An inducible CRISPR activation tool for accelerating plant regeneration

The inducible CRISPR activation (CRISPR-a) system offers unparalleled precision and versatility for regulating endogenous genes, making it highly sought after in plant research. In this study, we developed a chemically inducible CRISPR-a tool for plants called ER-Tag by combining the LexA-VP16-ER inducible system with the SunTag CRISPR-a system. We systematically compared different induction strategies and achieved high efficiency in target gene activation. We demonstrated that guide RNAs can be multiplexed and pooled for large-scale screening of effective morphogenic genes and gene pairs involved in plant regeneration. Further experiments showed that induced activation of these morphogenic genes can accelerate regeneration and improve regeneration efficiency in both eudicot and monocot plants, including alfalfa, woodland strawberry, and sheepgrass. Our study expands the CRISPR toolset in plants and provides a powerful new strategy for studying gene function when constitutive expression is not feasible or ideal.

Coronary microvascular dysfunction: prevalence and aetiology in patients with suspected myocardial ischaemia

AIM

To evaluate the prevalence, aetiology, and corresponding morbidity of coronary microvascular dysfunction (CMD) in patients with suspected myocardial ischaemia.

MATERIALS AND METHODS

The present study included 115 patients with suspected myocardial ischaemia who underwent stress perfusion cardiac magnetic resonance imaging. CMD was assessed visually based on the myocardial perfusion results. The CMR-derived myocardial perfusion reserve index (MPRI) and left ventricular (LV) strain parameters obtained using the post-processing software CVI42 were employed to evaluate LV myocardial perfusion and deformation. LV strain parameters included global longitudinal, circumferential, and radial strain (GLS, GCS, and GRS), global systolic/diastolic longitudinal, circumferential, and radial strain rates (SLSR, SCSR, SRSR, DLSR, DCSR, and DRSR).

RESULTS

Of the 115 patients, 12 patients were excluded and 103 patients were finally included in the study. CMD was observed in 79 % (81 patients, aged 53 ± 12 years) of patients. Regarding aetiology, 91 (88 %) patients had non-obstructive coronary artery disease (CAD), eight (8 %) had obstructive CAD, and four (4 %) had hypertrophic cardiomyopathy (HCM). The incidence of CMD was highest (100 %) in patients with HCM, followed by those with non-obstructive CAD (up to 79 %). There were no statistical differences between CMD and non-CMD groups in GCS, GRS, GLS, SRSR, SCSR, SLSR, DCSR, DRSR and DLSR.

CONCLUSION

The incidence of CMD was higher in patients with signs and symptoms of ischaemia. CMD occurred with non-obstructive CAD, obstructive CAD, and HCM, with the highest prevalence of CMD in HCM.

[Upregulating KLF11 ameliorates intestinal inflammation in mice with 2, 4, 6-trinitrobenesulfonic acid-induced colitis by inhibiting the JAK2/STAT3 signaling pathway]

OBJECTIVE

To investigate the expression level of Kruppel-like transcription factor family member KLF11 in intestinal mucosal tissues of Crohn's disease (CD) and its regulatory effect on intestinal inflammation in CD-like colitis.

METHODS

We examined KLF11 expression levels in diseased and normal colon mucosal tissues from 12 CD patients and 12 patients with colorectal cancer using immunofluorescence staining. KLF11 expression was also detected in the colon mucosal tissues of a mouse model of 2, 4, 6-trinitrobenesulfonic acid (TNBS)-induced colitis. A recombinant adenoviral vector was used to upregulate KLF11 expression in the mouse models and the changes in intestinal inflammation was observed. A Caco-2 cell model with stable KLF11 overexpression was constructed by lentiviral infection. The effect of KLF11 overexpression on expressions of JAK2/STAT3 signaling pathway proteins was investigated using immunoblotting in both the mouse and cell models. The mouse models were treated with coumermycin A1, a JAK2/STAT3 signaling pathway agonist, and the changes in intestinal inflammatory responses were observed.

RESULTS

The expression level of KLF11 was significantly lowered in both the clinical specimens of diseased colon mucosal tissues and the colon tissues of mice with TNBS-induced colitis (P < 0.05). Adenovirus-mediated upregulation of KLF11 significantly improved intestinal inflammation and reduced the expression levels of inflammatory factors in the intestinal mucosa of the colitis mouse models (P < 0.05). Overexpression of KLF11 significantly inhibited the expression levels of p-JAK2 and p-STAT3 in intestinal mucosal tissues of the mouse models and in Caco-2 cells (P < 0.05). Treatment with coumermycin A1 obviously inhibited the effect of KLF11 upregulation for improving colitis and significantly increased the expression levels of inflammatory factors in the intestinal mucosa of the mouse models (P < 0.05).

CONCLUSION

KLF11 is downregulated in the intestinal mucosa in CD, and upregulation of KLF11 can improve intestinal inflammation and reduce the production of inflammatory factors probably by inhibiting the JAK2/STAT3 signaling pathway.

