Genetically modified soybean lines exhibit less transcriptomic variation compared to natural varieties

Genetically modified (GM) soybeans provide a huge amount of food for human consumption and animal feed. However, the possibility of unexpected effects of transgenesis has increased food safety concerns. High-throughput sequencing profiling provides a potential approach to directly evaluate unintended effects caused by foreign genes. In this study, we performed transcriptomic analyses to evaluate differentially expressed genes (DEGs) in individual soybean tissues, including cotyledon (C), germ (G), hypocotyl (H), and radicle (R), instead of using the whole seed, from four GM and three non-GM soybean lines. A total of 3,351 DEGs were identified among the three non-GM soybean lines. When the GM lines were compared with their non-GM parents, 1,836 to 4,551 DEGs were identified. Furthermore, Gene Ontology (GO) analysis of the DEGs showed more abundant categories of GO items (199) among non-GM lines than between GM lines and the non-GM natural varieties (166). Results of Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that most KEGG pathways were the same for the two types of comparisons. The study successfully employed RNA sequencing to assess the differences in gene expression among four tissues of seven soybean varieties, and the results suggest that transgenes do not induce massive transcriptomic alterations in transgenic soybeans compared with those that exist among natural varieties. This work offers empirical evidence to investigate the genomic-level disparities induced by genetic modification in soybeans, specifically focusing on seed tissues.

Role of Cisplatin in Inducing Acute Kidney Injury and Pyroptosis in Mice via the Exosome miR-122/ELAVL1 Regulatory Axis

Although cisplatin is an effective chemotherapy drug for the treatment of various cancers, its clinical use is limited due to its side effects, especially nephrotoxicity. Unfortunately, acute kidney injury (AKI) caused by cisplatin remains one of the main challenges in effective cancer treatment. Evidence increasingly suggests that renal inflammation and pyroptotic inflammatory cell death of renal tubular epithelial cells (RTECs) mainly determine the progression and outcome of cisplatin-induced AKI. However, it is not clear how cisplatin regulates the pyroptosis of RTECs cells in AKI. The current study aimed to determine the regulation mechanism of AKI induced by cisplatin. We used cisplatin to induce AKI in vivo. We performed H&E staining of mouse kidney tissue sections and evaluated serological indicators of kidney injury (including blood urea nitrogen (BUN), serum creatinine, and tumor necrosis factor-alpha (TNF-alpha)). We used immunohistochemistry and western blot to detect the important substrate protein gasdermin D (GSDMD) and key target caspase-1 of pyroptosis, respectively. Cisplatin induced mouse AKI and RTECs pyroptosis. HK2 cell-derived exosomes treated with cisplatin influenced pyroptosis of the surrounding HK2 cells. Cisplatin-treated HK2 cells exosome-derived miR-122 regulated pyroptosis in the surrounding cells. Exosome-derived miR-122 affected cisplatin-induced AKI and HK2 cells pyroptosis by regulating the expression of embryonic lethal abnormal vision (ELAVL1). These results suggest that exosome miR-122 inhibited pyroptosis and AKI by targeting ELAVL1 under cisplatin treatment, and this offers a potential target for the treatment of AKI.

Genetic Diversity and Relationship of Shanlan Upland Rice Were Revealed Based on 214 Upland Rice SSR Markers

Shanlan upland rice (Oryza sativa L.) is a unique upland rice variety cultivated by the Li nationality for a long time, which has good drought resistance and high utilization value in drought resistance breeding. To explore the origin of Shanlan upland rice and its genetic relationship with upland rice from other geographical sources, 214 upland rice cultivars from Southeast Asia and five provinces (regions) in southern China were used to study genetic diversity by using SSR markers. Twelve SSR primers were screened and 164 alleles (Na) were detected, with the minimum number of alleles being 8 and the maximum number of alleles being 23, with an average of 13.667. The analysis of genetic diversity and analysis of molecular variance (AMOVA) showed that the differences among the materials mainly came from the individuals of upland rice. The results of gene flow and genetic differentiation revealed the relationship between the upland rice populations, and Hainan Shanlan upland rice presumably originated from upland rice in Guangdong province, and some of them were genetically differentiated from Hunan upland rice. It can be indirectly proved that the Li nationality in Hainan is a descendant of the ancient Baiyue ethnic group, which provides circumstantial evidence for the migration history of the Li nationality in Hainan, and also provides basic data for the advanced protection of Shanlan upland rice, and the innovative utilization of germplasm resources.

Identification of LncRNAs and Functional Analysis of ceRNA Related to Fatty Acid Synthesis during Flax Seed Development

Flax is a flowering plant cultivated for its oil and contains various unsaturated fatty acids. Linseed oil is known as the "deep-sea fish oil" of plants, and is beneficial to brain and blood lipids, among other positive effects. Long non-coding RNAs (lncRNAs) play an important role in plant growth and development. There are not many studies assessing how lncRNAs are related to the fatty acid synthesis of flax. The relative oil contents of the seeds of the variety Heiya NO.14 (for fiber) and the variety Macbeth (for oil) were determined at 5 day, 10 day, 20 day, and 30 day after flowering. We found that 10-20 day is an important period for ALA accumulation in the Macbeth variety. The strand-specific transcriptome data were analyzed at these four time points, and a series of lncRNAs related to flax seed development were screened. A competing endogenous RNA (ceRNA) network was constructed and the accuracy of the network was verified using qRT-PCR. MSTRG.20631.1 could act with miR156 on the same target, squamosa promoter-binding-like protein (SPL), to influence fatty acid biosynthesis through a gluconeogenesis-related pathway during flax seed development. This study provides a theoretical basis for future studies assessing the potential functions of lncRNAs during seed development.

