Co-expression network analysis and identification of core genes in the interaction between wheat and Puccinia striiformis f. sp. tritici

The epidemic of stripe rust, caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), would reduce wheat (Triticum aestivum) yields seriously. Traditional experimental methods are difficult to discover the interaction between wheat and Pst. Multi-omics data analysis provides a new idea for efficiently mining the interactions between host and pathogen. We used 140 wheat-Pst RNA-Seq data to screen for differentially expressed genes (DEGs) between low susceptibility and high susceptibility samples, and carried out Gene Ontology (GO) enrichment analysis. Based on this, we constructed a gene co-expression network, identified the core genes and interacted gene pairs from the conservative modules. Finally, we checked the distribution of Nucleotide-binding and leucine-rich repeat (NLR) genes in the co-expression network and drew the wheat NLR gene co-expression network. In order to provide accessible information for related researchers, we built a web-based visualization platform to display the data. Based on the analysis, we found that resistance-related genes such as TaPR1, TaWRKY18 and HSP70 were highly expressed in the network. They were likely to be involved in the biological processes of Pst infecting wheat. This study can assist scholars in conducting studies on the pathogenesis and help to advance the investigation of wheat-Pst interaction patterns.

Comparative transcriptome analysis reveals nicotine metabolism is a critical component for enhancing stress response intensity of innate immunity system in tobacco

The pyridine alkaloid nicotine acts as one of best-studied plant resistant traits in tobacco. Previous research has shown that NtERF199 and NtERF189, acting as master regulators within the NIC1 and NIC2 locus, quantitatively contribute to nicotine accumulation levels in N. tabacum. Genome editing-created Nic1(Nterf199) and Nic2 (Nterf189) double mutant provides an ideal platform for precisely dissecting the defensive role of nicotine and the connection between the nicotine biosynthetic pathway with other putative metabolic networks. Taking this advantage, we performed a comparative transcriptomic analysis to reevaluate the potential physiological and metabolic changes in response to nicotine synthesis defect by comparing the nic1nic2 and NIC1NIC2 plants. Our findings revealed that nicotine reduction could systematically diminishes the expression intensities of genes associated with stimulus perception, signal transduction and regulation, as well as secondary metabolic flux. Consequently, this global expression reduction might compromise tobacco adaptions to environmental fitness, herbivore resistances, and plant growth and development. The up-regulation of a novel set of stress-responsive and metabolic pathway genes might signify a newly established metabolic reprogramming to tradeoff the detrimental effect of nicotine loss. These results offer additional compelling evidence regarding nicotine's critical defensive role in nature and highlights the tight link between nicotine biosynthesis and gene expression levels of quantitative resistance-related genes for better environmental adaptation.

Establishment and application of Agrobacterium-delivered CRISPR/Cas9 system for wild tobacco (Nicotiana alata) genome editing

Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) system has been widely applied in cultivated crops, but limited in their wild relatives. Nicotiana alata is a typical wild species of genus Nicotiana that is globally distributed as a horticultural plant and well-studied as a self-incompatibility model. It also has valuable genes for disease resistance and ornamental traits. However, it lacks an efficient genetic transformation and genome editing system, which hampers its gene function and breeding research. In this study, we developed an optimized hypocotyl-mediated transformation method for CRISPR-Cas9 delivery. The genetic transformation efficiency was significantly improved from approximately 1% to over 80%. We also applied the CRISPR-Cas9 system to target the phytoene desaturase (NalaPDS) gene in N. alata and obtained edited plants with PDS mutations with over 50% editing efficiency. To generate self-compatible N. alata lines, a polycistronic tRNA-gRNA (PTG) strategy was used to target exonic regions of allelic S-RNase genes and generate targeted knockouts simultaneously. We demonstrated that our system is feasible, stable, and high-efficiency for N. alata genome editing. Our study provides a powerful tool for basic research and genetic improvement of N. alata and an example for other wild tobacco species.

Elevated MIF identified by multiple cytokine analyses facilitates macrophage M2 polarization contributing to postoperative recurrence in chronic rhinosinusitis with nasal polyps

BACKGROUND

Chronic rhinosinusitis with nasal polyps (CRSwNP) is characterized by tissue heterogeneity and high postoperative recurrence risk. This study aims to employ cytokine analyses to identify serum biomarkers associated with postoperative CRSwNP recurrence and elucidate underlying recurrent mechanisms.

METHODS

A prospective cohort study was conducted on CRSwNP patients undergoing functional endoscopic sinus surgery. Serum and tissue samples were collected and analyzed for multiple cytokines. Participants were followed for 3 years and categorized into recurrent and non-recurrent groups. Cytokine profiles were compared, and potential markers for recurrence were further assessed. Macrophage migration inhibitory factor (MIF) expression in macrophages was modulated, and their polarization and cytokine secretion were assessed.

