Integrative physiological, metabolomic, and transcriptomic analysis reveals the drought responses of two apple rootstock cultivars.

BACKGROUND: Drought is considered the main environmental factor restricting apple production and thus the development of the apple industry. Rootstocks play an important role in enhancing the drought tolerance of apple plants. Studies of the physiology have demonstrated that 'ZC9-3' is a strong drought-resistant rootstock, whereas 'Jizhen-2' is a weak drought-resistant rootstock. However, the metabolites in these two apple rootstock varieties that respond to drought stress have not yet been characterized, and the molecular mechanisms underlying their responses to drought stress remain unclear. RESULTS: In this study, the physiological and molecular mechanisms underlying differences in the drought resistance of 'Jizhen-2' (drought-sensitive) and 'ZC9-3' (drought-resistant) apple rootstocks were explored. Under drought stress, the relative water content of the leaves was maintained at higher levels in 'ZC9-3' than in 'Jizhen-2', and the photosynthetic, antioxidant, and osmoregulatory capacities of 'ZC9-3' were stronger than those of 'Jizhen-2'. Metabolome analysis revealed a total of 95 and 156 differentially accumulated metabolites in 'Jizhen-2' and 'ZC9-3' under drought stress, respectively. The up-regulated metabolites in the two cultivars were mainly amino acids and derivatives. Transcriptome analysis revealed that there were more differentially expressed genes and transcription factors in 'ZC9-3' than in 'Jizhen-2' throughout the drought treatment. Metabolomic and transcriptomic analysis revealed that amino acid biosynthesis pathways play key roles in mediating drought resistance in apple rootstocks. A total of 13 metabolites, including L-α-aminoadipate, L-homoserine, L-threonine, L-isoleucine, L-valine, L-leucine, (2S)-2-isopropylmalate, anthranilate, L-tryptophan, L-phenylalanine, L-tyrosine, L-glutamate, and L-proline, play an important role in the difference in drought resistance between 'ZC9-3' and 'Jizhen-2'. In addition, 13 genes encoding O-acetylserine-(thiol)-lyase, S-adenosylmethionine synthetase, ketol-acid isomeroreductase, dihydroxyacid dehydratase, isopropylmalate isomerase, branched-chain aminotransferase, pyruvate kinase, 3-dehydroquinate dehydratase/shikimate 5-dehydrogenase, N-acetylglutamate-5-P-reductase, and pyrroline-5-carboxylate synthetase positively regulate the response of 'ZC9-3' to drought stress. CONCLUSIONS: This study enhances our understanding of the response of apple rootstocks to drought stress at the physiological, metabolic, and transcriptional levels and provides key insights that will aid the cultivation of drought-resistant apple rootstock cultivars. Especially, it identifies key metabolites and genes underlying the drought resistance of apple rootstocks.

Melatonin alleviates cadmium toxicity by regulating root endophytic bacteria community structure and metabolite composition in apple.

The level of cadmium (Cd) accumulation in orchard soils is increasing, and excess Cd will cause serious damage to plants. Melatonin is a potent natural antioxidant and has a potential role in alleviating Cd stress. This study aimed to investigate the effects of exogenous melatonin on a root endophyte bacteria community and metabolite composition under Cd stress. The results showed that melatonin significantly scavenged the reactive oxygen species and restored the photosynthetic system (manifested by the improved photosynthetic parameters, total chlorophyll content and the chlorophyll fluorescence parameters (Fv/Fm)), increased the activity of antioxidant enzymes (the activities of catalase, superoxide dismutase, peroxidase and ascorbate oxidase) and reduced the concentration of Cd in the roots and leaves of apple plants. High-throughput sequencing showed that melatonin increased the endophytic bacterial community richness significantly and changed the community structure under Cd stress. The abundance of some potentially beneficial endophytic bacteria (Ohtaekwangia, Streptomyces, Tabrizicola and Azovibrio) increased significantly, indicating that the plants may absorb potentially beneficial microorganisms to resist Cd stress. The metabolomics results showed that melatonin significantly changed the composition of root metabolites, and the relative abundance of some metabolites decreased, suggesting that melatonin may resist Cd stress by depleting root metabolites. In addition, co-occurrence network analysis indicated that some potentially beneficial endophytes may be influenced by specific metabolites. These results provide a theoretical basis for studying the effects of melatonin on the endophytic bacterial community and metabolic composition in apple plants.

Dopamine alleviates cadmium stress in apple trees by recruiting beneficial microorganisms to enhance the physiological resilience revealed by high-throughput sequencing and soil metabolomics.