Understanding the molecular mechanism of drought resistance in Shanlan upland rice by transcriptome and phenotype analyses

Rice (Oryza sativa L.) is an important grain crop worldwide, and drought has become an important factor restricting rice yield. As a unique rice germplasm in Hainan (China), Shanlan upland rice has rich genetic diversity and certain advantage for breeding water-saving and drought-resistance rice. 48 varieties, including 41 Shanlan upland rice, 3 upland rice, and 4 irrigated rice varieties was cultivated in soil pots. The drought resistance was assessed at the seedling stage using the stress coefficients of seven indicators, as the D value calculating from five principal components to rank the varieties. Five cultivars with strong, medium, and low resistance, were selected for transcriptome sequencing. The results of the GSEA analysis showed that free amino acid content increased through the redistribution of energy in Shanlan upland rice to cope with drought stress. In addition, we found that Os03g0623100 was significantly up-regulated under drought stress conditions in varieties with high drought resistance, as compared with low resistance cultivars. The Os03g0623100 was predicted to interact with LEA protein in the STRING database, which may contribute to maintaining the energy metabolisms to under stress conditions. This study provides a view of Shanlan upland rice as a drought-resistant germplasm resource, and a deeper understanding of the molecular mechanism of crop drought resistance.

Overexpression of the Caragana korshinskii com58276 Gene Enhances Tolerance to Drought in Cotton (Gossypium hirsutum L.)

The increasing water scarcity associated with environmental change brings significant negative impacts to the growth of cotton plants, whereby it is urgent to enhance plant tolerance to drought. Here, we overexpressed the com58276 gene isolated from the desert plant Caragana korshinskii in cotton plants. We obtained three OE plants and demonstrated that com58276 confers drought tolerance in cotton after subjecting transgenic seeds and plants to drought. RNA-seq revealed the mechanisms of the possible anti-stress response, and that the overexpression of com58276 does not affect growth and fiber content in OE cotton plants. The function of com58276 is conserved across species, improving the tolerance of cotton to salt and low temperature, and demonstrating its applicability to improve plant resistance to environmental change.

Substituted benzoate-anchored decanuclear titanium-oxo clusters featuring unprecedented defective double-cubane geometry

Based on DMF solvent, four titanium-oxo clusters (TOCs) [Ti10(μ3-O)12(L)6 (OiPr)10 (DMF)2] (Ti-L) (L=4-methylbenzoate(MB), 3,5-Di-tert-butylbenzoate (DTBB), 4-Methoxybenzoate (MOB) and 4-Methyl-3,5-dinitrobenzoate(MDNB) with the same coordination environments have been solvothermally synthesized with high...

APOBEC mutagenesis, kataegis, chromothripsis in EGFR-mutant osimertinib-resistant lung adenocarcinomas

BACKGROUND

Studies of targeted therapy resistance in lung cancer have primarily focused on single-gene alterations. Based on prior work implicating apolipoprotein b mRNA-editing enzyme, catalytic polypeptide-like (APOBEC) mutagenesis in histological transformation of epidermal growth factor receptor (EGFR)-mutant lung cancers, we hypothesized that mutational signature analysis may help elucidate acquired resistance to targeted therapies.

PATIENTS AND METHODS

APOBEC mutational signatures derived from an Food and Drug Administration-cleared multigene panel [Memorial Sloan Kettering Cancer Center Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT)] using the Signature Multivariate Analysis (SigMA) algorithm were validated against the gold standard of mutational signatures derived from whole-exome sequencing. Mutational signatures were decomposed in 3276 unique lung adenocarcinomas (LUADs), including 93 paired osimertinib-naïve and -resistant EGFR-mutant tumors. Associations between APOBEC and mechanisms of resistance to osimertinib were investigated. Whole-genome sequencing was carried out on available EGFR-mutant lung cancer samples (10 paired, 17 unpaired) to investigate large-scale genomic alterations potentially contributing to osimertinib resistance.

RESULTS

APOBEC mutational signatures were more frequent in receptor tyrosine kinase (RTK)-driven lung cancers (EGFR, ALK, RET, and ROS1; 25%) compared to LUADs at large (20%, P < 0.001); across all subtypes, APOBEC mutational signatures were enriched in subclonal mutations (P < 0.001). In EGFR-mutant lung cancers, osimertinib-resistant samples more frequently displayed an APOBEC-dominant mutational signature compared to osimertinib-naïve samples (28% versus 14%, P = 0.03). Specifically, mutations detected in osimertinib-resistant tumors but not in pre-treatment samples significantly more frequently displayed an APOBEC-dominant mutational signature (44% versus 23%, P < 0.001). EGFR-mutant samples with APOBEC-dominant signatures had enrichment of large-scale genomic rearrangements (P = 0.01) and kataegis (P = 0.03) in areas of APOBEC mutagenesis.

CONCLUSIONS

APOBEC mutational signatures are frequent in RTK-driven LUADs and increase under the selective pressure of osimertinib in EGFR-mutant lung cancer. APOBEC mutational signature enrichment in subclonal mutations, private mutations acquired after osimertinib treatment, and areas of large-scale genomic rearrangements highlights a potentially fundamental role for APOBEC mutagenesis in the development of resistance to targeted therapies, which may be potentially exploited to overcome such resistance.

Research on lncRNA related to drought resistance of Shanlan upland rice

Background

Drought has become the major abiotic stress that causes losses in rice yields and consequently is one of the main environmental factors threatening food security. Long non-coding RNA (lncRNA) is known to play an important role in plant response to drought stress, while the mechanisms of competing endogenous RNA (ceRNA) in drought resistance in upland rice have been rarely reported.