RESULTS

In the discovery cohort (21 recurrent and 40 non-recurrent patients), circulating cytokine profiles differed significantly, with 8 cytokines showing differential expression between the two groups. Among them, serum eotaxin, MIF, RANTES, and TRAIL exhibited promise in predicting recurrence. In the validation cohort (24 recurrent and 44 non-recurrent patients), serum eotaxin, MIF, and TRAIL levels were higher in recurrent cases. Tissue MIF was elevated in recurrent cases and had a strong predictive value for recurrence. Moreover, tissue MIF was co-expressed with CD206 in recurrent cases. Mechanistically, MIF overexpression promoted macrophage M2 polarization and TGF-β1, CCL-24, and MIF secretion, and MIF recombinant protein facilitated M2 polarization, and TGF-β1 and CCL-24 production, contributing to CRSwNP recurrence.

CONCLUSIONS

Serum-specific cytokine signatures were associated with postoperative recurrence risk in CRSwNP. Elevated MIF enhanced macrophage M2 polarization and cytokine secretion, contributing to the recurrent mechanisms of CRSwNP.

Analysis of water quality influencing factors under multi-source data fusion based on PLS-SEM model: An example of East-Liao River in China

Owing to alterations in the environment and human activities, the quality of surface water is declining. Despite a substantial number of studies on the factors that impact water quality, there is still a need for a better understanding of the major causes of water quality degradation. This study fused multi-source data using partial least squares structural equation modeling to evaluate the effects of weather, soil composition, and geographical features on the water quality of the East Liao River (ELR), Jilin Province, China. The impacts of land-use practices on water quality at different buffer scales were analyzed. The most significant correlation between land use and water quality was observed at a distance of 4 km. The severity of water pollution was significantly influenced by soil type, with a path coefficient of 0.689 (p < 0.001). Conversely, landscape factors exhibited a notable adverse effect, indicated by a path coefficient of -0.608 (p < 0.001). Additionally, meteorological factors exhibited a significant impact, with a path coefficient of 0.463 (p < 0.001). The indirect effects of landscape elements on water quality were also examined. Water quality could be indirectly influenced by landscape through soil factors, as evidenced by a path coefficient of -0.572 (p < 0.01). In this study, new ideas for studying water quality drivers using multi-source data fusion are introduced. Managers can leverage the findings of this study to improve their decision-making and effectively address water quality issues in ELR located in Jilin Province, China.

CRISPR/Cas9-mediated seamless gene replacement in protoplasts expands the resistance spectrum to TMV-U1 strain in regenerated Nicotiana tabacum

CRISPR/Cas-based genome editing is now extensively used in plant breeding and continues to evolve. Most CRISPR/Cas current applications in plants focus on gene knock-outs; however, there is a pressing need for new methods to achieve more efficient delivery of CRISPR components and gene knock-ins to improve agronomic traits of crop cultivars. We report here a genome editing system that combines the advantages of protoplast technologies with recent CRISPR/Cas advances to achieve seamless large fragment insertions in the model Solanaceae plant Nicotiana tabacum. With this system, two resistance-related regions of the N' gene were replaced with homologous fragments from the N'alata gene to confer TMV-U1 resistance in the T0 generation of GMO-free plants. Our study establishes a reliable genome-editing tool for efficient gene modifications and provides a detailed description of the optimization process to assist other researchers adapt this system for their needs.

First Dark Matter Search Results from the LUX-ZEPLIN (LZ) Experiment

The LUX-ZEPLIN experiment is a dark matter detector centered on a dual-phase xenon time projection chamber operating at the Sanford Underground Research Facility in Lead, South Dakota, USA. This Letter reports results from LUX-ZEPLIN's first search for weakly interacting massive particles (WIMPs) with an exposure of 60 live days using a fiducial mass of 5.5 t. A profile-likelihood ratio analysis shows the data to be consistent with a background-only hypothesis, setting new limits on spin-independent WIMP-nucleon, spin-dependent WIMP-neutron, and spin-dependent WIMP-proton cross sections for WIMP masses above 9  GeV/c^{2}. The most stringent limit is set for spin-independent scattering at 36  GeV/c^{2}, rejecting cross sections above 9.2×10^{-48}  cm at the 90% confidence level.

