Background: Hypoxia signaling plays a critical role in the development of lung adenocarcinoma (LUAD). We herein aimed to explore the prognostic value of hypoxia-related genes and construct the hypoxia-related prognostic signature for LUAD patients. Methods: A total of 26 hypoxia-related genes were collected. Five hundred thirteen and 246 LUAD samples were obtained from the Cancer Genome Atlas and Gene Expression Omnibus databases, respectively. Univariate Cox regression and LASSO Cox regression analyses were conducted to screen the hypoxia-related genes associated with the prognosis of LUAD patients, which would be used for constructing prognosis predictive model for LUAD patients. Multivariate Cox regression analysis was done to determine the independent prognostic factors. The Nomogram model was constructed to predict the prognosis of LUAD patients. Results: Based on 26 hypoxia-related genes, LUAD samples could be divided into 4 clusters with different prognoses. Among which, 6 genes were included to construct the Risk Score and the LUAD patients with higher Risk Score had worse prognosis. Besides, the Nomogram based on all the independent risk factors could relatively reliably predict the survival probability. And 9 types of immune cells’ infiltration was significantly differential between high and low risk LUAD patients. Conclusion: The Risk Score model based on the 6 crucial hypoxia-related genes could relatively reliably predict the prognosis of LUAD patients.

Background/Objectives: The oil grape (Idesia polycarpa), often called the “golden tree”, is an essential woody plant valued for its edible oil. Although its economic significance is recognized, the specifics of its chloroplast genome and evolutionary connections remain unclear. This study sequenced the chloroplast genome of I. polycarpa and performed a comparative analysis of its genome structure, genetic diversity, and phylogenetics using chloroplast data from related species. Methods: In this study, we sequenced and annotated the whole chloroplast genome of I. polycarpa via GISEQ-500 sequencing and de novo assembly. Results: The chloroplast genome of I. polycarpa exhibits a typical tetrad structure, with a length of 155,899 bp and a GC content of 36.78%. It comprises 130 unique genes, including 85 coding genes, 37 tRNAs, and eight rRNAs, showing notable conservation in gene composition and arrangement compared to closely related species. However, the inverted repeat region boundaries are narrower. Phylogenetic analysis showed strong relationships among I. polycarpa, Bennettiodendron brevipes, Poliothyrsis sinensis, Itoa orientalis, and Carrierea calycina within the Salicaceae family. Additionally, positive selection analysis revealed that rpl16, ycf1, rps18, and rpl22 are under significant selective pressure in related species, likely linked to adaptations for photosynthesis and environmental responses. Conclusions: This research provides vital molecular foundations for the conservation, classification, and enhancement of I. polycarpa germplasm resources, advancing the study of adaptive evolutionary mechanisms and broadening the genomic database for I. polycarpa.

Colorectal cancer (CRC) is the third leading cancer type worldwide and accounts for the second highest rate of cancer-related mortality. Liver metastasis significantly contributes to the mortality associated with CRC, but the fundamental mechanisms behind it remain unclear. Signal-induced proliferation-associated protein 1 (SIPA1), a GTPase activating protein, has been shown to promote metastasis in breast cancer. In this study, our objective was to explore the role of SIPA1 in regulating epithelial-mesenchymal transition (EMT) in CRC. The analysis of The Cancer Genome Atlas (TCGA) database revealed that the expression level of SIPA1 mRNA was notably upregulated and exhibited a positively correlated with EMT and STAT3 signaling pathways in CRC. Knockdown of SIPA1 impairs CRC cell proliferation and migration. Further studies on the reliance of SIPA1 on STAT3 signaling for EMT regulation have shown that SIPA1 stimulates the activation of STAT3, resulting in its nuclear translocation. The co-treatment of overexpressed SIPA1 with the STAT3 inhibitor STTITA has shown that SIPA1 regulates the expression of EMT-related markers through STAT3. Our study indicate that SIPA1 promotes CRC metastasis by activating the STAT3 signaling pathway, underscoring the potential of SIPA1 as a therapeutic target for metastatic CRC patients.

Asparagus cochinchinensis (Lour.) Merr. (Chinese asparagus) is a trailing plant used in Chinese traditional medicine with major bioactive compounds concentrated in the rhizome. Rhizome rot, a major disease of A. cochinchinensis, affects plants during propagation, after harvest, and during storage. High-throughput sequencing and culture techniques were used to identify causal pathogenic fungi. Sequences of amplicons obtained from symptomatic and asymptomatic rhizomes revealed that the richness and diversity index of the endophytic fungal community was significantly greater in asymptomatic rhizomes than in symptomatic rhizomes (p < 0.05), indicating that the fungal community undergoes a compositional shift during the development of rhizome decay. A total of 32 and 51 fungal isolates were identified in asymptomatic and symptomatic rhizomes, respectively. Among them, Aspergillus niger, A. flavus, Penicillium venetum, P. crustosum, Fusarium equiseti, F. oxysporum, Irpex lacteus and Chaetomium globosum were common to both asymptomatic and symptomatic rhizomes. Neodeightonia subglobosa, Neurospora tetrasperma, Trichoderma harzianum, Talaromyces pinophilus, and A. terreus were only detected in symptomatic rhizomes. Importantly, T. pinophilus, T. harzianum, A. terreus, N. tetrasperma, and I. lacteus isolated from symptomatic rhizomes were non-pathogenic, while the remaining eight species, A. niger, A. flavus, P. venetum, P. crustosum, F. equiseti, F. oxysporum, N. subglobosa, and C. globosum, were capable of inducing prominent symptoms of rhizome soft rot in Asparagus cochinchinensis. Co-inoculation with any two of the three species—A. niger, F. equiseti, and P. venetum—significantly increased soft rot development after 7 dpi (p < 0.05). Notably, T. harzianum exhibited biocontrol activity against A. niger, F. equiseti, and P. venetum in dual-culture tests. T. harzianum also exhibited strong inhibitory activity against Fusarium wilt, suggesting the use of T. harzianum as a potential biocontrol agent for managing rhizome decay and wilt in Chinese asparagus. Our data indicate that the endophytic community of A. cochinchinensis rhizomes contains pathogenic, non-pathogenic, and probiotic fungi. Furthermore, our study provides a microbiological foundation for understanding rhizome rot in A. cochinchinensis and developing targeted biocontrol strategies against rhizome rot.