Dopamine has demonstrated promise as a stress-relief substance. However, the function of dopamine in Cd tolerance and its mechanism remains largely unknown. The current study was performed to investigate the mechanism of dopamine on alleviating apple Cd stress through regular application of CdCl2 and dopamine solution to potting soil. The results indicated that dopamine significantly reduced reactive oxygen species (ROS) and Cd accumulation and alleviated the inhibitory effect of Cd stress on the growth of apple plants through activation of the antioxidant system, enhancement of photosynthetic capacity, and regulation of gene expression related to Cd absorption and detoxification. The richness of the rhizosphere microbial community increased, and community composition and assembly were affected by dopamine treatment. Network analysis of microbial communities showed that the numbers of nodes and total links increased significantly after dopamine treatment, while the keystone species shifted. Linear discriminant analysis effect size indicated that some biomarkers were significantly enriched after dopamine treatment, suggesting that dopamine induced plants to recruit potentially beneficial microorganisms (Pseudoxanthomonas, Aeromicrobium, Bradyrhizobium, Frankia, Saccharimonadales, Novosphingobium, and Streptomyces) to resist Cd stress. The co-occurrence network showed several metabolites that were positively correlated with relative growth rate and negatively correlated with Cd accumulation, suggesting that potentially beneficial microorganisms may be attracted by several metabolites (L-threonic acid, profenamine, juniperic acid and (3ß,5ξ,9ξ)-3,6,19-trihydroxyurs-12-en-28-oic acid). Our results demonstrate that dopamine alleviates Cd stress in apple trees by recruiting beneficial microorganisms to enhance the physiological resilience revealed. This study provides an effective means to reduce the harm to agricultural production caused by heavy metals.

Effect of renin-angiotensin-aldosterone system inhibitors on survival outcomes in cancer patients treated with immune checkpoint inhibitors: a systematic review and meta-analysis.

Background: Effect of renin-angiotensin-aldosterone system inhibitors (RAASIs) in combination with immune checkpoint inhibitors (ICIs) on prognoses in cancer patients remains controversial. This study systematically evaluated the effect of RAASIs on survival outcomes in cancer patients receiving ICIs treatment and provided an evidence-based reference for the rational use of RAASIs and ICIs combination therapy in clinical practice. Methods: Studies evaluating the prognosis of RAASIs-used versus RAASIs-free in cancer patients receiving ICIs treatment from inception to 1 November 2022 were retrieved by searching PubMed, Cochrane Library, Web of Science, Embase, and major conference proceedings. Studies in English reporting hazard ratios (HRs) with 95% confidence intervals (CIs) for overall survival (OS) and/or progression-free survival (PFS) were included. Statistical analyses were conducted using the software Stata 17.0. Results: A total of 12 studies containing 11739 patients were included, comprising ~4861 patients in the RAASIs-used and ICIs-treated group and ~6878 patients in RAASIs-free and ICIs-treated group. The pooled HR was 0.85 (95%CI, 0.75-0.96; P = 0.009) for OS and 0.91 (95%CI, 0.76-1.09; P = 0.296) for PFS, indicating a positive effect of RAASIs concomitant with ICIs on cancer patients. This effect was observed especially in patients with urothelial carcinoma (HR, 0.53; 95%CI, 0.31-0.89; P = 0.018) and renal cell carcinoma (HR, 0.56; 95%CI, 0.37-0.84; P = 0.005) on OS. Conclusion: Concomitant use of RAASIs and ICIs enhanced the efficacy of ICIs and this combination regimen was associated with significantly improved OS and a trend towards better PFS. RAASIs can be considered as adjuvant drugs when hypertensive patients receive ICIs treatment. Our results provide an evidence-based reference for the rational use of the RAASIs and ICIs combination therapy to improve the efficacy of ICIs in clinical practice. Systematic review registration: https://www.crd.york.ac.uk/prospero/, identifier CRD42022372636; https://inplasy.com/, identifier INPLASY2022110136.

Interpretable deep learning survival predictive tool for small cell lung cancer.