Residues, potential source and ecological risk assessment of polycyclic aromatic hydrocarbons (PAHs) in surface water of the East Liao River, Jilin Province, China

The environmental risks posed by polycyclic aromatic hydrocarbons (PAHs) and the diversity of their anthropogenic origins make them a global issue. Therefore, it is of utmost significance for protecting the aquatic environment and the growth of neighboring populations to identify their possible origins and ecological risk. Here, we detail the contamination profiles of 15 PAHs found in the East Liao River's surface waters in Jilin Province and use the receptor model Absolute Principal Component Analysis - Multiple Linear Regression (APCS-MLR) and diagnostic ratios method to identify the primary potential sources of pollution. Based on the natural hazard risk formation theory (NHRFT), an ecological risk assessment (ERA) model for PAHs in the East Liao River was developed. The method assesses the ecological risk status of PAHs by integrating the risk quotient (RQ) approach and the DPSIRM (driving force, pressure, state, impact, response, management) conceptual framework. Total concentrations in the surface water body were between 396.42 and 624.06 ng/L, with an average of 436.99 ng/L. The source research revealed that coal, biomass, and traffic emission sources are the most likely PAH contributors to the East Liao River. The ERA found that the majority of the sites' locations of the study were at low risk for PAHs in surface water bodies (30.7 % and 32.2 %, respectively), while only a tiny percentage of sites were at high or very high risk (1.8 % and 13.6 %). The study results provide theoretical support for the East Liao River's ecological, environmental protection, and policy formulation.

Construction of a high-density genetic map and dissection of genetic architecture of six agronomic traits in tobacco (Nicotiana tabacum L.)

Tobacco (Nicotiana tabacum L.) is an economic crop and a model organism for studies on plant biology and genetics. A population of 271 recombinant inbred lines (RIL) derived from K326 and Y3, two elite flue-cured tobacco parents, has been constructed to investigate the genetic basis of agronomic traits in tobacco. Six agronomic traits including natural plant height (nPH), natural leaf number (nLN), stem girth (SG), inter-node length (IL), length of the largest leaf (LL) and width of the largest leaf (LW) were measured in seven environments, spanning the period between 2018 and 2021. We firstly developed an integrated SNP-indel-SSR linkage map with 43,301 SNPs, 2,086 indels and 937 SSRs, which contained 7,107 bin markers mapped on 24 LGs and covered 3334.88 cM with an average genetic distance of 0.469cM. Based on this high-density genetic map, a total of 70 novel QTLs were detected for six agronomic traits by a full QTL model using the software QTLNetwork, of which 32 QTLs showed significant additive effects, 18 QTLs showed significant additive-by-environment interaction effects, 17 pairs showed significant additive-by-additive epistatic effects and 13 pairs showed significant epistasis-by-environment interaction effects. In addition to additive effect as a major contributor to genetic variation, both epistasis effects and genotype-by-environment interaction effects played an important role in explaining phenotypic variation for each trait. In particular, qnLN6-1 was detected with considerably large main effect and high heritability ( h a 2 =34.80%). Finally, four genes including Nt16g00284.1, Nt16g00767.1, Nt16g00853.1, Nt16g00877.1 were predicted as pleiotropic candidate genes for five traits.

The complete chloroplast genome of Nicotiana plumbaginifolia

Nicotiana plumbaginifolia Vivianiis 1802 is an annual herb, native to Mexico and South America. It is one of the most widely distributed tobacco species. As a wild tobacco, N. plumbaginifolia has provided several economically important disease-resistance genes to cultivated tobacco. We assembled the complete chloroplast genome of N. plumbaginifolia. The chloroplast genome is 155,945 bp in length, which includes a large single copy region (86,621 bp), a small single copy region (18,528 bp) and two separated inverted repeat regions (25,398 bp). A total of 117 unique genes were annotated, consisting of 84 protein-coding genes, 29 tRNA genes and 4 rRNA genes. Based on chloroplast genomes of 17 Nicotiana species, phylogenetic analyses indicated that N. plumbaginifolia was closely related to N. suaveolens and N. amplexicaulis.

Wan-Nian-Qing, a Herbal Composite Prescription, Suppresses the Progression of Liver Cancer in Mice by Regulating Immune Response

The Wan-Nian-Qing prescription (WNQP), an herbal composite containing Ornithogalum caudatum, has been used in China for several years for cancer treatment. However, the mechanism of its pharmacological action against liver cancer is not clear. This study aimed to investigate the role of WNQP in inhibiting tumor growth in hepatocellular carcinoma model mice and determine its mechanism of action. We established HepG2- and SMMC-7721-xenografted tumor models in nude mice and BALB/c mice. The mice were administered WNQP for 2 weeks. The bodyweight of each mouse was monitored every day, and the tumor size was measured using vernier caliper before each round of WNQP administration. After the last dose, mice were sacrificed. The tumors were removed, lysed, and subjected to proteome profiling, enzyme-linked immunosorbent assay, and western blotting. The liver, spleen, and kidney were collected for histopathological examination. The effects of WNQP against liver cancer were first systematically confirmed in HepG2- and SMMC-7721-xenografted nude mice and BALB/c mice models. WNQP inhibited tumor growth, but failed to affect bodyweight and organ structures (liver and spleen), confirming that it was safe to use in mice. In BALB/c mice, WNQP regulated immune function, inferred from the modulation of immune-related cytokines such as interleukins, interferon, tumor necrosis factors, and chemokines. Further results confirmed that this regulation occurred via the regulatory effects of WNQP on Nrf2 signaling. WNQP can inhibit the growth of HepG2- and SMMC-7721-xenografted tumors in nude mice and BALB/c mice. This effect manifests at least partially through immunomodulation mediated apoptosis.

