicine Systems Pharmacology (TCMSP) database was adopted to screen the target genes of paeonol, and the STRING database was employed to construct a protein-protein interaction (PPI) network. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the target genes was performed employing DAVID online database. The expressions of these target genes in GC tissues and para-cancerous tissues were analyzed with GEPIA database, and GEO datasets (GSE109476 and GSE93415) were utilized to analyze differentially expressed lncRNAs and miRNAs in GC tissues and para-cancerous tissues. The expressions of LINC00665, miR-665 and MAPK1 mRNA in Apatinib-resistant GC cells were detected through quantitative real-time polymerase chain reaction (qRT-PCR). Cell counting kit-8 (CCK-8) assay was conducted to detect cell proliferation; Transwell assays were employed to detect cell migration and invasion, and TdT-mediated dUTP nick end labeling (TUNEL) assay was utilized to detect cell apoptosis. Dual-luciferase reporter gene assay was performed to detect the binding relationships between miR-665 and LINC00665, as well as between miR-665 and MAPK1 mRNA. The expressions of MAPK1 protein and glycolysis-associated proteins (GLUT1, LDHB and HK2) were detected by Western blot. Additionally, a tumor xenograft mice model was constructed to evaluate the effects of paeonol on lung metastasis.

RESULTS

Paeonol could inhibit the proliferation, migration, invasion and glycolysis, and promote the apoptosis of Apatinib-resistant GC cells. TCMSP database suggested that Paeonol had 17 target genes, and 17 target genes were mainly enriched in signaling pathways related to apoptosis, glucose and lipid metabolism, etc.; GEPIA database suggests that MAPK1, among the 17 target genes, was markedly elevated in GC tissues. Paeonol could decrease LINC00665 and MAPK1 expressions in GC cells but increase the expression of miR-665. LINC00665 overexpression, MAPK1 overexpression or inhibition of miR-665 could abolish the inhibitive effects of paeonol on the malignant phenotypes of Apatinib-resistant GC cells. miR-665 is verified as an upstream regulator of MAPK1 and a target of LINC00665. Additionally, paeonol could significantly inhibit the lung metastasis in the tumor xenograft mice model.

CONCLUSIONS

Paeonol can inhibit the malignancy of Apatinib-resistant GC cells through LINC00665/miR-665/MAPK1 axis. For the first time, our study imply that paeonol may be a potential drug to reverse Apatinib-resistant of GC cells.

LOXL1-AS1 Drives The Progression Of Gastric Cancer Via Regulating miR-142-5p/PIK3CA Axis

Background

Gastric cancer (GC) is a deadly disease, and its incidence is especially high in East Asia including China. Recently, some long non-coding RNA (lncRNAs) have been identified as oncogenes or tumor suppressors. This study aimed to determine the function and mechanism of lncRNA LOXL1-AS1 on the progression of GC.

Methods

RT-PCR was done to measure the expression levels of LOXL1-AS1 and miR-142-5p in GC tissues. The association between pathological indexes and LOXL1-AS1 expression was also analyzed. Human GC cell lines AGS and BGC823 were used as cell models. CCK-8 and colony formation assays were conducted to assess the effect of LOXL1-AS1 on the proliferation of GC cell lines. Transwell assay was conducted to determine the influence of LOXL1-AS1 on cell migration and invasion. Furthermore, luciferase reporter assay was carried out to confirm the relationship of miR-142-5p with LOXL1-AS1. Additionally, Western blot was done to detect the regulatory function of LOXL1-AS1 on PIK3CA, a target of miR-142-5p. In vivo experiment was also performed to validate the roles and mechanism of LOXL1-AS1 on the growth and metastasis of GC cells.

Results

LOXL1-AS1 expression in GC samples was significantly increased, which was correlated with unfavorable pathological indexes. Highly expressed LOXL1-AS1 was closely linked to shorter overall survival time and post-progression survival time of the patients. LOXL1-AS1 markedly modulated the malignant phenotypes of GC cells. Additionally, overexpressed LOXL1-AS1 notably reduced the expression of miR-142-5p, but enhanced the expression level of PIK3CA. In vivo experiments further validated that knockdown of LOXL1-AS1 inhibited the growth and metastasis of GC cells via regulating miR-142-5p and PIK3CA.

Conclusion

LOXL1-AS1 was a sponge of tumor suppressor miR-142-5p in GC, enhanced the expression of PIK3CA indirectly and functioned as an oncogenic lncRNA.