[Effect of HBV DNA load on the safety and prognosis of systematic therapy in advanced hepatocellular carcinoma]

Objective: To study the effect of hepatitis B virus (HBV) infection on the occurrence of liver damage, HBV reactivation (HBVr) and the influence of HBVr on the prognosis of patients with advanced hepatocellular carcinoma (HCC) receiving systemic therapy. Methods: The clinical data of 403 patients with HBV-related HCC at the Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-Sen University et al, from July 2018 to December 2020 were collected. The incidence of liver damage and HBVr during systematic therapy, and the influence of HBVr on survival prognosis were analyzed. Results: Of the 403 patients, 89.1% were male (n=359), with a median age of 51 years (51.5±12.1). Before propensity score matching (PSM), the proportion of patients with cirrhosis, TNM and advanced BCLC stage was higher in high HBV-DNA (baseline HBV-DNA>1000 U/ml, n=147) group comparing with the low HBV-DNA (baseline HBV DNA≤1000 u/ml, n=256) group (P<0.05). There was no significant difference in baseline indexes between the two groups after PSM. In 290 patients after PSM, there was no significant difference in the incidence of liver damage and HBVr between high HBV-DNA group and low HBV-DNA group (P>0.05). Survival analysis was performed on 169 patients with survival data, the median overall survival (OS) was found to be 11.49 months (95%CI: 7.77-12.89) and 16.65 months (95%CI: 10.54-21.99, P=0.008) in the high and low HBV-DNA groups, respectively. And median progression-free survival (PFS) was 7.41 months (95%CI: 5.06-8.67) and 10.55 months (95%CI: 6.72-13.54, P=0.038), respectively, with a statistically significant difference. There were no differences in overall survival (OS) and progression-free survival (PFS) between patients with and without HBVr and those with or without liver damage (P>0.05). Conclusions: HBV-DNA levels above 1 000 U/ml before systemic therapy do not increase the risk of liver damage or HBVr during systemic therapy in patients with HBV-related hepatocellular carcinoma, and such patients can safely receive systemic therapy.

Antiviral effect of palmatine against infectious bronchitis virus through regulation of NF-κB/IRF7/JAK-STAT signalling pathway and apoptosis

1. Infectious bronchitis virus (IBV), a gamma-coronavirus, can infect chickens of all ages and leads to an acute contact respiratory infection. This study evaluated the anti-viral activity of palmatine, a natural non-flavonoid alkaloid, against IBV in chicken embryo kidney (CEK) cells.2. The half toxic concentration (CC50) of palmatine was 672.92 μM, the half inhibitory concentration (IC50) of palmatine against IBV was 7.76 μM and the selection index (SI) was 86.74.3. Mode of action assay showed that palmatine was able to directly inactivate IBV and inhibited the adsorption, penetration and intracellular replication of IBV.4. Palmatine significantly upregulated TRAF6, TAB1 and IKK-β compared with the IBV-infected group, leading to the increased expressions of pro-inflammatory cytokines IL-1β and TNF-α in the downstream NF-κB signalling pathway.5. Palmatine significantly up-regulated the levels of MDA5, MAVS, IRF7, IFN-α and IFN-β in the IRF7 pathway, inducing type I interferon production. It up-regulated the expression of 2'5'-oligoadenylate synthase (OAS) in the JAK-STAT pathway.6. IBV infection induced cell apoptosis and palmatine-treatment delayed the process of apoptosis by regulation of the expression of apoptosis-related genes (BAX, BCL-2, CASPASE-3 and CASPASE-8).7. Palmatine could exert anti-IBV activity through regulation of NF-κB/IRF7/JAK-STAT signalling pathways and apoptosis, providing a theoretical basis for the utilisation of palmatine to treat IBV infection.

Efficacy and safety of intrathecal pemetrexed for TKI-failed leptomeningeal metastases from EGFR+ NSCLC: an expanded, single-arm, phase II clinical trial

BACKGROUND

This study aimed to evaluate the efficacy and safety of intrathecal pemetrexed (IP) for treating patients with leptomeningeal metastases (LM) from non-small-cell lung cancer (NSCLC) who progressed from epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitor (TKI) treatment in an expanded, prospective, single-arm, phase II clinical study (ChiCTR1800016615).

PATIENTS AND METHODS

Patients with confirmed NSCLC-LM who progressed from TKI received IP (50 mg, day 1/day 5 for 1 week, then every 3 weeks for four cycles, and then once monthly) until disease progression or intolerance. Objectives were to assess overall survival (OS), response rate, and safety. Measurable lesions were assessed by investigator according to RECIST version 1.1. LM were assessed according to the Response Assessment in Neuro-Oncology (RANO) criteria.

RESULTS

The study included 132 patients; 68% were female and median age was 52 years (31-74 years). The median OS was 12 months (95% confidence interval 10.4-13.6 months), RANO-assessed response rate was 80.3% (106/132), and the most common adverse event was myelosuppression (n = 42; 31.8%), which reversed after symptomatic treatment. The results of subgroup analysis showed that absence of brain parenchymal metastasis, good Eastern Cooperative Oncology Group score, good response to IP treatment, negative cytology after treatment, and patients without neck/back pain/difficult defecation had longer survival. Gender, age, previous intrathecal methotrexate/cytarabine, and whole-brain radiotherapy had no significant influence on OS.

CONCLUSIONS

This study further showed that IP is an effective and safe treatment method for the EGFR-TKI-failed NSCLC-LM, and should be recommended for these patients in clinical practice and guidelines.

Relationship between coronary microvascular dysfunction (CMD) and left ventricular diastolic function in patients with symptoms of myocardial ischemia with non-obstructive coronary artery disease (INOCA) by cardiovascular magnetic resonance feature-tracking

AIM

To investigate whether there was an association between coronary microvascular dysfunction (CMD) and left ventricular (LV) diastolic function in patients with myocardial ischemia with non-obstructive coronary artery disease (INOCA).