GIS- and MCD-based suitability assessment for optimized location of solid waste landfills in Dar es Salaam, Tanzania

Despite recent advancements in waste management technologies, landfills remain the dominant approach for the final disposal of solid waste (SW) around the world. However, landfills are associated with adverse environmental and health-related impacts. This study is primarily applied to Dar es Salaam, a city in the East African region that has failed to follow appropriate approaches for site selection and that the methods used to select the current sites are manually operated. The study used a geographical information system (GIS) combined with multicriteria decision analysis (MCDA) to objectively determine the optimal landfill sites. A comprehensive list of assessment criteria was examined through a computerized site selection procedure based on GIS to analyze the ground that was surveyed and to remotely obtain data. Analytical hierarchy process (AHP)-one of the best MCDA approaches-was used to assign relative weight and evaluate each criterion. Finally, the study computed site suitability indices (SSIs), which aids in the identification of site suitability levels (SSLs) for the entire region. The final suitability map produced by overlaying the criteria map layers showed that a large part of the study area (60.92%) was completely unsuitable for landfill siting. The remaining areas consisted of land with varying suitability level, which were grouped into four classes: very low (30.92%), low (2.05%), moderate (5.65%), and high (0.46). To this end, only the high suitability class (0.46%) was of acceptable suitability levels (ASLs) (SSI ≥ 2.0). From the numerous identified sites with ASL, only three sites were suggested. Due to concerns regarding the lifespan and environment-related risks associated with these suggested sites, there is a need to further study new environmentally friendly techniques, considering the importance of circular economy agenda of waste to resource/energy for sustainable solid waste management.

Comprehensive assessment of heavy metals pollution of farmland soil and crops in Jilin Province

As a major agricultural province in China, it is necessary to study the content of heavy metals in farmland soil and crop in Jilin Province and to evaluate the risks to ecology and human health. This study presented the work completed on 79 soil samples, 10 rice samples, 66 maize samples and 15 soybean samples collected from Jilin Province farmland and evaluated six heavy metals (Zn, Cu, Pb, Cd, Hg and As) concentrations. The results showed that the concentrations of the six heavy metals in farmland soil and crop samples from Jilin Province basically met the soil standards and food health standards of China. The agricultural soil pollution spatial distribution was the most serious in the south of Jilin Province and the lightest in the west. The non-carcinogenic risks faced by children eating crops were higher than those of adults, but the carcinogenic risks were lower than those of adults. Both of the two health risks to adults and children from eating crops were very limited. The results would help determine the heavy metals pollution in farmland soil in Jilin Province efficiently and accurately and helped decision makers to achieve a balance between production and environmental regulation.

Efficacy of utidelone plus capecitabine versus capecitabine for heavily pretreated, anthracycline- and taxane-refractory metastatic breast cancer: final analysis of overall survival in a phase III randomised controlled trial

BACKGROUND

Primary analysis of the phase III trial BG01-1323L demonstrated that utidelone plus capecitabine significantly improved progression-free survival (PFS) and overall response rate (ORR) versus capecitabine alone in heavily-pretreated patients with metastatic breast cancer (MBC). Here, we report the final overall survival (OS) analysis and updates of other endpoints.

PATIENTS AND METHODS

In total, 405 patients were randomised 2:1 to receive utidelone (30 mg/m² IV daily, days 1-5, over 90 min) plus capecitabine (1000 mg/m² orally b.i.d., days 1-14) or capecitabine alone (1250 mg/m² orally b.i.d., days 1-14) every 21 days. The secondary endpoint, OS, was estimated using the Kaplan-Meier product-limit approach at a two-sided alpha level of 0.05 after the prespecified 310 death events had been reached. Exploratory analyses of the primary endpoint, PFS, and the secondary endpoint, ORR, were also done. Safety was analysed in patients who had at least one dose of study drug.

RESULTS

At the final OS analysis, the median duration of follow-up was 19.6 months in the utidelone plus capecitabine group and 15.4 months in the capecitabine alone group. In the intention-to-treat population, 313 deaths had occurred at data cut-off, 203 of 270 patients in the combination group and 110 of 135 in the monotherapy group. Median OS in the combination group was 19.8 months compared with 16.0 months in the monotherapy group [hazard ratio (HR) = 0.75, 95% confidence intervals (CI) 0.59-0.94, P = 0.0142]. The updated analysis of PFS and ORR showed that the combination therapy remained superior to monotherapy. Safety results were similar to those previously reported with respect to incidence, severity and specificity. No late-emerging toxicities or new safety concerns occurred.

