Integrated whole-exome and bulk transcriptome sequencing delineates the dynamic evolution from preneoplasia to invasive lung adenocarcinoma featured with ground-glass nodules.

OBJECTIVE: The genomic and molecular ecology involved in the stepwise continuum progression of lung adenocarcinoma (LUAD) from adenocarcinoma in situ (AIS) to minimally invasive adenocarcinoma (MIA) and subsequent invasive adenocarcinoma (IAC) remains unclear and requires further elucidation. We aimed to characterize gene mutations and expression landscapes, and explore the association between differentially expressed genes (DEGs) and significantly mutated genes (SMGs) during the dynamic evolution from AIS to IAC. METHODS: Thirty-five patients with ground-glass nodules (GGNs) lung adenocarcinomas were enrolled. Whole-exome sequencing (WES) and transcriptome sequencing (RNA-Seq) were conducted on all patients, encompassing both tumor samples and corresponding noncancerous tissues. Data obtained from WES and RNA-Seq were subsequently analyzed. RESULTS: The findings from WES delineated that the predominant mutations were observed in EGFR (49%) and ANKRD36C (17%). SMGs, including EGFR and RBM10, were associated with the dynamic evolution from AIS to IAC. Meanwhile, DEGs, including GPR143, CCR9, ADAMTS16, and others were associated with the entire process of invasive LUAD. We found that the signaling pathways related to cell migration and invasion were upregulated, and the signaling pathways of angiogenesis were downregulated across the pathological stages. Furthermore, we found that the messenger RNA (mRNA) levels of FAM83A, MAL2, DEPTOR, and others were significantly correlated with CNVs. Gene set enrichment analysis (GSEA) showed that heme metabolism and cholesterol homeostasis pathways were significantly upregulated in patients with EGFR/RBM10 co-mutations, and these patients may have poorer overall survival than those with EGFR mutations. Based on the six calculation methods for the immune infiltration score, NK/CD8+ T cells decreased, and Treg/B cells increased with the progression of early LUAD. CONCLUSIONS: Our findings offer valuable insights into the unique genomic and molecular features of LUAD, facilitating the identification and advancement of precision medicine strategies targeting the invasive progression of LUAD from AIS to IAC.

The clinical effects of Orff music therapy on children with autism spectrum disorder: a comprehensive evaluation.

Objective: This study aimed to investigate the clinical effects of Orff music therapy on children with Autism Spectrum Disorder (ASD) from the perspectives of parents, evaluators, and therapists. Methods: 93 children with ASD aged 3-6 years participated in the study. They were divided into an observation group (n = 48) receiving comprehensive rehabilitation intervention including Orff music therapy, and a control group (n = 45) receiving only comprehensive rehabilitation intervention. The Autism Behavior Checklist (ABC), Childhood Autism Rating Scale (CARS), and Psycho-educational Profile-3rd edition (PEP-3) were used for assessments before and after the intervention. Results: There were no significant demographic differences between the two groups. Both groups showed significant improvements in Sensory, Relating, Language, CVP, EL, RL, VMI, AE, SR, and CARS scores at T1, T2, and T3 (T1 vs. T2, T2 vs. T3, T1 vs. T3) (all p < 0.05). The observation group demonstrated significant changes in Body and Object use and FM, while the control group showed some changes in these domains. Social and self-help, GM, CMB, and CVB also significantly improved in both groups after 6 months of intervention (all p < 0.05). In terms of different time intervals, the observation group showed greater improvements in Sensory, Relating, Language, CARS scores, EL, RL, and SR compared to the control group (all p < 0.05). The improvement levels in Body and Object use, CVP, FM, VMI, and AE did not differ significantly between the two groups in the T1-T2 interval, but were significantly higher in the observation group in the T2-T3 and T1-T3 intervals (all p < 0.05). The magnitude of changes in Social and self-help, GM, CMB, and CVB did not differ significantly between the groups. Conclusion: Orff music therapy showed significant improvements in language expression, language comprehension, social skills, cognitive abilities, imitation abilities, emotional expression and fine motor in children with ASD. These findings provide support for the use of Orff music therapy as an effective intervention for children with ASD.

A Novel Methylation-based Model for Prognostic Prediction in Lung Adenocarcinoma.

Objectives: Specific methylation sites have shown promise in the early diagnosis of lung adenocarcinoma (LUAD). However, their utility in predicting LUAD prognosis remains unclear. This study aimed to construct a reliable methylation-based predictor for accurately predicting the prognosis of LUAD patients. Methods: DNA methylation data and survival data from LUAD patients were obtained from the TCGA and a GEO series. A DNA methylation-based signature was developed using univariate least absolute shrinkage and selection operators and multivariate Cox regression models. Results: Eight CpG sites were identified and validated as optimal prognostic signatures for the overall survival of LUAD patients. Receiver operating characteristic analysis demonstrated the high predictive ability of the eight-site methylation signature combined with clinical factors for overall survival. Conclusion: This research successfully identified a novel eight-site methylation signature for predicting the overall survival of LUAD patients through bioinformatic integrated analysis of gene methylation markers used in the early diagnosis of lung cancer.