Results

In our study, a total of 191 lncRNAs, 2115 mRNAs and 32 miRNAs (microRNAs) were found by strand-specific sequencing and small RNA sequencing to be differentially expressed in drought-stressed rice. Functional analysis of results indicate that they play important roles in hormone signal transduction, chlorophyll synthesis, protein synthesis and other pathways. Construction of a ceRNA network revealed that MSTRG.28732.3 may interact with miR171 in the chlorophyll biosynthesis pathway and affect the ability of plants to withstand drought stress by regulating Os02g0662700, Os02g0663100 and Os06g0105350. The accuracy of the regulatory network was verified by qRT-PCR.

Conclusion

Our results provide a theoretical basis for future studies on the potential function of lncRNA in plant drought resistance, and they provide new genetic resources for drought-resistant rice breeding.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08546-0.

Gestational bisphenol A exposure impairs hepatic lipid metabolism by altering mTOR/CRTC2/SREBP1 in male rat offspring

Lipid metabolism is an important biochemical process in the body. Recent studies have found that environmental endocrine disruptors play an important role in the regulation of lipid metabolism. Bisphenol A (BPA), a common environmental endocrine disruptor, has adverse effects on lipid metabolism, but the mechanism is still unclear. This study aimed to investigate the effects of gestational BPA exposure on hepatic lipid metabolism and its possible mechanism in male offspring. The pregnant Sprague-Dawley rats were exposed to BPA (0, 0.05, 0.5, 5 mg/kg/day) from day 5 to day 19 of gestation to investigate the levels of triglyceride (TG) and total cholesterol (TC), and the expression of liver lipid metabolism-related genes in male offspring rats. The results showed that compared with the control group, the TG and TC levels in serum and liver in BPA-exposed groups was increased. And the expressions of liver fatty acid oxidation related genes, such as peroxisome proliferators-activated receptor α (PPARα) and carnitine palmitoyl transferase 1α (CPT1α), were down-regulated. However, the expressions of fatty acid synthesis related genes, such as sterol regulatory element binding proteins 1 (SREBP-1), acetyl-CoA carboxylase 1 (ACC1), fatty acid synthase (FAS) and stearoyl-CoA desaturase 1 (SCD-1), were up-regulated. The increased protein levels of mTOR and p-CRTC2 suggested that CREB-regulated transcription coactivator 2 (CRTC2) might be an important mediator in the mTOR/SREBP-1 pathway. In conclusion, these results demonstrated that mTOR/CRTC2/SREBP-1 could be affected by gestational BPA exposure, which may involve in the lipid metabolic disorders in later life.

Development of a Duck Genomic Reference Material by Digital PCR Platforms for the Detection of Meat Adulteration

Low-cost meat, such as duck, is frequently used to adulterate more expensive foods like lamb or beef in many countries. However, the lack of DNA-based reference materials has limited the quality control and detection of adulterants. Here, we report the development and validation of duck genomic DNA certified reference materials (CRMs) through the detection of the duck interleukin 2 (IL2) gene by digital PCR (dPCR) for the identification of duck meat in food products. The certified value of IL2 in CRMs was 5.78 ± 0.51 × 10³ copies/μL with extended uncertainty (coverage factor k = 2) based on IL2 quantification by eight independent collaborating laboratories. Quantification of the mitochondrial gene cytb revealed a concentration of 2.0 × 10⁶ copies/μL, as an information value. The CRMs were also used to determine the limit of detection (LOD) for six commercial testing kits, which confirmed that these kits meet or exceed their claimed sensitivity and are reliable for duck detection.

Genome-wide identification and functional characterization of LEA genes during seed development process in linseed flax (Linum usitatissimum L.)

BACKGROUND

LEA proteins are widely distributed in the plant and animal kingdoms, as well as in micro-organisms. LEA genes make up a large family and function in plant protection against a variety of adverse conditions.

RESULTS

Bioinformatics approaches were adopted to identify LEA genes in the flax genome. In total, we found 50 LEA genes in the genome. We also conducted analyses of the physicochemical parameters and subcellular location of the genes and generated a phylogenetic tree. LuLEA genes were unevenly mapped among 15 flax chromosomes and 90% of the genes had less than two introns. Expression profiles of LuLEA showed that most LuLEA genes were expressed at a late stage of seed development. Functionally, the LuLEA1 gene reduced seed size and fatty acid contents in LuLEA1-overexpressed transgenic Arabidopsis lines.

CONCLUSION

Our study adds valuable knowledge about LEA genes in flax which can be used to improve related genes of seed development.

Enhanced tolerance to drought stress resulting from Caragana korshinskii CkWRKY33 in transgenic Arabidopsis thaliana

Background

It is well known that WRKY transcription factors play important roles in plant growth and development, defense regulation and stress responses.

Results

In this study, a WRKY transcription factor, WRKY33, was cloned from Caragana korshinskii. A sequence structure analysis showed that it belonged to the Group-I type. Subcellular localization experiments in tobacco epidermal cells showed the presence of CkWRKY33 in the nucleus. Additionally, CkWRKY33 was overexpressed in Arabidopsis thaliana. A phenotypic investigation revealed that compared with wild-type plants, CkWRKY33-overexpressing transgenic plants had higher survival rates, as well as relative soluble sugar, proline and peroxidase contents, but lower malondialdehyde contents, following a drought stress treatment.

Conclusions

This suggested that the overexpression of CkWRKY33 led to an enhanced drought-stress tolerance in transgenic A. thaliana. Thus, CkWRKY33 may act as a positive regulator involved in the drought-stress responses in Caragana korshinskii.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12863-021-00965-4.