CONCLUSIONS

For heavily-pretreated, anthracycline- and taxane-resistant MBC patients, utidelone plus capecitabine significantly improved OS versus capecitabine alone. These results support the use of utidelone plus capecitabine as a novel therapeutic regimen for patients with MBC.

Genome-wide association study of leaf chemistry traits in tobacco

Leaf chemistry traits are some of the key factors influencing tobacco quality, which can be significantly reduced by lower chemical components in cured leaf. To improve tobacco quality through breeding, genetic diversity analysis, population structure analysis, and genome-wide association studies were performed in a panel of 347 tobacco germplasms and the markers associated with five leaf chemistry traits, including total sugar (TS), reducing sugar (RS), total nitrogen (TN), nicotine (NIC), and total potassium (TP) contents were identified. Four groups were classified at a genetic distance of 0.316 by genetic diversity analysis based on coefficient parameter NEI72 using a program NTSYS-pc2.10e, whereas four well-differentiated subpopulations were postulated in the 347 tobacco accessions. A total of 47 target trait-associated SNPs was detected in at least three environments as well as the best linear unbiased predictions (BLUPs) across all environments, among which two, two, four, six, and one highly suggestive associated SNPs were repeatedly detected in all environments and BLUPs for TS, RS, TN, NIC, and TP, respectively. On the basis of the phenotypic effects of the alleles corresponding to suggestive associated SNPs, five tobacco accessions harboring favorable alleles with elite phenotypic performance in leaf chemistry traits were identified. The results could facilitate quality tobacco breeding for higher leaf chemistry trait contents through molecular marker-assisted approaches.

Construction of a high-density genetic map with whole genome sequencing in Nicotiana tabacum L

Tobacco (Nicotiana tabacum L.) is an essential commercial crop and an ideal model plant for biological mechanism studies. As an allopolyploid species, tobacco harbors a massive and complex genome, which makes the application of molecular markers complicated and challenging. In our study, we performed whole-genome sequencing of an intraspecific recombinant inbred line (RIL) population, a F1 generation and their parents. With the Nicotiana tabacum (K326 cultivar) genome as reference, a total of 45,081 markers were characterized to construct the genetic map, which spanned a genetic distance of 3486.78 cM. Evaluation of a two-dimensional heat map proved the high quality of the genetic map. We utilized these markers to anchor scaffolds and analyzed the ancestral genome origin of linkage groups (LGs). Furthermore, such a high-density genetic map will be applied for quantitative trait locus (QTL) detection, gene localization, genome-wide association studies (GWAS), and marker-assisted breeding in tobacco.

Non-Structural Protein NSm of Tomato Spotted Wilt Virus Is an Avirulence Factor Recognized by Resistance Genes of Tobacco and Tomato via Different Elicitor Active Sites

Tomato spotted wilt virus (TSWV) is one of the most destructive viral pathogens of plants. Recently, a single dominant gene conferring complete resistance to TSWV (RTSW) was identified in Nicotina alata and introgressed into cultivated tobacco (N. tabacum). However, whether the TSWV carries an avirulence (Avr) factor directed against RTSW remains obscure. In the present study, we identified the non-structural protein (NSm), the movement protein of TSWV, which is an RTSW-specific Avr factor, by using two different transient expression systems. Using amino acid (aa) substitution mutants, we demonstrated the ability to induce RTSW-mediated hypersensitive response (HR) of NSm is independent of its movement function. Moreover, key substitutions (C118Y and T120N), a 21-aa viral effector epitope, and different truncated versions of NSm, which are responsible for the recognition of the Sw-5b resistance gene of tomato, were tested for their ability to trigger HR to TSWV in tobacco. Together, our results demonstrated that RTSW-mediated resistance is triggered by NSm in the same way as by Sw-5b, however, via different elicitor active sites. Finally, an Avr gene-based diagnostic approach was established and used to determine the presence and effectiveness of resistance genes in tobacco.