Background: Small cell lung cancer (SCLC) is an aggressive and almost universally lethal neoplasm. There is no accurate predictive method for its prognosis. Artificial intelligence deep learning may bring new hope. Methods: By searching the Surveillance, Epidemiology, and End Results database (SEER), 21,093 patients' clinical data were eventually included. Data were then divided into two groups (train dataset/test dataset). The train dataset (diagnosed in 2010-2014, N = 17,296) was utilized to conduct a deep learning survival model, validated by itself and the test dataset (diagnosed in 2015, N = 3,797) in parallel. According to clinical experience, age, sex, tumor site, T, N, M stage (7th American Joint Committee on Cancer TNM stage), tumor size, surgery, chemotherapy, radiotherapy, and history of malignancy were chosen as predictive clinical features. The C-index was the main indicator to evaluate model performance. Results: The predictive model had a 0.7181 C-index (95% confidence intervals, CIs, 0.7174-0.7187) in the train dataset and a 0.7208 C-index (95% CIs, 0.7202-0.7215) in the test dataset. These indicated that it had a reliable predictive value on OS for SCLC, so it was then packaged as a Windows software which is free for doctors, researchers, and patients to use. Conclusion: The interpretable deep learning survival predictive tool for small cell lung cancer developed by this study had a reliable predictive value on their overall survival. More biomarkers may help improve the prognostic predictive performance of small cell lung cancer.

Prevalence of Novel and Traditional Synthetic Phenolic Antioxidants in Baby Food from China: A Dominant Pathway for Infant Exposure.

Synthetic phenolic antioxidants (SPAs) are a group of ubiquitous contaminants with multiple toxicities. However, current knowledge on the occurrence of SPAs in baby food and associated infant exposure is lacking. Herein, we analyzed three categories of baby food from China: infant formula, cereal, and puree, for a broad suite of 11 traditional and 19 novel SPAs. In addition to 11 traditional SPAs, up to 13 novel SPAs were detected in the baby food samples. The median concentrations of novel SPAs for infant formula, cereal, and puree were 604, 218, and 24.1 ng/g, respectively, surpassing those of traditional SPAs (53.4, 62.1, and 10.0 ng/g). The prevalent SPAs in the samples were butylated hydroxytoluene, 2,4-di-tert-butylphenol, pentaerythritol tetrakis[3-(3,5-di-tert-butyl-4-hydroxyphenyl)propionate] (AO 1010), and octadecyl 3-(3,5-di-tert-butyl-4-hydroxyphenyl) propionate (AO 1076). Source analysis indicated that the prevalence of these four SPAs in baby food was associated with contamination of packaging materials, mechanical processing, or raw ingredients. Migration experiments demonstrated that contamination of plastic packaging constituted an important source. Exposure assessment suggested that there may be no appreciable health risk posed by the SPAs in baby food. Even so, baby food consumption was still a dominant pathway for infant exposure to SPAs, with a higher contribution than breast milk consumption, dust ingestion, dermal dust absorption, and air inhalation, which requires special attention.

Identification of human peripheral blood monocyte gene markers for early screening of solid tumors.

As cancer mortality is high in most regions of the world, early screening of cancer has become increasingly important. Minimally invasive screening programs that use peripheral blood mononuclear cells (PBMCs) are a new and reliable strategy that can achieve early detection of tumors by identifying marker genes. From 797 datasets, four (GSE12771, GSE24536, GSE27562, and GSE42834) including 428 samples, 236 solid tumor cases, and 192 healthy controls were chosen according to the inclusion criteria. A total of 285 genes from among 440 reported genes were selected by meta-analysis. Among them, 4 of the top significantly differentially expressed genes (ANXA1, IFI44, IFI44L, and OAS1) were identified as marker genes of PBMCs. Pathway enrichment analysis identified, two significant pathways, the 'primary immunodeficiency' pathway and the 'cytokine-cytokine receptor interaction' pathway. Protein- protein interaction (PPI) network analysis revealed the top 27 hubs with a degree centrality greater than 23 to be hub genes. We also identified 3 modules in Molecular Complex Detection (MCODE) analysis: Cluster 1 (related to ANXA1), Cluster 2 (related to IFI44 and IFI44L) and Cluster 3 (related to OAS1). Among the 4 marker genes, IFI44, IFI44L, and OAS1 are potential diagnostic biomarkers, even though their results were not as remarkable as those for ANXA1 in our study. ANXA1 is involved in the immunosuppressive mechanism in tumor-bearing hosts and may be used in a new strategy involving the use of the host's own immunity to achieve tumor suppression.

Gene expression profile-based drug screen identifies SAHA as a novel treatment for NAFLD.

Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease worldwide. Being part of the metabolic syndrome, NAFLD is characterized by the deposition of triglycerides (TGs) as lipid droplets in the cytoplasm of hepatic cells. Recently, the rapid development of high-throughput genome analysis technologies provided opportunities to screen for new drugs for NAFLD. In this study, we screened for potential drugs based on the gene expression profiles of 73 compounds and identified histone deacetylase (HDAC) inhibitors as a novel treatment for the accumulation of lipids in hepatocytes. In the subsequent analysis and experiments, we discovered that SAHA inhibited the fatty acid and lipid metabolism pathways in hepatic cells and induced a significant deficiency of lipid accumulation in HepG2 and SMMC-7721 cells. Furthermore, SAHA inhibited lipid synthesis in hepatic cells by directly suppressing the expression of DGAT2. Hence, our study provides a novel method to screen for effective drugs for liver diseases and identifies SAHA as a potent treatment for NAFLD.

Identification of core genes in ovarian cancer by an integrative meta-analysis.

BACKGROUND: Epithelial ovarian cancer is one of the most severe public health threats in women. Since it is still challenging to screen in early stages, identification of core genes that play an essential role in epithelial ovarian cancer initiation and progression is of vital importance. RESULTS: Seven gene expression datasets (GSE6008, GSE18520, GSE26712, GSE27651, GSE29450, GSE36668, and GSE52037) containing 396 ovarian cancer samples and 54 healthy control samples were analyzed to identify the significant differentially expressed genes (DEGs). We identified 563 DEGs, including 245 upregulated and 318 downregulated genes. Enrichment analysis based on the gene ontology (GO) functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that the upregulated genes were significantly enriched in cell division, cell cycle, tight junction, and oocyte meiosis, while the downregulated genes were associated with response to endogenous stimuli, complement and coagulation cascades, the cGMP-PKG signaling pathway, and serotonergic synapse. Two significant modules were identified from a protein-protein interaction network by using the Molecular Complex Detection (MCODE) software. Moreover, 12 hub genes with degree centrality more than 29 were selected from the protein-protein interaction network, and module analysis illustrated that these 12 hub genes belong to module 1. Furthermore, Kaplan-Meier analysis for overall survival indicated that 9 of these hub genes was correlated with poor prognosis of epithelial ovarian cancer patients. CONCLUSION: The present study systematically validates the results of previous studies and fills the gap regarding a large-scale meta-analysis in the field of epithelial ovarian cancer. Furthermore, hub genes that could be used as a novel biomarkers to facilitate early diagnosis and therapeutic approaches are evaluated, providing compelling evidence for future genomic-based individualized treatment of epithelial ovarian cancer.

Overexpression of MpCYS4, a phytocystatin gene from Malus prunifolia (Willd.) Borkh., delays natural and stress-induced leaf senescence in apple.

Phytocystatins are a well-characterized class of naturally occurring protease inhibitors that prevent the catalysis of papain-like cysteine proteases. The action of cystatins in stress tolerance has been studied intensively, but relatively little is known about their functions in plants during leaf senescence. Here, we examined the potential roles of the apple cystatin, MpCYS4, in leaf photosynthesis as well as the concentrations and composition of leaf proteins when plants encounter natural or stress-induced senescence. Overexpression of this gene in apple rootstock M26 effectively slowed the senescence-related declines in photosynthetic activity and chlorophyll concentrations and prevented the action of cysteine proteinases during the process of degrading proteins (e.g., Rubisco) in senescing leaves. Moreover, MpCYS4 alleviated the associated oxidative damage and enhanced the capacity of plants to eliminate reactive oxygen species by activating antioxidant enzymes such as ascorbate peroxidase, peroxidase, and catalase. Consequently, plant cells were protected against damage from free radicals during leaf senescence. Based on these results, we conclude that MpCYS4 functions in delaying natural and stress-induced senescence of apple leaves.

Overexpression of MpCYS4, A Phytocystatin Gene from Malus prunifolia (Willd.) Borkh., Enhances Stomatal Closure to Confer Drought Tolerance in Transgenic Arabidopsis and Apple.

Phytocystatins (PhyCys) comprise a group of inhibitors for cysteine proteinases in plants. They play a wide range of important roles in regulating endogenous processes and protecting plants against various environmental stresses, but the underlying mechanisms remain largely unknown. Here, we detailed the biological functions of MpCYS4, a member of cystatin genes isolated from Malus prunifolia. This gene was activated under water deficit, heat (40°C), exogenous abscisic acid (ABA), or methyl viologen (MV) (Tan et al., 2014a). At cellular level, MpCYS4 protein was found to be localized in the nucleus, cytoplasm, and plasma membrane of onion epidermal cells. Recombinant MpCYS4 cystatin expressed in Escherichia coli was purified and it exhibited cysteine protease inhibitor activity. Transgenic overexpression of MpCYS4 in Arabidopsis (Arabidopsis thaliana) and apple (Malus domestica) led to ABA hypersensitivity and series of ABA-associated phenotypes, such as enhanced ABA-induced stomatal closing, altered expression of many ABA/stress-responsive genes, and enhanced drought tolerance. Taken together, our results demonstrate that MpCYS4 is involved in ABA-mediated stress signal transduction and confers drought tolerance at least in part by enhancing stomatal closure and up-regulating the transcriptional levels of ABA- and drought-related genes. These findings provide new insights into the molecular mechanisms by which phytocystatins influence plant growth, development, and tolerance to stress.