MATERIALS AND METHODS

Our study included 115 subjects with suspected myocardial ischemia that underwent stress perfusion cardiac magnetic resonance (CMR). They were divided into non-CMD and CMD two groups. CMR-derived volume-time curves and CMR-FT parameters were used to assess LV diastolic function using CVI42 software. The latter included global/regional LV peak longitudinal, circumferential, radial diastolic strain rate (LDSR, CDSR, RDSR). Logistic regression analysis was performed with CMR-FT strain parameters as independent variables and CMD as dependent variables, and the effect value was expressed as an odds ratio (OR).

RESULTS

Of the 115 patients, we excluded data from 23 patients and 92 patients (56.5% male；52 ± 12 years) were finally included in the study. Of these, 19 patients were included in the non-CMD group (49 ± 11 years) and CMD group included 73patient (52 ± 12 years). The regional CDSR (P=0.019), and regional RDSR (P=0.006) were significantly lower in the CMD group than in non-CMD group. But, regional LDSR in CMD group was higher than non-CMD (P=0.003). In logistic regression analysis, regional LDSR (adjusted β= 0.1, 95%CI 0.077, 0.349, p=0.002) and RDSR (adjusted β= 0.1, 95 % CI 0.066, 0.356, p=0.004) were related to CMD.

CONCLUSIONS

LV myocardial perfusion parameter MPRI was negatively correlated with LV diastolic function (CDSR) which needs to take into account the degree of diastolic dysfunction.

Acyl carrier protein OsMTACP2 confers rice cold tolerance at the booting stage

Low temperatures occurring at the booting stage in rice (Oryza sativa L.) often result in yield loss by impeding male reproductive development. However, the underlying mechanisms by which rice responds to cold at this stage remain largely unknown. Here, we identified MITOCHONDRIAL ACYL CARRIER PROTEIN 2 (OsMTACP2), the encoded protein of which mediates lipid metabolism involved in the cold response at the booting stage. Loss of OsMTACP2 function compromised cold tolerance, hindering anther cuticle and pollen wall development, resulting in abnormal anther morphology, lower pollen fertility and seed setting. OsMTACP2 was highly expressed in tapetal cells and microspores during anther development, with the encoded protein localizing to both mitochondria and the cytoplasm. Comparative transcriptomic analysis revealed differential expression of genes related to lipid metabolism between the wild type and the Osmtacp2-1 mutant in response to cold. Through a lipidomic analysis, we demonstrated that wax esters, which are the primary lipid components of the anther cuticle and pollen walls, function as cold-responsive lipids. Their levels increased dramatically in the wild type but not in Osmtacp2-1 when exposed to cold. Additionally, mutants of two cold induced genes of wax ester biosynthesis, ECERIFERUM1 and WAX CRYSTAL-SPARSE LEAF2, showed decreased cold tolerance. These results suggest that OsMTACP2-mediated wax ester biosynthesis is essential for cold tolerance in rice at the booting stage.

[The cutoff value of small airway dysfunction in children with bronchial asthma]

Objective: To explore the cutoff value for assessing small airway dysfunction in children with asthma. Methods: A total of 364 asthmatic children aged 5 to 14 years, with normal ventilatory function, followed up at the Asthma Clinic of the Children's Hospital of Capital Institute of Pediatrics from January 2017 to January 2018, were selected as the case group. Concurrently, 403 healthy children of the same age range and without any symptoms in the community were chosen as the control group, and pulmonary function tests were conducted. The values of forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC), forced expiratory flow at 50% of FVC (FEF50), forced expiratory flow at 75% of FVC (FEF75) and maximum mid-expiratory flow (MMEF) were compared between case group and control group. Statistical tests such as t-test, χ2 test, or Mann-Whitney U test were used to analyze the differences between the groups. Receiver operating characteristic (ROC) curves were constructed, and the maximum Youden Index was utilized to determine the optimal cutoff values and thresholds for identifying small airway dysfunction in asthmatic children. Results: This study comprised 364 children in the case group (220 boys and 144 girls) and 403 children in the control group (198 boys and 205 girls). The small airway parameters (FEF50%pred, FEF75%pred, MMEF%pred) in the asthmatic group were significantly lower than in the control group (77% (69%, 91%) vs. 95% (83%, 109%), 67% (54%, 82%) vs. 84% (70%, 102%), 76% (66%, 90%) vs. 97% (86%, 113%), Z=12.03, 11.35, 13.66, all P<0.001). The ROC curve area under the curve for FEF50%pred, FEF75%pred, MMEF%pred was 0.75, 0.74, and 0.79, respectively. Using a cutoff value of 80% for FEF50%pred achieved a sensitivity of 56.9% and specificity of 81.4%. A cutoff value of 74% for FEF75%pred resulted in a sensitivity of 67.3% and specificity of 69.2%. Finally, using a cutoff value of 84% for MMEF%pred achieved a sensitivity of 67.9% and specificity of 77.2%. Conclusion: In the presence of normal ventilatory function, utilizing FEF50<80% predicted or MMEF<84% predicted can accurately serve as criteria for identifying small airway dysfunction in children with controlled asthma.

Blocking miR528 function promotes tillering and regrowth in switchgrass

MiRNAs have been reported to be the key regulators involving a wide range of biological processes in diverse plant species, but their functions in switchgrass, an important biofuel and forage crop, are largely unknown. Here, we reported the novel function of miR528, which has expanded to four copies in switchgrass, in controlling biomass trait of tillering number and regrowth rate after mowing. Blocking miR528 activity by expressing short tandem target mimic (STTM) increased tiller number and regrowth rate after mowing. The quadruple pvmir528 mutant lines derived from genome editing also showed such improved traits. Degradome and RNA-seq analysis, combined with in situ hybridization assay revealed that up-regulation of two miR528 targets coding for Cu/Zn-SOD enzymes, might be responsible for the improved traits of tillering and regrowth in pvmir528 mutant. Additionally, natural variations in the miR528-SOD interaction exist in C3 and C4 monocot species, implying the distinct regulatory strength of the miR528-SOD module during monocot evolution. Overall, our data illuminated a novel role of miR528 in controlling biomass traits and provided a new target for genetic manipulation-mediated crop improvement.