Cuproptosis-related ceRNA axis triggers cell proliferation and cell cycle through CBX2 in lung adenocarcinoma.

BACKGROUND: Lung adenocarcinoma (LUAD) has high morbidity and mortality. Despite substantial advances in treatment, the prognosis of patients with LUAD remains unfavorable. The ceRNA axis has been reported to play an important role in the pathogenesis of LUAD. In addition, cuproptosis is considered an important factor in tumorigenesis. The expression of CBX2 has been associated with the development of multiple tumors, including LUAD. However, the precise molecular mechanisms through which the cuproptosis-related ceRNA network regulates CBX2 remain unclear. METHODS: The DEGs between tumor and normal samples of LUAD were identified in TCGA database. The "ConsensusClusterPlus" R package was used to perform consensus clustering based on the mRNA expression matrix and cuproptosis-related gene expression profile. Then, LASSO-COX regression analysis was performed to identify potential prognostic biomarkers associated with cuproptosis, and the ceRNA network was constructed. Finally, the mechanisms of ceRNA in LUAD was studied by cell experiments. RESULTS: In this study, the AC144450.1/miR-424-5p axis was found to promote the progression of LUAD by acting on CBX2. The expression of AC144450.1 and miR-424-5p can be altered to regulate CBX2 and is correlated with cell proliferation and cell cycle of LUAD. Mechanistically, AC144450.1 affects the expression of CBX2 by acting as the ceRNA of miR-424-5p. In addition, a cuproptosis-related model were constructed in this study to predict the prognosis of LUAD. CONCLUSIONS: This study is the first to demonstrate that the AC144450.1/miR-424-5p/CBX2 axis is involved in LUAD progression and may serve as a novel target for its diagnosis and treatment.

Ivermectin induces nonprotective autophagy by downregulating PAK1 and apoptosis in lung adenocarcinoma cells.

INTRODUCTION: LUAD (Lung adenocarcinoma), the most common subtype of lung carcinoma and one of the highest incidences and mortality cancers in the world remains still a substantial treatment challenge. Ivermectin, an avermectin derivative, has been traditionally used as an antiparasitic agent in human and veterinary medicine practice during the last few decades. Though ivermectin has been shown to be effective against a variety of cancers, however, there is few available data reporting the antitumor effects of ivermectin in LUAD. METHODS: The effect of ivermectin on cell viability and proliferative ability of LUAD cells was evaluated using CCK-8 and colony formation assay. Apoptosis rate and autophagy flux were detected using flow cytometry based on PI/Annexin V staining and confocal laser scanning microscope based on LC3-GFP/RFP puncta, respectively. Western blotting experiment was conducted to verify the results of changes in apoptosis and autophagy. LUAD-TCGA and GEO databases were used to analyse the expression and predictive value of PAK1 in LUAD patients. Xenograft model and immumohistochemical staining were used for verification of the inhibitor effect of ivermectin in vivo. RESULTS: Ivermectin treatment strikingly impeded the colony formation, and the viability of the cell, along with cell proliferation, and caused the apoptosis and enhanced autophagy flux in LUAD cells. In addition, ivermectin-induced nonprotective autophagy was confirmed by treating LUAD cells with 3-MA, an autophagy inhibitor. Mechanistically, we found that ivermectin inhibited PAK1 protein expression in LUAD cells and we confirmed that overexpression of PAK1 substantially inhibited ivermectin-induced autophagy in LUAD cells. Based on TCGA and GEO databases, PAK1 was highly expressed in LUAD tissues as compared with normal tissues. Furthermore, LUAD patients with high PAK1 level have poor overall survival. Finally, in vivo experiments revealed that ivermectin efficiently suppressed the cellular growth of LUAD among nude mice. CONCLUSION: This study not only revealed the mechanism of ivermectin inhibited the growth of LUAD but also supported an important theoretical basis for the development of ivermectin during the therapy for LUAD.

Marine reserves promote cycles in fish populations on ecological and evolutionary time scales.

Marine reserves are considered essential for sustainable fisheries, although their effectiveness compared to traditional fisheries management is debated. The effect of marine reserves is mostly studied on short ecological time scales, whereas fisheries-induced evolution is a well-established consequence of harvesting. Using a size-structured population model for an exploited fish population of which individuals spend their early life stages in a nursery habitat, we show that marine reserves will shift the mode of population regulation from low size-selective survival late in life to low, early-life survival due to strong resource competition. This shift promotes the occurrence of rapid ecological cycles driven by density-dependent recruitment as well as much slower evolutionary cycles driven by selection for the optimal body to leave the nursery grounds, especially with larger marine reserves. The evolutionary changes increase harvesting yields in terms of total biomass but cause disproportionately large decreases in yields of larger, adult fish. Our findings highlight the importance of carefully considering the size of marine reserves and the individual life history of fish when managing eco-evolutionary marine systems to ensure both population persistence as well as stable fisheries yields.