The DPSIR Model for Environmental Risk Assessment of Municipal Solid Waste in Dar es Salaam City, Tanzania

Environmental risk has become an area of major concern and research, drawing special attention. This study on the environmental risk assessment (ERA) of Dar es Salaam Municipal Solid Waste comes at a time when the Government of Tanzania is becoming increasingly concerned about dealing with high levels of pollution from municipal solid waste (MSW). The paper employed the Driving force-Pressure-State-Impact-Response (DPSIR) model to establish an environmental risk indicator system and the analytical hierarchy process (AHP) to calculate and analyze risk values, based on the actual situation of MSW in the city of Dar es Salaam. It lists several measures that have been taken in response to the current significantly high levels of pollution, which have assisted in maintaining the environmental risk index (ERI) at a medium level (0.4–0.6) during the period from 2006–2017. However, these measures have not been adequate enough to manage the external pressure. The ERI has been increasing gradually, calling for timely formulation of demand-specific waste management policies to reduce the possibility of reaching the critical point in near future. With the use of the DPSIR model for ERA, this study has become highly valuable, providing empirical justification to reduce environmental risk from MSW, which is one of the main sources of environmental pollution in the urban areas of developing countries.

Overexpression of EPS8L3 promotes cell proliferation by inhibiting the transactivity of FOXO1 in HCC

The homology of epidermal growth factor receptor pathway substrate 8 (EPS8), EPS8L3, is elevated significantly in hepatocellular carcinoma (HCC) tissues and cell lines compared with the normal liver tissues and cell lines. The MTT and colony formation assays demonstrated that overexpressing EPS8L3 enhances, while silencing reduces the proliferation of HCC cells. Further experiments illustrated that overexpressing EPS8L3 promotes the expression of p-AKT, Cyclin D1, but inhibits the transcriptional activity of FOXO1. Besides, colony formation assay demonstrated that AKT inhibitor suppresses the effect of EPS8L3 on proliferation in EPS8L3-overexpressing cells, whereas AKT restores the proliferation of EPS8L3-silenced cells, suggesting that EPS8L3 might promote proliferation by hyperactivating the AKT signaling pathway and subsequently inhibiting the FOXO1 transcriptional activity. Our results provide new view between EPS8L3 and progression of human HCC, suggesting that EPS8L3 may be a novel therapeutic target for HCC.

Abstract PD3-08: A randomized phase II trial of pyrotinib plus capecitabine versus lapatinib plus capecitabine in patients with HER2-positive metastatic breast cancer previously treated with taxanes, anthracyclines and/or trastuzumab

Background:Pyrotinib is an oral, irreversible pan-ErbB receptor tyrosine kinase inhibitor (TKI) with activity against epidermal growth factor receptor (EGFR) / HER1, HER2, and HER4. Lapatinib in combination with capecitabine is one of the standards of care for patients with HER2-positive metastatic breast cancer (MBC) who have received prior taxanes, anthracyclines and/or trastuzumab.

Methods: We conducted an open label, multicenter, randomized phase II trial to comparatively evaluate efficacy and safety of pyrotinib + capecitabine (PC) or lapatinib + capecitabine (LC) in women with HER2-positive MBC. Key eligibility criteria included prior treatment with taxanes, anthracyclines and/or trastuzumab, ≤2 prior chemotherapies for metastatic disease, no CNS metastases, and no prior treatment with HER2 targeted TKI. Eligible patients were randomized 1:1 to PC Arm (P 400 mg QD D1–21 + C 1000 mg/m2BID D1–14, 21-D cycle) or LC Arm (L 1250 mg QD D1–21 + C 1000 mg/m2BID D1–14, 21-D cycle). The primary endpoint was objective response rate (ORR) as assessed by investigator, and secondary endpoints included progression-free survival (PFS), time to progression (TTP), duration of response (DoR), overall survival (OS), and safety.

Results: Between May 2015 and Mar 2016, 128 patients (65 in PC arm and 63 in LC arm) were enrolled in this study. Median age was 48 years (range 25-70), ECOG performance status was 0 (53.9%) or 1 (46.1%), 62.5% had hormone receptor-positive disease, 76.6% had visceral disease and 53.9% had received prior trastuzumab in (neo)adjuvant and/or mestastatic setting. Baseline characteristics were well balanced in two arms. Median follow-up time was 15.0 months. ORR was 78.5% in PC arm and 57.1% in LC arm (p=0.01), Median PFS was 18.1 months in PC arm and 7.0 months in LC arm (hazard ratio 0.363; 95% CI 0.228, 0.579; p&lt;0.0001), PFS benefit in PC arm compared to LC arm was observed irrespective of prior trastuzumab or not. Treatment related Grade 3-4 toxicities occurred in &gt;2% patients in PC arm vs LC arm included hand-foot syndrome (21.5% vs 19.0%), diarrhea (13.8% vs 4.8%), decreased neutrophil (7.7% vs 1.6%), decreased WBC (6.2% vs 1.6%), vomiting (4.6% vs 0%), increased AST (3.1% vs 1.6%), decreased hemoglobin (3.1% vs 1.6%), increased total bilirubin (0% vs 4.8%) and increased conjugated bilirubin (0% vs 3.2%).