Dynamic root microbiome sustains soybean productivity under unbalanced fertilization

Root-associated microbiomes contribute to plant growth and health, and are dynamically affected by plant development and changes in the soil environment. However, how different fertilizer regimes affect quantitative changes in microbial assembly to effect plant growth remains obscure. Here, we explore the temporal dynamics of the root-associated bacteria of soybean using quantitative microbiome profiling (QMP) to examine its response to unbalanced fertilizer treatments (i.e., lacking either N, P or K) and its role in sustaining plant growth after four decades of unbalanced fertilization. We show that the root-associated bacteria exhibit strong succession during plant development, and bacterial loads largely increase at later stages, particularly for Bacteroidetes. Unbalanced fertilization has a significant effect on the assembly of the soybean rhizosphere bacteria, and in the absence of N fertilizer the bacterial community diverges from that of fertilized plants, while lacking P fertilizer impedes the total load and turnover of rhizosphere bacteria. Importantly, a SynCom derived from the low-nitrogen-enriched cluster is capable of stimulating plant growth, corresponding with the stabilized soybean productivity in the absence of N fertilizer. These findings provide new insights in the quantitative dynamics of the root-associated microbiome and highlight a key ecological cluster with prospects for sustainable agricultural management.

The Simons Observatory: Cryogenic half wave plate rotation mechanism for the small aperture telescopes

We present the requirements, design, and evaluation of the cryogenic continuously rotating half-wave plate (CHWP) for the Simons Observatory (SO). SO is a cosmic microwave background polarization experiment at Parque Astronómico de Atacama in northern Chile that covers a wide range of angular scales using both small (⌀0.42 m) and large (⌀6 m) aperture telescopes. In particular, the small aperture telescopes (SATs) focus on large angular scales for primordial B-mode polarization. To this end, the SATs employ a CHWP to modulate the polarization of the incident light at 8 Hz, suppressing atmospheric 1/f noise and mitigating systematic uncertainties that would otherwise arise due to the differential response of detectors sensitive to orthogonal polarizations. The CHWP consists of a 505 mm diameter achromatic sapphire HWP and a cryogenic rotation mechanism, both of which are cooled down to ∼50 K to reduce detector thermal loading. Under normal operation, the HWP is suspended by a superconducting magnetic bearing and rotates with a constant 2 Hz frequency, controlled by an electromagnetic synchronous motor. We find that the number of superconductors and the number of magnets that make up the superconducting magnetic bearing are important design parameters, especially for the rotation mechanism's vibration performance. The rotation angle is detected through an angular encoder with a noise level of 0.07 μrad s. During a cooldown process, the rotor is held in place by a grip-and-release mechanism that serves as both an alignment device and a thermal path. In this paper, we provide an overview of the SO SAT CHWP: its requirements, hardware design, and laboratory performance.

Pericoronary adipose tissue attenuation predicts outcome of percutaneous intervention for chronic total occlusion

AIM

To investigate the association between pericoronary adipose tissue (PCAT) attenuation (PCATA) and outcomes of chronic total occlusion (CTO) after percutaneous coronary intervention (PCI), and to establish a clinical model that can be easily generalised to predict the outcomes of PCI-CTO.

MATERIALS AND METHODS

Between September 2015 and September 2019, patients from two centres were enrolled retrospectively. The primary endpoint was a procedural success (defined as achieving residual stenosis of <30% and a grade 3 thrombolysis in myocardial infarction [TIMI] flow). The new predictive model was generated by factors that were determined by multivariate analysis. The PCATA of CTO (PCATA-CTO) score was developed by assigning 1 point for each independent predictor, and then summing all points accrued. In addition, the predictive efficacy and interobserver and intraobserver agreement of PCATA-CTO and other scoring systems based on coronary computed tomography angiography (CCTA) were compared.

RESULTS

A total of 201 patients (mean age 58.9 ± 10.8 years, 85% male) were enrolled. The PCI success was achieved in 76% of the lesions. PCAT was higher in the PCI success group (-72.44 ± 10.45HU versus -76.76 ± 10.54 HU, p<0.05). Multivariable analysis yielded severe calcification, lesion length ≥15 mm, and perivascular fat attenuation index (FAI) ≤-69.5HU as independent negative predictors for procedural success. The area under the receiver operating characteristic curves for the PCATA-CTO score was 0.72. Comparing the PCATA-CTO score with other predictive scores, the PCATA-CTO score showed the highest interobserver (kappa = 0.74) and intraobserver agreement (kappa = 0.90, all p<0.01).

CONCLUSION

FAI ≤-69.5HU is an independent negative predictor of procedural success. The PCATA-CTO score improved the reliability of the prediction model. Its potential for clinical implementation requires evaluation.