Nomogram Predicting the Prognosis of Patients with Surgically Resected Stage IA Non-small Cell Lung Cancer.

The American Joint Committee on Cancer (AJCC) 8th stage system was limited in accuracy for predicting prognosis of stage IA non-small cell lung cancer (NSCLC) patients. This study aimed to establish and validate two nomograms that predict overall survival (OS) and lung cancer-specific survival (LCSS) in surgically resected stage IA NSCLC patients. Postoperative patients with stage IA NSCLC in SEER database between 2004 and 2015 were examined. Survival and clinical information according to the inclusion and exclusion criteria were collected. All patients were randomly divided into the training cohort and validation cohort with a ratio of 7:3. Independent prognosis factors were evaluated using univariate and multivariate Cox regression analyses, and predictive nomogram was established based on these factors. Nomogram performance was measured using the C-index, calibration plots, and DCA. Patients were grouped by quartiles of nomogram scores and survival curves were plotted by Kaplan-Meier analysis. In total, 33,533 patients were included in the study. The nomogram contained 12 prognostic factors in OS and 10 prognostic factors in LCSS. In the validation set, the C-index was 0.652 for predicting OS and 0.651 for predicting LCSS. The calibration curves for the nomogram-predicted probability of OS and LCSS showed good agreement between the actual observation and nomogram prediction. DCA indicated that the clinical value of the nomograms were higher than AJCC 8th stage for predicting OS and LCSS. Nomogram scores related risk stratification revealed statistically significant difference which have better discrimination than AJCC 8th stage. The nomogram can accurately predict OS and LCSS in surgically resected patients with stage IA NSCLC. Supplementary Information: The online version contains supplementary material available at 10.1007/s13193-022-01700-w.

Self-organized mud cracking amplifies the resilience of an iconic "Red Beach" salt marsh.

Self-organized patterning, resulting from the interplay of biological and physical processes, is widespread in nature. Studies have suggested that biologically triggered self-organization can amplify ecosystem resilience. However, if purely physical forms of self-organization play a similar role remains unknown. Desiccation soil cracking is a typical physical form of self-organization in coastal salt marshes and other ecosystems. Here, we show that physically self-organized mud cracking was an important facilitating process for the establishment of seepweeds in a "Red Beach" salt marsh in China. Transient mud cracks can promote plant survivorship by trapping seeds, and enhance germination and growth by increasing water infiltration in the soil, thus facilitating the formation of a persistent salt marsh landscape. Cracks can help the salt marsh withstand more intense droughts, leading to postponed collapse and faster recovery. These are indications of enhanced resilience. Our work highlights that self-organized landscapes sculpted by physical agents can play a critical role in ecosystem dynamics and resilience to climate change.

Predicting residual friction angle of lunar regolith based on Chang'e-5 lunar samples.

With the rapid development of human lunar exploration projects, the lunar base establishment and resource utilization are on the way, and hence it is urgent and significant to reasonably predict engineering properties of the lunar regolith, which remains to be unclear due to limited lunar samples currently accessible for geotechnical tests. In this contribution, we aim to address this outstanding challenge from the perspective of granular material mechanics. To this end, the 3D multi-aspect geometrical characteristics and mechanical properties of Chang'e-5 lunar samples are for the first time evaluated with a series of non-destructive microscopic tests. Based on the measured particle surface roughness and Young's modulus, the interparticle friction coefficients of lunar regolith particles are well predicted through an experimental fitting approach using previously published data on terrestrial geomaterials or engineering materials. Then the residual friction angle of the lunar regolith under low confining pressure is predicted as 53° to 56° according to the particle overall regularity and interparticle friction coefficients of Chang'e-5 lunar samples. The presented results provide a novel cross-scale method to predict engineering properties of the lunar regolith from particle scale information to serve for the future lunar surface engineering construction.

Phase-separation physics underlies new theory for the resilience of patchy ecosystems.

Spatial self-organization of ecosystems into large-scale (from micron to meters) patterns is an important phenomenon in ecology, enabling organisms to cope with harsh environmental conditions and buffering ecosystem degradation. Scale-dependent feedbacks provide the predominant conceptual framework for self-organized spatial patterns, explaining regular patterns observed in, e.g., arid ecosystems or mussel beds. Here, we highlight an alternative mechanism for self-organized patterns, based on the aggregation of a biotic or abiotic species, such as herbivores, sediment, or nutrients. Using a generalized mathematical model, we demonstrate that ecosystems with aggregation-driven patterns have fundamentally different dynamics and resilience properties than ecosystems with patterns that formed through scale-dependent feedbacks. Building on the physics theory for phase-separation dynamics, we show that patchy ecosystems with aggregation patterns are more vulnerable than systems with patterns formed through scale-dependent feedbacks, especially at small spatial scales. This is because local disturbances can trigger large-scale redistribution of resources, amplifying local degradation. Finally, we show that insights from physics, by providing mechanistic understanding of the initiation of aggregation patterns and their tendency to coarsen, provide a new indicator framework to signal proximity to ecological tipping points and subsequent ecosystem degradation for this class of patchy ecosystems.