CRISPR/Cas9 editing of wheat TaQ genes alters spike morphogenesis and grain threshability

The TaQ alleles as one of the AP2-like transcription factors in common wheat (Triticum aestivum) play an important role in the evolution of spike characteristics from wild and domesticated emmer to modern wheat cultivars. Its loss-of-function mutant not only changed threshability and spike architecture but also affected plant height, flowering time, and floret structure. However, the comprehensive functions of TaAQ and TaDq genes in wheat have not been fully elucidated yet. Here, CRISPR/SpCas9 was used to edit wheat TaAQ and TaDq. We obtained homozygous plants in the T₁ generation with loss of function of only TaAQ or TaDq and simultaneous loss of function of TaAQ and TaDq to analyze the effect of these genes on wheat spikes and floret shapes. The results demonstrated that the TaAQ-edited plants and the TaAQ and TaDq simultaneously-edited plants were nearly similar in spike architecture, whereas the TaDq-edited plants were different from the wild-type ones only in plant height. Moreover, the TaAQ-edited plants or the TaAQ and TaDq simultaneously-edited plants were more brittle than the wild-type and the TaDq-edited plants. Based on the expression profiling, we postulated that the VRN1, FUL2, SEP2, SEP5, and SEP6 genes might affect the number of spikelets and florets per spike in wheat by regulating the expression of TaQ. Combining the results of this report and previous reports, we conceived a regulatory network of wheat traits, including plant height, spike shape, and floral organs, which were influenced by AP2-like family genes. The results achieved in this study will help us to understand the regulating mechanisms of TaAQ and TaDq alleles on wheat floral organs and inflorescence development.

An electrochemical DNA biosensor based on nitrogen-doped graphene nanosheets decorated with gold nanoparticles for genetically modified maize detection

A reliable electrochemical biosensor is reported based on nitrogen-doped graphene nanosheets and gold nanoparticle (Au/N-G) nanocomposites for the event-specific detection of GM maize MIR162. The differential pulse voltammetry response of methylene blue (MB) was chosen to monitor the target DNA hybridization event. Under the optimum conditions, the peak current increased linearly with the logarithm of the concentration of DNA in the range 1.0 × 10^-14 to 1.0 × 10^-8 M, and the detection limit was 2.52 × 10^-15 M (S/N = 3). It is also demonstrated that the DNA biosensor has high selectivity, good stability, and fabrication reproducibility. The biosensor has been effectively applied to detect MIR162 in real samples, showing its potential as an effective tool for GM crop analysis. These results will contribute to the development of new portable transgenic detection systems. Graphical abstract .

Increased pollen source area does not always enhance the risk of pollen dispersal and gene flow in Oryza sativa L

Pollen dispersal is one of the main ways of gene flow. In the past years, rice pollen dispersal and gene flow have been well studies. However, there is much dispute whether the risk of pollen dispersal and gene flow continuously increases with the source area. A Lagrangian stochastic model was used to simulate the pollen depositions at different distances from different pollen source areas. The field experiments showed a good fit in the pollen depositions. The larger the source area, the more the pollen grains were deposited at each distance, with the pollen dispersal distance increasing accordingly. However, this effect gradually leveled off as the source area increased. In the large-area of pollen source, we found a significantly higher saturation point for the amount of pollen deposition. Once the source area exceeded 1000 × 1000 m2, the pollen deposition no longer increased, even if the source area continued to increase, indicating the "critical source area" of rice pollen dispersal. However, a 100 × 100 m2 critical source area for conventional rice and hybrid rice was sufficient, while the critical source area for the sterile line was about 230 × 230 m2.

Genomic Comparison and Population Diversity Analysis Provide Insights into the Domestication and Improvement of Flax

Flax has been cultivated for its oil and fiber for thousands of years. However, it remains unclear how the modifications of agronomic traits occurred on the genetic level during flax cultivation. In this study, we conducted genome-wide variation analyses on multiple accessions of oil-use, fiber-use, landraces, and pale flax to identify the genomic variations during flax cultivation. Our findings indicate that, during flax domestication, genes relevant to flowering, dehiscence, oil production, and plant architecture were preferentially selected. Furthermore, regardless of origins, the improvement of the modern oil-use flax preceded that of the fiber-use flax, although the dual selection on oil-use and fiber-use characteristics might have occurred in the early flax domestication. We also found that the expansion of MYB46/MYB83 genes may have contributed to the unique secondary cell wall biosynthesis in flax and the directional selections on MYB46/MYB83 may have shaped the morphological profile of the current oil-use and fiber-use flax.

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Assemblies of genomes, including oil-use flax, fiber-use flax and pale flax

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Comparative genomic analysis between pale flax and cultivated flax

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Dual-selection mode on oil-use and fiber-use characteristics might be existing

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Expansion and selection of MYB46/MYB83 may shape the morphological profile of flax

Efficient induction of haploid plants in wheat by editing of TaMTL using an optimized Agrobacterium-mediated CRISPR system

The use of CRISPR/LbCpf1 and CRISPR/xCas9 systems in wheat have not yet been reported. In this study, we compared the efficiencies of three CRISPR editing systems (SpCas9, LbCpf1, and xCas9), and three different promoters (OsU6a, TaU3, and TaU6) that drive single-guide (sg)RNA, which were introduced into wheat via Agrobacterium-mediated transformation. The results indicated that TaU3 was a better choice than OsU6a or TaU6. The editing efficiency was higher using two sgRNAs than one sgRNA, and mutants with a large fragment deletion between the two sgRNAs were produced. The LbCpf1 and xCas9 systems could both be used successfully. Two endogenous genes, TaWaxy and TaMTL, were edited with high efficiency by the optimized SpCas9 system, with the highest efficiency (80.5%) being achieved when using TaU3 and two sgRNAs to target TaWaxy. Rates of seed set in the TaMTL-edited T0 transgenic plants were much lower than that of the wild-type. A haploid induction rate of 18.9% was found in the TaMTL-edited T1 plants using the CRISPR/SpCas9 system. Mutants with reverse insertion of the deleted sequences of TaMTL and TaWaxy between the two sgRNAs were identified in the edited T0 plants. In addition, wheat grains lacking embryos or endosperms were observed in the TaMTL-edited T1 generation.