[Analysis on the use of HIV post-exposure prophylaxis and related factors in men who have sex with men in Qingdao]

Objective: To understand the use of post-exposure prophylaxis (PEP) and analyze related factors among men who have sex with men (MSM) in Qingdao, and provide a reference for the AIDS prevention and control in this population. Methods: A cross-sectional survey conducted from April 2022 to February 2023. Relying on MSM social groups in Qingdao, a snowball sampling method was applied to recruit research subjects who met the inclusion criteria of age ≥18 years old, having had homosexual anal or oral sex in the past six months, and HIV-negative or infection status unknown. The sample size was estimated at 566. Data on demographic characteristics, sexual behavior characteristics, PEP use, and others of the research subjects was collected through on-site questionnaires. The logistic regression model was used to analyze the factors associated with using PEP. Results: A total of 811 participants were recruited, mainly aged 25-34 (53.6%, 435/811), unmarried (74.7%, 606/811), with an average monthly income of ≥5 000 yuan (52.2%, 423/811), and having lived in Qingdao for ≥10 years (75.6%, 613/811). The proportion of those who knew the HIV status of their sexual partners in the last six months was 67.1% (544/811), and those with HIV-positive partners were 3.6% (29/811). In the last six months, the proportion of participants who had group sex (86.4%, 701/811), unprotected anal sex (98.2%, 796/811), and use of club drugs (80.3%, 651/811) was high. Moreover, 28.4% (230/811) had used PEP. The multivariate logistic regression analysis showed that the factors related to the use of PEP included divorced or widowed (aOR=5.46,95%CI:1.96-15.17), average monthly income ≥5 000 yuan (aOR=2.04,95%CI:1.44-2.89), same-sex sexual orientation (aOR=0.40,95%CI:0.22-0.71), having HIV-positive sexual partners in the last six months (aOR=2.54,95%CI:1.13-5.71) and having been tested for HIV ≥3 times in the last six months (aOR=1.46,95%CI:1.04-2.06). Conclusions: The prevalence of risk behaviors among MSM in Qingdao was high, and the use of PEP was low. In the future, it is essential to increase HIV/AIDS prevention education among MSM, promote MSM to know the HIV status of their sexual partners, and reduce the prevalence of risk behaviors among this population. Additionally, explore medical insurance reimbursement plans for PEP to reduce utilization costs and promote the use of PEP by MSM after HIV exposure occurs as soon as possible.

Telomere-to-telomere genome of the allotetraploid legume Sesbania cannabina reveals transposon-driven subgenome divergence and mechanisms of alkaline stress tolerance

Alkaline soils pose an increasing problem for agriculture worldwide, but using stress-tolerant plants as green manure can improve marginal land. Here, we show that the legume Sesbania cannabina is very tolerant to alkaline conditions and, when used as a green manure, substantially improves alkaline soil. To understand genome evolution and the mechanisms of stress tolerance in this allotetraploid legume, we generated the first telomere-to-telomere genome assembly of S. cannabina spanning ∼2,087 Mb. The assembly included all centromeric regions, which contain centromeric satellite repeats, and complete chromosome ends with telomeric characteristics. Further genome analysis distinguished A and B subgenomes, which diverged approximately 7.9 million years ago. Comparative genomic analysis revealed that the chromosome homoeologs underwent large-scale inversion events (>10 Mb) and a significant, transposon-driven size expansion of the chromosome 5A homoeolog. We further identified four specific alkali-induced phosphate transporter genes in S. cannabina; these may function in alkali tolerance by relieving the deficiency in available phosphorus in alkaline soil. Our work highlights the significance of S. cannabina as a green tool to improve marginal lands and sheds light on subgenome evolution and adaptation to alkaline soils.

Effects of empagliflozin on progression of chronic kidney disease: a prespecified secondary analysis from the empa-kidney trial

BACKGROUND

Sodium-glucose co-transporter-2 (SGLT2) inhibitors reduce progression of chronic kidney disease and the risk of cardiovascular morbidity and mortality in a wide range of patients. However, their effects on kidney disease progression in some patients with chronic kidney disease are unclear because few clinical kidney outcomes occurred among such patients in the completed trials. In particular, some guidelines stratify their level of recommendation about who should be treated with SGLT2 inhibitors based on diabetes status and albuminuria. We aimed to assess the effects of empagliflozin on progression of chronic kidney disease both overall and among specific types of participants in the EMPA-KIDNEY trial.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA), and included individuals aged 18 years or older with an estimated glomerular filtration rate (eGFR) of 20 to less than 45 mL/min per 1·73 m2, or with an eGFR of 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher. We explored the effects of 10 mg oral empagliflozin once daily versus placebo on the annualised rate of change in estimated glomerular filtration rate (eGFR slope), a tertiary outcome. We studied the acute slope (from randomisation to 2 months) and chronic slope (from 2 months onwards) separately, using shared parameter models to estimate the latter. Analyses were done in all randomly assigned participants by intention to treat. EMPA-KIDNEY is registered at ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and then followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroups of eGFR included 2282 (34·5%) participants with an eGFR of less than 30 mL/min per 1·73 m2, 2928 (44·3%) with an eGFR of 30 to less than 45 mL/min per 1·73 m2, and 1399 (21·2%) with an eGFR 45 mL/min per 1·73 m2 or higher. Prespecified subgroups of uACR included 1328 (20·1%) with a uACR of less than 30 mg/g, 1864 (28·2%) with a uACR of 30 to 300 mg/g, and 3417 (51·7%) with a uACR of more than 300 mg/g. Overall, allocation to empagliflozin caused an acute 2·12 mL/min per 1·73 m2 (95% CI 1·83-2·41) reduction in eGFR, equivalent to a 6% (5-6) dip in the first 2 months. After this, it halved the chronic slope from -2·75 to -1·37 mL/min per 1·73 m2 per year (relative difference 50%, 95% CI 42-58). The absolute and relative benefits of empagliflozin on the magnitude of the chronic slope varied significantly depending on diabetes status and baseline levels of eGFR and uACR. In particular, the absolute difference in chronic slopes was lower in patients with lower baseline uACR, but because this group progressed more slowly than those with higher uACR, this translated to a larger relative difference in chronic slopes in this group (86% [36-136] reduction in the chronic slope among those with baseline uACR <30 mg/g compared with a 29% [19-38] reduction for those with baseline uACR ≥2000 mg/g; ptrend<0·0001).