Conclusions: In women with HER2-positive MBC previously treated with taxanes, anthracyclines and/or trastuzumab, pyrotinib + capecitabine yield statistically significant better PFS and ORR than lapatinib + capecitabine in this randomized phase II trial. Phase III study is ongoing to validate this finding.

Citation Format: Xu B, Ma F, Ouyang Q, Li W, Jiang Z, Tong Z, Liu Y, Li H, Yu S, Feng J, Wang S, Hu X, Zhu X, Zou J. A randomized phase II trial of pyrotinib plus capecitabine versus lapatinib plus capecitabine in patients with HER2-positive metastatic breast cancer previously treated with taxanes, anthracyclines and/or trastuzumab [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD3-08.

Transcriptomic profile of tobacco in response to Tomato zonate spot orthotospovirus infection

BACKGROUND

Tomato zonate spot virus (TZSV), a dominant species of thrips-transmitted orthotospoviruses in Yunnan and Guangxi provinces in China, causes significant loss of yield in lots of crops and is a major threat to incomes of rural families. However, the detailed molecular mechanism of crop disease caused by TZSV remains obscure.

METHODS

Next-generation sequencing (NGS)-based transcriptome analysis (RNA-seq) was performed to investigate and compare the gene expression changes in systemic leaves of tobacco upon infection with TZSV and mock-inoculated plants as a control.

RESULTS

De novo assembly and analysis of tobacco transcriptome data by RNA-Seq identified 135,395 unigenes. 2102 differentially expressed genes (DEGs) were obtained in tobacco with TZSV infection, among which 1518 DEGs were induced and 584 were repressed. Gene Ontology enrichment analysis revealed that these DEGs were associated with multiple biological functions, including metabolic process, oxidation-reduction process, photosynthesis process, protein kinase activity. The KEGG pathway analysis of these DEGs indicated that pathogenesis caused by TZSV may affect multiple processes including primary and secondary metabolism, photosynthesis and plant-pathogen interactions.

CONCLUSION

Our global survey of transcriptional changes in TZSV infected tobacco provides crucial information into the precise molecular mechanisms underlying pathogenesis and symptom development. This is the first report on the relationships in the TZSV-plant interaction using transcriptome analysis. Findings of present study will significantly help enhance our understanding of the complicated mechanisms of plant responses to orthotospoviral infection.

Large-scale development of SSR markers in tobacco and construction of a linkage map in flue-cured tobacco

Tobacco (Nicotiana tabacum L.), particularly flue-cured tobacco, is one of the most economically important nonfood crops and is also an important model system in plant biotechnology. Despite its importance, only limited molecular marker resources are available for genome analysis, genetic mapping, and breeding. Simple sequence repeats (SSR) are one of the most widely-used molecular markers, having significant advantages including that they are generally co-dominant, easy to use, abundant in eukaryotic organisms, and produce highly reproducible results. In this study, based on the genome sequence data of flue-cured tobacco (K326), we developed a total of 13,645 mostly novel SSR markers, which were working in a set of eighteen tobacco varieties of four different types. A mapping population of 213 backcross (BC1) individuals, which were derived from an intra-type cross between two flue-cured tobacco varieties, Y3 and K326, was selected for mapping. Based on the newly developed SSR markers as well as published SSR markers, we constructed a genetic map consisting of 626 SSR loci distributed across 24 linkage groups and covering a total length of 1120.45 cM with an average distance of 1.79 cM between adjacent markers, which is the highest density map of flue-cured tobacco till date.

Effects of particle size on bidirectional reflectance factor measurements from particulate surfaces

The bidirectional reflectance factor (BRF) is commonly used to study the structure of a particulate surface based on photometric measurements. In this paper, we describe the bidirectional reflectance factor distribution of natural particulate surfaces with particles sizes varying from 0.15 mm to 0.9 mm. Two types of natural particulate surfaces (one with low reflectance and the other with moderate reflectance) were measured at visible and near-infrared wavelengths using the Northeast Normal University Laboratory Goniospectrometer System (NENULGS). Both the BRFs and anisotropic reflectance factors (ARFs) at selected wavelengths were compared with previously published results to verify the accuracy of our measurements, and we also quantitatively analyzed the effects of particle size on the BRF. It was found that the maximum reflectance difference, which was more distinct for the low-reflectance samples, between particulate surfaces with particle sizes of 0.15 mm and 0.9 mm occurred in the forward scattering direction for all samples, and the value of this maximum difference reached 59% for the low-reflectance samples. Then, we conducted a test of a photometric model to determine which parameters could be confidently linked to the surfaces' reflectance behavior. The inverted parameters were compared with the known physical parameters of our samples, such as the particle size. We found that the single-scattering albedo could be empirically used to determine the particle sizes of our samples when measurements of particulate surfaces with different particle sizes were performed under the same incidence conditions and with wide viewing angles. The potential applications of our results appear very promising for empirically resolving the spatial distribution of particle size within a given particulate sample as well as for deepening our understanding of the scattering properties of particulate media.