Body mass index cut-off points for predicting chronic non-communicable disease should differ by gender and age group

OBJECTIVES

The objective of this study to determine whether body mass index (BMI) in different genders and age groups need different thresholds when predicting chronic non-communicable diseases (CNCDs).

STUDY DESIGN

This is a cross-sectional study.

METHODS

Data were obtained from the China Health and Nutrition Survey conducted in 2009. Sequential sample cluster analysis was used to group age according to BMI. Propensity score matching was used to eliminate the influence of age. Receiver operating characteristic curve based on gender and age group was used to evaluate the cut-off values and efficiency of BMI in each group.

RESULTS

A total of 8469 individuals were enrolled in this study. Results of sequential sample cluster analyses showed age was divided into three groups: 18-39, 40-59 and 60-99 years. There were significant differences in the distribution of BMI among the three groups for both males and females (P < 0.001). Statistical differences were observed in the distribution of BMI between genders in the 18-39- and 60-99-year-old age groups (P < 0.001). For men, the cut-off values of BMI were ≥25 kg/m², ≥24 kg/m² and ≥23 kg/m² in the 18-39, 40-59 and 60-99 years old groups, respectively; for women, the corresponding cut-off points were ≥25 kg/m², ≥23 kg/m² and ≥25 kg/m² in groups.

CONCLUSIONS

The thresholds for BMI might be different between gender and age group. In addition, it might not be suitable to determine cut-off values of BMI to predict CNCDs for people aged ≥60 years.

Low frequency, weak MCP-1 secretion and exhausted immune status of peripheral monocytes were associated with progression of severe enterovirus A71-infected hand, foot and mouth disease

A minority of hand, foot and mouth disease (HFMD) caused by enterovirus A71 (EV-A71) results in severe neural complications. However, whether monocyte-mediated immunity is involved in the disease progression of HFMD remains unknown. One hundred and twenty mild and 103 severe HFMD patients were recruited and enzyme-linked immunosorbent assay (ELISA), flow cytometry and Transwell culture were performed in the study. Peripheral monocyte counts were lower in both absolute counts and frequencies in severe cases compared to mild cases. After screening 10 monocyte-related cytokines by ELISA, only monocyte chemoattractant protein-1 (MCP-1) was found at higher levels in sera of mild cases compared to those with severe symptoms. Monocytes purified from mild cases produced more MCP-1 than the cells from severe patients when stimulated in vitro. We observed that immune exhaustion markers programmed death 1 (PD-1) and programmed death ligand 1 (PD-L1) were highly regulated on the surface of monocytes from severe cases compared to mild cases. PD-L1 blockade induced a higher production of MCP-1 in the supernatant of a Transwell system. The production of MCP-1 also increased following PD-L1 blockade of purified monocytes activated by granulocyte-macrophage colony-stimulating factor (GM-CSF) combined with R848 or EV-A71 virus. Our results indicate that absolute count, frequency and levels of MCP-1 secretion of peripheral monocytes, together with their immune status, probably contribute to differential disease prognosis in EV-A71-associated HFMD.

Abstract P4-04-01: The landscape of somatic genetic alterations in breast cancers from CHEK2 germline mutation carriers

Introduction: Checkpoint kinase 2 (CHEK2) is a tumor suppressor gene, which regulates cell cycle in response to DNA damage response. Selected CHEK2 germline mutations have been shown to confer an increased risk of breast cancer development. Multiple founder mutations in CHEK2 have been identified, and meta analyses have shown that CHEK2 truncating variants confer a higher breast cancer risk than missense variants. Here, we assessed the phenotype and repertoire of genetic alterations of breast cancers from 33 patients with CHEK2 pathogenic germline variants.

Materials and methods: We performed targeted capture massively parallel sequencing (≥410 genes) of tumor and normal samples from 13 patients with CHEK2 pathogenic germline variants, and retrieved whole exome sequencing (WES) data (BAM files) of tumor and normal samples from 20 patients with CHEK2 germline pathogenic variants included in the TCGA breast cancer study. In addition, we retrieved WES data of BRCA1, BRCA2 and ATM associated breast cancers from TCGA and Weigelt et al. (JNCI 2018). Somatic mutations, copy number alterations, mutational signatures and large-scale transitions (LSTs) were defined using state-of-the-art bioinformatics algorithms.

Results: Of the 33 CHEK2-associated breast cancers included in this study, 21 had missense and 12 had loss-of-function (LoF) germline mutations, and 81% were ER-positive and 12% HER2-positive. CHEK2-associated breast cancers statistically significantly less frequently displayed an ER-negative/HER2-negative phenotype (0%) than BRCA1- (80%) or BRCA2-associated (33%) breast cancers (BRCA1, p&lt;0.0001 for both comparisons), but were similar to ATM-associated breast cancers. Biallelic inactivation of CHEK2 through loss of heterozygosity (LOH) of the wild-type allele was present in 17 of 33 samples (52%). LOH of the CHEK2 wild-type allele was significantly more frequent in tumors with LOF mutations than in those with missense mutations (78% vs 36%, respectively; p=0.0394). PIK3CA (36%) and GATA3 (33%) were the two most recurrently mutated genes in these samples. TP53 somatic mutations were detected in five cases, four of which harbored missense CHEK2 germline mutations. Unlike BRCA1- and BRCA2-associated breast cancers, but akin to ATM-associated breast cancers, CHEK2-associated breast cancers lacked the mutational signature associated with homologous recombination (HR) DNA repair defects (i.e. signature 3) and only five cases displayed high LST scores.