INTERPRETATION

Empagliflozin slowed the rate of progression of chronic kidney disease among all types of participant in the EMPA-KIDNEY trial, including those with little albuminuria. Albuminuria alone should not be used to determine whether to treat with an SGLT2 inhibitor.

FUNDING

Boehringer Ingelheim and Eli Lilly.

Impact of primary kidney disease on the effects of empagliflozin in patients with chronic kidney disease: secondary analyses of the EMPA-KIDNEY trial

BACKGROUND

The EMPA-KIDNEY trial showed that empagliflozin reduced the risk of the primary composite outcome of kidney disease progression or cardiovascular death in patients with chronic kidney disease mainly through slowing progression. We aimed to assess how effects of empagliflozin might differ by primary kidney disease across its broad population.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA). Patients were eligible if their estimated glomerular filtration rate (eGFR) was 20 to less than 45 mL/min per 1·73 m2, or 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher at screening. They were randomly assigned (1:1) to 10 mg oral empagliflozin once daily or matching placebo. Effects on kidney disease progression (defined as a sustained ≥40% eGFR decline from randomisation, end-stage kidney disease, a sustained eGFR below 10 mL/min per 1·73 m2, or death from kidney failure) were assessed using prespecified Cox models, and eGFR slope analyses used shared parameter models. Subgroup comparisons were performed by including relevant interaction terms in models. EMPA-KIDNEY is registered with ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroupings by primary kidney disease included 2057 (31·1%) participants with diabetic kidney disease, 1669 (25·3%) with glomerular disease, 1445 (21·9%) with hypertensive or renovascular disease, and 1438 (21·8%) with other or unknown causes. Kidney disease progression occurred in 384 (11·6%) of 3304 patients in the empagliflozin group and 504 (15·2%) of 3305 patients in the placebo group (hazard ratio 0·71 [95% CI 0·62-0·81]), with no evidence that the relative effect size varied significantly by primary kidney disease (pheterogeneity=0·62). The between-group difference in chronic eGFR slopes (ie, from 2 months to final follow-up) was 1·37 mL/min per 1·73 m2 per year (95% CI 1·16-1·59), representing a 50% (42-58) reduction in the rate of chronic eGFR decline. This relative effect of empagliflozin on chronic eGFR slope was similar in analyses by different primary kidney diseases, including in explorations by type of glomerular disease and diabetes (p values for heterogeneity all >0·1).

INTERPRETATION

In a broad range of patients with chronic kidney disease at risk of progression, including a wide range of non-diabetic causes of chronic kidney disease, empagliflozin reduced risk of kidney disease progression. Relative effect sizes were broadly similar irrespective of the cause of primary kidney disease, suggesting that SGLT2 inhibitors should be part of a standard of care to minimise risk of kidney failure in chronic kidney disease.

FUNDING

Boehringer Ingelheim, Eli Lilly, and UK Medical Research Council.

[A cohort study of HIV infection in club drug abusers among men who have sex with men in Qingdao]

Objective: To understand and analyze the incidence of HIV infection in club drug abusers among men who have sex with men (MSM) in Qingdao and provide a reference for the prevention and intervention of this population. Methods: From March 2017 to July 2022, club drug abusers among MSM who are HIV-negative were recruited by snowball sampling of MSM social organizations in Qingdao, a prospective cohort was established, and a follow-up survey was conducted every six months, with the sample size estimated to be 436. The survey contents included demographic characteristics, sexual characteristics, AIDS knowledge awareness, club drug abuse, HIV testing, and other information. HIV infection was the outcome-dependent variable, and the interval between the recruitment into the cohort and the HIV infection was the time-dependent variable. Cox proportional hazards regression analysis was conducted to identify the related factors for HIV infection. Results: A total of 987 participants of club drug abusers among MSM were recruited during the baseline survey and 826 eligible participants were enrolled in this cohort. A total of 46 HIV infection cases were found, and the cumulative follow-up time was 1 960.68 person-years. The incidence of HIV infection was 2.35/100 person-years. The multivariate Cox regression analysis showed that <30 (aHR=3.04, 95%CI: 1.62-5.71) non-Shandong residents (aHR=2.29,95%CI:1.20-4.39) found their partners through offline (aHR=4.62,95%CI:2.05-10.41), homosexual sexual partners >4 (aHR=3.06,95%CI:1.59-5.88), condom broken during sex (aHR=2.24,95%CI:1.21-4.17) and hemorrhage sexual intercourse (aHR=2.56,95%CI:1.31-5.03) were significantly associated with HIV infection in this cohort. Conclusions: The incidence of HIV infection in club drug abusers among MSM in Qingdao is generally low, but knowledge and practice have separated, and the risk of HIV infection is high. The related factors of HIV infection included younger age, non-Shandong residents, finding their partners offline, multiple sexual partners, condom break during sex, and hemorrhage sexual intercourse; HIV-related behavioral intervention should be strengthened.