SNP-based genetic linkage map of tobacco (Nicotiana tabacum L.) using next-generation RAD sequencing

Background

Tobacco (Nicotiana tabacum L.) is an important model system, which has been widely used in plant physiological studies and it is particularly useful as a bioreactor. Despite its importance, only limited molecular marker resources are available for genome analysis, genetic mapping and breeding. Restriction-site associated DNA sequencing (RAD-seq) is a powerful new method for targeted sequencing across the genomes of many individuals. This approach has broad potential for genetic analysis through linkage mapping.

Results

We constructed a RAD library using genomic DNA from a BC₁ backcross population. Sequencing of 196 individuals was performed on an Illumina HiSeq 2500. Two linkage maps were constructed, one with a reference genome and another, termed as de novo identification of single nucleotide polymorphism (SNP) by RAD-seq, without a reference genome. Overall, 4138 and 2162 SNP markers with a total length of 1944.74 and 2000.9 cM were mapped to 24 linkage groups in the genetic maps based on reference genome and without reference, respectively.

Conclusions

Using two different SNP discovery methods based on next generation RAD sequencing technology, we have respectively mapped 2162 and 4318 SNPs in our backcross population. This study gives an excellent example for high density linkage map construction, irrespective of genome sequence availability, and provides saturated information for downstream genetic investigations such as quantitative trait locus analyses or genomic selection (e.g. bioreactor suitable cultivars).

Electronic supplementary material

The online version of this article (doi:10.1186/s40709-015-0034-3) contains supplementary material, which is available to authorized users.

Irradiation after surgery for breast cancer patients with primary tumours and one to three positive axillary lymph nodes: yes or no?

OBJECTIVE AND METHODS

We retrospectively analyzed clinicopathologic features and survival in breast cancer patients who had T1 or T2 primary tumours and 1-3 histologically involved axillary lymph nodes and who were treated with modified radical mastectomy without adjuvant radiotherapy (rt). We also explored prognosis to find the high- and low-risk groups.

RESULTS

From May 2001 to April 2005, 368 patients treated at Tianjin Tumor Hospital met the study criteria. The 5- and 8-year rates were 7.2% and 10.7% for locoregional recurrence (lrr), 85.1% and 77.7% for disease-free survival (dfs), and 92.8% and 89.3% for overall survival (os). Multivariate Cox regression analysis showed that age, tumour size, estrogen receptor (er) status, and lymphovascular invasion (lvi) were independent prognostic factors for lrr and dfs. Based on 4 patient-related factors that indicate poor prognosis (age < 40 years, tumour > 3 cm, er negativity, and lvi), the high-risk group (patients with 3 or 4 factors, accounting for 12.5% of the cohort) had 5- and 8-year rates of 24.3% and 36.9% for lrr, 57.2% and 39.2% for dfs, and 74.8% and 43.8% for os compared with 5.0% and 7.1% for lrr, 88.9% and 83.1% for dfs, 91.6% and 83.4% for os in the low-risk group (patients with 0-2 factors, accounting for 87.5% of the cohort; p < 0.001).

CONCLUSIONS

Our study identified several risk factors that correlated independently with a greater incidence of lrr and distant metastasis in patients with T1 and T2 breast cancer and 1-3 positive nodes. Patients with 0-2 risk factors may not be likely to benefit from post-mastectomy rt, but patients with 3-4 risk factors may need rt to optimize locoregional control and improve survival.

Succinate is an inflammatory signal that induces IL-1β through HIF-1α

Macrophages activated by the Gram-negative bacterial product lipopolysaccharide switch their core metabolism from oxidative phosphorylation to glycolysis. Here we show that inhibition of glycolysis with 2-deoxyglucose suppresses lipopolysaccharide-induced interleukin-1β but not tumour-necrosis factor-α in mouse macrophages. A comprehensive metabolic map of lipopolysaccharide-activated macrophages shows upregulation of glycolytic and downregulation of mitochondrial genes, which correlates directly with the expression profiles of altered metabolites. Lipopolysaccharide strongly increases the levels of the tricarboxylic-acid cycle intermediate succinate. Glutamine-dependent anerplerosis is the principal source of succinate, although the 'GABA (γ-aminobutyric acid) shunt' pathway also has a role. Lipopolysaccharide-induced succinate stabilizes hypoxia-inducible factor-1α, an effect that is inhibited by 2-deoxyglucose, with interleukin-1β as an important target. Lipopolysaccharide also increases succinylation of several proteins. We therefore identify succinate as a metabolite in innate immune signalling, which enhances interleukin-1β production during inflammation.