Conclusion:CHEK2-associated breast cancers are phenotypically and genetically distinct from BRCA1- and BRCA2-associated breast cancers, but similar to ATM-associated breast cancers. Akin to ATM-associated breast cancers, CHEK2-associated breast cancers are preferentially ER-positive, lack genomics features consistent with defective HR, and have a repertoire of somatic genetic alterations similar to those of non-BRCA1/2 ER-positive breast cancers. Our results suggest that either CHEK2 germline mutations contribute to an increased risk of breast cancer independently of the HR DNA repair defects or that the mutational signatures caused by CHEK2 pathogenic germline mutations differ from those caused by pathogenic germline mutations affecting bona fide HR-related genes (e.g. BRCA1, BRCA2 and PALB2).

Citation Format: Kumar R, Pei X, Selenica P, Wen HY, Powell S, Robson M, Riaz N, Reis-Filho JS, Weigelt B, Mandelker D. The landscape of somatic genetic alterations in breast cancers from CHEK2 germline mutation carriers [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-04-01.

Consensus genetic linkage map construction and QTL mapping for plant height-related traits in linseed flax (Linum usitatissimum L.)

BACKGROUND

Flax is an important field crop that can be used for either oilseed or fiber production. Plant height and technical length are important characters for flax. For linseed flax, plants usually have a short technical length and plant height than those for fiber flax. As an important agronomical character for fiber and linseed flax, plant height is usually a selection target for breeding. However, because of limited technologies and methods available, there has been little research focused on discovering the molecular mechanism controlling plant height.

RESULTS

In this study, two related recombinant inbred line (RIL) populations developed from crosses of linseed and fiber parents were developed and phenotyped for plant height and technical length in four environments. A consensus linkage map based on two RIL populations was constructed using SNP markers generated by genotyping by sequencing (GBS) technology. A total of 4497 single nucleotide polymorphism (SNP) markers were included on 15 linkage groups with an average marker density of one marker every 2.71 cM. Quantitative trait locus (QTL) mapping analysis was performed for plant height and technical length using the two populations. A total of 19 QTLs were identified for plant height and technical length. For the MH population, eight plant height QTLs and seven technical length QTLs were identified, five of which were common QTLs for both traits. For the PH population, six plant height and three technical length QTLs were identified. By comparing the QTLs and candidate gene information in the two population, two common QTLs and three candidate genes were discovered.

CONCLUSIONS

This study provides a foundation for map-based cloning of QTLs and marker-assisted selection for plant height-related traits in linseed and fiber flax.

Consensus genetic linkage map construction and QTL mapping for plant height-related traits in linseed flax (Linum usitatissimum L.)

BACKGROUND

Flax is an important field crop that can be used for either oilseed or fiber production. Plant height and technical length are important characters for flax. For linseed flax, plants usually have a short technical length and plant height than those for fiber flax. As an important agronomical character for fiber and linseed flax, plant height is usually a selection target for breeding. However, because of limited technologies and methods available, there has been little research focused on discovering the molecular mechanism controlling plant height.

RESULTS

In this study, two related recombinant inbred line (RIL) populations developed from crosses of linseed and fiber parents were developed and phenotyped for plant height and technical length in four environments. A consensus linkage map based on two RIL populations was constructed using SNP markers generated by genotyping by sequencing (GBS) technology. A total of 4497 single nucleotide polymorphism (SNP) markers were included on 15 linkage groups with an average marker density of one marker every 2.71 cM. Quantitative trait locus (QTL) mapping analysis was performed for plant height and technical length using the two populations. A total of 19 QTLs were identified for plant height and technical length. For the MH population, eight plant height QTLs and seven technical length QTLs were identified, five of which were common QTLs for both traits. For the PH population, six plant height and three technical length QTLs were identified. By comparing the QTLs and candidate gene information in the two population, two common QTLs and three candidate genes were discovered.

CONCLUSIONS

This study provides a foundation for map-based cloning of QTLs and marker-assisted selection for plant height-related traits in linseed and fiber flax.

Combined analysis and miRNA expression profiles of the flowering related genes in common wild rice (oryza rufipogon Griff.)

Common wild rice (Oryza rufipogon Griff.) is the most closely related ancestral species to Asian cultivated rice (Oryza sativa L.). It contains various valuable traits with regard to tolerance to cold, drought and salinity, flowering diversity and many quantitative trait loci with agronomic important traits. Flowering is one of the most important agronomic traits. However, flowering-related transcriptome and how to be regulated by miRNAs have not been estimated in O.rufipogon. To identify how the genes and miRNAs regulating flowering in O.rufipogon. Three O.rufipogon RNA libraries, two vegetative stages (CWRT-V1 and CWRT-V2) and one flowering stage (CWRT-F2) were constructed using leaves tissue and sequenced using Illumina deep sequencing. 27,405, 27,333, 28,979 unique genes were obtained after mapping to the reference genome from CWRT-V1, CWRT-V2 and CWRT-F2, respectively. Then differentially expressed genes (DEGs) were screened and got 1419 unique genes are likely to involve in flower development. Detailed information showed that MADS box and floral meristem identity genes, such as MADS 1, MADS14, Hd1 are involved in common wild rice. Then, combined analysis of miRNA and mRNA expression profiles was performed. Twenty three known miRNA-mRNA pairs and five new candidates were presented an anti-correlationship. Interestingly, 12 miRNAs were negatively correlated with 20 mRNAs encoding flowering-related proteins, indicating that miRNAs regulated target genes to promote flowering in CWRT-F2 group. The results provided here genomic resources for flowering related genes and how these flowering genes were regulated by miRNAs in common wild rice.

Isolation and Characterization of a Green-Tissue Promoter from Common Wild Rice (Oryza rufipogon Griff.)