Exogenous melatonin improved potassium content in Malus under different stress conditions.

Melatonin mediates many physiological processes in plants. We investigated its role in regulating growth, potassium uptake, and root system architecture under three types of stress: salinity or a deficiency of all nutrients in Malus hupehensis Rehd., as well as a K deficiency in Malus rockii Rehd. Each treatment caused a reduction in growth rates and disrupted the absorption of potassium. However, pretreatment with 0.1 mmol/L melatonin significantly alleviated such inhibitions. The addition of melatonin also upregulated genes for antioxidant enzymes involved in the ascorbate-glutathione cycle (MdcAPX, MdDHAR1, MdDHAR2, MdMDHAR, and MdcGR) and helped decrease the accumulation of H2 O2 while improving the expression of K transporters and genes for the CBL1-CIPK23 pathway. These results indicated that melatonin can regulate the ROS signal and activate the CBL1-CIPK23 pathway to regulate the expression of a potassium channel protein gene, thereby promoting the absorption of potassium ions. Our findings demonstrate that inducing melatonin production is an important mechanism for plant defenses that can serve as a platform for possible applications in agricultural or related fields of research.

Two new pyrrolosesquiterpenes produced by a Streptomyces species.

Two new pyrrolosesquiterpenes, 1 and 2, were isolated from cultures of the soil actinomycete Streptomyces sp. Hd7-21. The structures of these compounds were established as (2Z,4E,9E)-6,7,11-trihydroxy-3,7,11-trimethyl-1-(1H-pyrrol-2-yl)dodeca-2,4,9-trien-1-one (1) and (2Z,4E)-5-{3-[(2E)-4-hydroxy-4-methylpent-2-en-1-yl]-3-methyloxiran-2-yl}-3-methyl-1-(1H-pyrrol-2-yl)penta-2,4-dien-1-one (2) by extensive spectroscopic analyses including MS, and 1D- and 2D-NMR data. Their cytotoxic activities against a panel of human cancer cell lines were evaluated.

Induced production of new diterpenoids in the fungus Penicillium funiculosum.

The supplementation of a DNA methyltransferase inhibitor, 5-azacytidine (5-AZ), to the culture medium of Penicillium funiculosum, dramatically altered its metabolic profiles. Analysis of the culture broth extract led to the isolation of two new prenyleudesmane diterpenoids (1-2). The isolated compounds were further evaluated for their cytotoxic and antibacterial activities. Our findings confirmed that the use of chemical epigenetic modifiers is an effective technique for promoting the expression of silent biosynthetic pathways to produce unique secondary metabolites.

Epigenetic modifier-induced biosynthesis of novel acetylenic sterols from Cladosporium colocasiae.

The addition of an HDAC inhibitor, suberoylanilide hydroxamic acid (SBHA), to the culture medium of Cladosporium colocasiae, dramatically altered its metabolic profiles. Analysis of the culture broth extract led to the isolation of two new acetylenic sterols (1-2). The isolated compounds were further evaluated for their cytotoxic and antibacterial activities. Compound 1 showed activity against Bacillus subtilis, affording a zone of inhibition of 12mm at 100µg/disk. However, none of them showed noticeable growth inhibitory effects.

A new pyrrolosesquiterpene isolated from cultures of Streptomyces sp.

One new pyrrolosesquiterpene 1 was isolated from the cultures of the soil actinomycete Streptomyces sp. Hd7-21. Its structure was elucidated by extensive spectroscopic analyses including MS and one-dimensional and two-dimensional NMR data. Compound 1 showed moderate cytotoxic activity against a panel of human cancer cell lines.

Structural elucidation and NMR assignments of two new pyrrolosesquiterpenes from Streptomyces sp. Hd7-21.

Two new pyrrolosesquiterpenes were isolated from cultures of the soil actinomycete Streptomyces sp. Hd7-21. The structures of these compounds were elucidated by extensive spectroscopic analyses including MS and 1D and 2D NMR data. Their cytotoxic activity against a panel of human cancer cell lines were biologically evaluated.