Efficient CRISPR/Cas9-mediated genome editing in sheepgrass (Leymus chinensis)

The lack of genome editing platforms has hampered efforts to study and improve forage crops that can be grown on lands not suited to other crops. Here, we established efficient Agrobacterium-mediated clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) genome editing in a perennial, stress-tolerant forage grass, sheepgrass (Leymus chinensis). By screening for active single-guide RNAs (sgRNAs), accessions that regenerate well, suitable Agrobacterium strains, and optimal culture media, and co-expressing the morphogenic factor TaWOX5, we achieved 11% transformation and 5.83% editing efficiency in sheepgrass. Knocking out Teosinte Branched1 (TB1) significantly increased tiller number and biomass. This study opens avenues for studying gene function and breeding in sheepgrass.

Genome evolution and initial breeding of the Triticeae grass Leymus chinensis dominating the Eurasian Steppe

Leymus chinensis, a dominant perennial grass in the Eurasian Steppe, is well known for its remarkable adaptability and forage quality. Hardly any breeding has been done on the grass, limiting its potential in ecological restoration and forage productivity. To enable genetic improvement of the untapped, important species, we obtained a 7.85-Gb high-quality genome of L. chinensis with a particularly long contig N50 (318.49 Mb). Its allotetraploid genome is estimated to originate 5.29 million years ago (MYA) from a cross between the Ns-subgenome relating to Psathyrostachys and the unknown Xm-subgenome. Multiple bursts of transposons during 0.433-1.842 MYA after genome allopolyploidization, which involved predominantly the Tekay and Angela of LTR retrotransposons, contributed to its genome expansion and complexity. With the genome resource available, we successfully developed a genetic transformation system as well as the gene-editing pipeline in L. chinensis. We knocked out the monocot-specific miR528 using CRISPR/Cas9, resulting in the improvement of yield-related traits with increases in the tiller number and growth rate. Our research provides valuable genomic resources for Triticeae evolutionary studies and presents a conceptual framework illustrating the utilization of genomic information and genome editing to accelerate the improvement of wild L. chinensis with features such as polyploidization and self-incompatibility.

A mitochondrial pentatricopeptide repeat protein enhances cold tolerance by modulating mitochondrial superoxide in rice

Cold stress affects rice growth and productivity. Defects in the plastid-localized pseudouridine synthase OsPUS1 affect chloroplast ribosome biogenesis, leading to low-temperature albino seedlings and accumulation of reactive oxygen species (ROS). Here, we report an ospus1-1 suppressor, sop10. SOP10 encodes a mitochondria-localized pentatricopeptide repeat protein. Mutations in SOP10 impair intron splicing of the nad4 and nad5 transcripts and decrease RNA editing efficiency of the nad2, nad6, and rps4 transcripts, resulting in deficiencies in mitochondrial complex I, thus decrease ROS generation and rescuing the albino phenotype. Overexpression of different compartment-localized superoxide dismutases (SOD) genes in ospus1-1 reverses the ROS over-accumulation and albino phenotypes to various degrees, with Mn-SOD reversing the best. Mutation of SOP10 in indica rice varieties enhances cold tolerance with lower ROS levels. We find that the mitochondrial superoxide plays a key role in rice cold responses, and identify a mitochondrial superoxide modulating factor, informing efforts to improve rice cold tolerance.

The Effect of MDSC-Derived Exosomes Played in Esophageal Squamous Carcinoma Cells after Ionizing Radiation

PURPOSE/OBJECTIVE(S)

Radiotherapy is the main treatment for esophageal cancer. Previous studies have shown that radiotherapy not only kills tumor cells directly, but also reshapes the immune microenvironment of the tumor. It has been reported an increase in the recruitment of myeloid-derived suppressor cells (MDSC) can occur in tumor tissue after ionizing radiation. Exosomes are mediators of intercellular information exchange and are also involved in the regulation of the tumor microenvironment. In this study, we wanted to understand whether MDSC in esophageal cancer tissue are involved in the regulation of tumor cell response to ionizing radiation via exosomes.

MATERIALS/METHODS

KYSE-150 was used to construct a subcutaneous transplantation tumor model in nude mice. And then mice irradiated with 5 Gy×5fx and 0 Gy×5fx respectively. After irradiation, the spleens of the mice were used to isolate MDSC, and collect the cell supernatants to extract the exosomes. Based on the exosomes, we divided the experiment into three groups (control, exosomes, exosomes+radiation). Exosomes were injected into a nude mouse model of esophageal cancer via the tail vein or co-cultured with KYSE-150 cells. Mice were irradiated with a 5 Gy×5fx after completion of injection, and KYSE-150 cells were irradiated with a single dose 4 Gy. After radiation, KYSE-150 cells were used to detect cell cloning, apoptosis and cell cycle by flow cytometry, cell proliferation by CCK 8. XRCC4,XRCC5,XRCC6,γH2AX,ATM expression in cells and tumor tissue were measured by Western blot and RT-PCR.

RESULTS

The tumor volume was significantly reduced after 5 Gy x 5fx radiation. When exosomes co-cultured with KYSE-150 cells, decrease in apoptosis and increase in cell cloning and cell proliferation were found in the exosomes+radiation group and exosomes group after radiation when compared with the control group, with this change being more pronounced in the exosome+radiation group. The results of the cell cycle assay showed that after ionizing radiation, the proportion of cells in the G0/G1 phase was significantly lower, and the proportion of cells in the S and G2/M phases were significantly higher in the exosomes+radiation group and exosomes group when compared to the Control group. The protein and mRNA expression of XRCC4,XRCC5,XRCC6,γH2AX,ATM in cells were increased in exosomes+radiation group and exosomes group after radiation when compared with the control group, with this change being more obvious in the exosome+radiation group. After irradiation, tumor volumes were measured in nude mice and the results showed that exosomes+radiation group tumors were the largest in volume, while the control group regressed most significantly after irradiation.