Promoters play a very important role in the initiation and regulation of gene transcription. Green-tissue promoter is of great significance to the development of genetically modified crops. Based on RNA-seq data and RT-PCR expression analysis, this study screened a gene, OrGSE (GREEN SPECIAL EXPRESS), which is expressed specifically in green tissues. The study also isolated the promoter of the OrGSE gene (OrGSEp), and predicted many cis-acting elements, such as the CAAT-Box and TATA-Box, and light-responding elements, including circadian, G-BOX and GT1 CONSENSUS. Histochemical analysis and quantification of GUS activity in transgenic Arabidopsis thaliana plants expressing GUS under the control of OrGSEp revealed that this promoter is not only green tissue-specific, but also light-inducible. The ability of a series of 5’-deletion fragments of OrGSEp to drive GUS expression in Arabidopsis was also evaluated. We found that the promoter region from −54 to −114 is critical for the promoter function, and the region from −374 to −114 may contain core cis-elements involved in light response. In transgenic rice expressing GUS under the control of OrGSEp, visualization and quantification of GUS activity showed that GUS was preferentially expressed in green tissues and not in endosperm. OrGSEp is a useful regulatory element for breeding pest-resistant crops.

Combination of apatinib and continuous nutritional support for a gastric cancer patient with brain metastasis prolongs survival

WHAT IS KNOWN AND OBJECTIVES

Gastric cancer is the most common gastrointestinal malignant tumour in China, which rarely metastasizes into the central nervous system. However, brain metastasis leads to increased risk of death.

CASE SUMMARY

Here, we report a case of brain metastasis from gastric cancer, which was treated with apatinib and continual nutritional support, with a survival time of 2 years.

WHAT IS NEW AND CONCLUSION

The combination of apatinib and continual nutritional support may be an option for the treatment of brain metastasis from gastric cancer. A prospective study should be performed to confirm this.

Biomechanics of Immediate Postextraction Implant Osseointegration

The aim of this study was to gain insights into the biology and mechanics of immediate postextraction implant osseointegration. To mimic clinical practice, murine first molar extraction was followed by osteotomy site preparation, specifically in the palatal root socket. The osteotomy was positioned such that it removed periodontal ligament (PDL) only on the palatal aspect of the socket, leaving the buccal aspect undisturbed. This strategy created 2 distinct peri-implant environments: on the palatal aspect, the implant was in direct contact with bone, while on the buccal aspect, a PDL-filled gap existed between the implant and bone. Finite element modeling showed high strains on the palatal aspect, where bone was compressed by the implant. Osteocyte death and bone resorption predominated on the palatal aspect, leading to the loss of peri-implant bone. On the buccal aspect, where finite element modeling revealed low strains, there was minimal osteocyte death and robust peri-implant bone formation. Initially, the buccal aspect was filled with PDL remnants, which we found directly provided Wnt-responsive cells that were responsible for new bone formation and osseointegration. On the palatal aspect, which was devoid of PDL and Wnt-responsive cells, adding exogenous liposomal WNT3A created an osteogenic environment for rapid peri-implant bone formation. Thus, we conclude that low strain and high Wnt signaling favor osseointegration of immediate postextraction implants. The PDL harbors Wnt-responsive cells that are inherently osteogenic, and if the PDL tissue is healthy, it is reasonable to preserve this tissue during immediate implant placement.

A Comparative Assessment of Implant Site Viability in Humans and Rats

Our long-term objective is to devise methods to improve osteotomy site preparation and, in doing so, facilitate implant osseointegration. As a first step in this process, we developed a standardized oral osteotomy model in ovariectomized rats. There were 2 unique features to this model: first, the rats exhibited an osteopenic phenotype, reminiscent of the bone health that has been reported for the average dental implant patient population. Second, osteotomies were produced in healed tooth extraction sites and therefore represented the placement of most implants in patients. Commercially available drills were then used to produce osteotomies in a patient cohort and in the rat model. Molecular, cellular, and histologic analyses demonstrated a close alignment between the responses of human and rodent alveolar bone to osteotomy site preparation. Most notably in both patients and rats, all drilling tools created a zone of dead and dying osteocytes around the osteotomy. In rat tissues, which could be collected at multiple time points after osteotomy, the fate of the dead alveolar bone was followed. Over the course of a week, osteoclast activity was responsible for resorbing the necrotic bone, which in turn stimulated the deposition of a new bone matrix by osteoblasts. Collectively, these analyses support the use of an ovariectomy surgery rat model to gain insights into the response of human bone to osteotomy site preparation. The data also suggest that reducing the zone of osteocyte death will improve osteotomy site viability, leading to faster new bone formation around implants.

The applied value of medical history, physical examination, colour-Doppler ultrasonography and testis scintigraphy in the differential diagnosis of acute scrotum

Acute scrotum, especially testicular torsion, is a common surgical emergency. A delay in diagnosis or management may lead to permanent testicular ischaemic damage. Thus, it is particularly important to differentiate testicular torsion from other acute scrotum conditions as soon as possible. Our study has retrospectively investigated 358 patients with acute scrotum admitted to our hospital from the year 2007 to 2016. We have collected a thorough history and clinical data and drew the conclusion by comparing clinical features of different acute scrotum cases, medical history, imaging and surgical findings. Therefore, we propose an innovative "Testicular Torsion (TT) Green Channel" concept. Through the combination of a comprehensive medical history, physical examination and auxiliary colour-Doppler ultrasonography, the diagnosis of testicular torsion is definite in most circumstances. Testis scintigraphy is a novel and complementary diagnostic modality that can reduce the negative exploration rate in ambiguous and certain cases. The TT Green Channel is a new concept in the management of testicular torsion.

A Wnt-Responsive PDL Population Effectuates Extraction Socket Healing

Stem cells residing in the periodontal ligament (PDL) support the homeostasis of the periodontium, but their in vivo identity, source(s), and function(s) remain poorly understood. Here, using a lineage-tracing mouse strain, we identified a quiescent Wnt-responsive population in the PDL that became activated in response to tooth extraction. The Wnt-responsive population expanded by proliferation, then migrated from the PDL remnants that remained attached to bundle bone, into the socket. Once there, the Wnt-responsive progeny upregulated osteogenic protein expression, differentiated into osteoblasts, and generated the new bone that healed the socket. Using a liposomal WNT3A protein therapeutic, we showed that a single application at the time of extraction was sufficient to accelerate extraction socket healing 2-fold. Collectively, these data identify a new stem cell population in the intact periodontium that is directly responsible for alveolar bone healing after tooth removal.

Identification and functional analysis of two alternatively spliced transcripts of ABSCISIC ACID INSENSITIVE3 (ABI3) in linseed flax (Linum usitatissimum L.)

Alternative splicing is a popular phenomenon in different types of plants. It can produce alternative spliced transcripts that encode proteins with altered functions. Previous studies have shown that one transcription factor, ABSCISIC ACID INSENSITIVE3 (ABI3), which encodes an important component in abscisic acid (ABA) signaling, is subjected to alternative splicing in both mono- and dicotyledons. In the current study, we identified two homologs of ABI3 in the genome of linseed flax. We screened two alternatively spliced flax LuABI3 transcripts, LuABI3-2 and LuABI3-3, and one normal flax LuABI3 transcript, LuABI3-1. Sequence analysis revealed that one of the alternatively spliced transcripts, LuABI3-3, retained a 6 bp intron. RNA accumulation analysis showed that all three transcripts were expressed during seed development, while subcellular localization and transgene experiments showed that LuABI3-3 had no biological function. The two normal transcripts, LuABI3-1 and LuABI3-2, are the important functional isoforms in flax and play significant roles in the ABA regulatory pathway during seed development, germination, and maturation.

Role of Autophagy in Ovarian Cryopreservation by Vitrification

BACKGROUND

Ovarian cryopreservation by vitrification and transplantation are useful methods to recover female fertility after radiotherapy and chemotherapy. As type II programmed cell death, autophagy plays important roles in ovarian follicle development, ovarian follicle atresia and anti-stress injury.

OBJECTIVE

The potential role of autophagy in ovarian vitrification was investigated.

MATERIALS AND METHODS

Mouse ovaries were cryopreserved by vitrification, and autophagy was treated, after which the ovarian histology was checked, and ovarian follicles were counted. The apoptotic rate was detected by TUNEL, and apoptotic molecular marker cleaved caspase-3 was checked by immunofluorescence and western blot analysis.

RESULTS

Our results suggested that autophagy was increased in the process of vitrification compared with the fresh ovaries (p<0.05). The number of primordial follicles was decreased through inhibiting or over-activating the autophagy by autophagy inhibitor or activator (p<0.05). However, the number of primary follicles, antral follicles and atretic follicles was not significantly different compared with vitrified/warmed groups. The apoptotic rate was significantly increased in the vitrified/warmed, autophagy-inhibiting and over-activating groups compared with the fresh group (p<0.05), and this result was further confirmed by western blot analysis.

CONCLUSIONS

Taken together, autophagy was activated in the ovarian cryopreservation by vitrification and plays a role in a natural adaptive response to cold stress in ovarian cryopreservation by vitrification.

Levothyroxine monotherapy versus levothyroxine and selenium combination therapy in chronic lymphocytic thyroiditis

PURPOSE

New strategies are needed for prevention and treatment of chronic lymphocytic thyroiditis (CLT). This study aimed to assess whether combination of levothyroxine treatment and selenium (Se) supplementation results in improved therapeutic effects in CLT compared with levothyroxine monotherapy.

METHODS

An open-label, randomized controlled study was performed in 60 CLT patients assigned to two groups. Levothyroxine group (LT) patients (n = 24) received levothyroxine alone for 3 months; meanwhile, the combination (LTSS) group (n = 36) was administered levothyroxine with selenium yeast capsule. Blood selenium concentrations, anti-thyroid peroxidase (TPO) and anti-thyroglobulin (Tg) antibody levels, and inflammatory cytokine amounts were compared between both groups before and after treatment.

RESULTS

At baseline, similar values were obtained in both groups for all the parameters assessed (p > 0.05). After treatment, significantly increased blood selenium levels (µg/L) [90.05 (80.69, 107.76) vs. 39.64 (29.42, 51.10), p < 0.001] and decreased anti-TPO antibody (23.63 ± 9.31 vs. 32.00 ± 10.41%, p = 0.002), anti-Tg antibody (35.84 ± 15.21 vs. 45.47 ± 14.24%, p = 0.015) and IL-2 amounts (pg/mL) [159.29 (124.54, 189.70) vs. 226.48 (190.74, 266.56), p < 0.001] were observed in the LTSS group compared with the LT group post-treatment; meanwhile, similar IL-10 concentrations [23.14 (21.65, 28.56) pg/mL vs. 24.68 (21.71, 29.67) pg/mL] were obtained in both groups. Subgroup analysis of patients with hypothyroidism showed the same trend observed in the whole population; in patients with normal thyroid function, only Se and IL-2 amounts differed between the two treatment groups. Correlation analysis of of the indexes: in HT patients, the basal serum selenium concentration was positively correlated with TT₄ (r = 0.294, p < 0.05), significantly negatively correlated with TSH (r = -0.343, p < 0.01), and had no significant correlation with TT3 (p > 0.05).

CONCLUSIONS

These findings indicated that levothyroxine and selenium combination results in improved therapeutic effects than the levothyroxine monotherapy in preventing CLT progression.