CONCLUSION

MDSC-derived exosomes have a tumor growth-promoting effect in esophageal squamous carcinoma, which is enhanced by ionizing radiation, and this may be related to the accelerated repair of damage in tumor tissue after radiation.

Facial expression of patients with Graves' orbitopathy

PURPOSE

Patients with Graves' orbitopathy (GO) have characteristic facial expressions that are different from those of healthy individuals due to the combination of somatic and psychiatric symptoms. However, the facial expressions of GO patients have not yet been described and analyzed systematically. Thus, the present study aimed to present the facial expressions of GO patients and explore their applications in clinical practice.

METHODS

Facial image and clinical data of 943 GO patients were included, and 126 patients answered quality of life (GO-QOL) questionnaires. Each patient was labeled for one facial expression. Then, a portrait was drawn for every facial expression. Logistic and linear regression was performed to analyze the correlation between facial expression and clinical indicators, including QOL, disease activity and severity. The VGG-19 network model was utilized to discriminate facial expressions automatically.

RESULTS

Two groups, i.e., the non-negative emotion (neutral, happy) and the negative emotion (disgust, angry, fear, sadness, surprise), and seven expressions of GO patients were systematically analyzed. Facial expression was statistically associated with GO activity (P = 0.002), severity (P < 0.001), QOL visual functioning subscale scores (P = 0.001), and QOL appearance subscale score (P = 0.012). The deep learning model achieved satisfactory results (accuracy 0.851, sensitivity 0.899, precision 0.899, specificity 0.720, F1 score 0.899, and AUC 0.847).

CONCLUSIONS

As a novel clinical sign, facial expression holds the potential to be incorporated into GO assessment system in the future. The discrimination model may assist clinicians in real-life patient care.

Verification and Mechanism Exploration of CDK4 Alterations on Influencing Radiotherapy Sensitivity in Small Cell Lung Cancer

PURPOSE/OBJECTIVE(S)

In this study, we aimed to explore the changes of functional phenotype before and after radiotherapy through vitro and vivo experiments. The potential pathway was preliminarily clarified.

MATERIALS/METHODS

Firstly, the relationships between the prognosis and the expression of CDK4 protein in SCLC patients treated with definitive chemoradiotherapy were explored. Then the stable overexpressed/knockdown CDK4 and negative control transfecting SCLC cell lines were established to monitor the changes of cell proliferation, migration, invasion, apoptosis and cell cycle after increasing radiation doses according to a cell counting kit assay, transwell cell migration and invasion assay, apoptosis cell cycle assay and BALB/c mouse model of subcutaneously transplanted tumor. The potential signal pathways were confirmed via KEGG pathway enrichment analysis and western blot.

RESULTS

Compared with patients with lower CDK4 protein expression, prognosis of those with high CDK4 protein expression was decreased significantly (p < 0.05). The cell activity, migration and invasion ability of overexpression/knockdown CDK4 and negative control group were all decreased with increasing radiation doses, but the activity, migration and invasion ability of cells with overexpression CDK4 was stronger after same dose X-ray irradiation (p<0.01). For group with knockdown CDK4, it showed lower cell activity, migration and invasion than negative control group. After X-ray irradiation, the apoptotic ratio of all groups increased. And cells with overexpressed CDK4 displayed significantly reduced apoptosis, less G0/G1 phase cells, and improved M phase cells than the control group. In addition, compared with negative control group, gross tumor volume of overexpression CDK4 group decreased much smaller after X-ray irradiation. H1339 cells with overexpression CDK4 and negative control group were sequenced by transcriptomic sequencing before and after radiotherapy. Taken together, differential genes were consistently enriched in MAPK pathway. Western blot showed that, compared with the negative control group, overexpression CDK4 group of H1339 and SW1271 cells after radiotherapy all showed significant changes on pERK proteins in the ERK pathway increased significantly (P<0.001).

CONCLUSION

In this study, the overexpression/knockdown CDK4 and negative control group were successfully constructed in H1339 and SW1271 cells, revealing the radiotherapy resistance of CDK4 alterations in vitro and in vivo experiment. And CDK4 alterations was shown to promote radiotherapy resistance through phosphorylation of MAPK/ERK signaling pathway in SCLC.

The radiomic biomarker in non-small cell lung cancer: 18F-FDG PET/CT characterisation of programmed death-ligand 1 status

AIM

To present an integrated 2-[18F]-fluoro-2-deoxy-d-glucose (18F-FDG) positron-emission tomography (PET)/computed tomography (CT) radiomic characterisation of programmed death-ligand 1 (PD-L1) status in non-small-cell lung cancer (NSCLC).

MATERIALS AND METHODS

In this retrospective study, 18F-FDG PET/CT images and clinical data of 394 eligible patients were divided into training (n=275) and test sets (n=119). Next, the corresponding nodule of interest was segmented manually on the axial CT images by radiologists. After which, the spatial position matching method was used to match the image positions of CT and PET, and radiomic features of the CT and PET images were extracted. Radiomic models were built using five different machine-learning classifiers and the performance of the radiomic models were further evaluated. Finally, a radiomic signature was established to predict the PD-L1 status in patients with NSCLC using the features in the best performing radiomic model.

RESULTS

The radiomic model based on the PET intranodular region determined using the logistic regression classifier preformed best, yielding an area under the receiver operating characteristics curve (AUC) of 0.813 (95% CI: 0.812, 0.821) on the test set. The clinical features did not improve the test set AUC (0.806, 95% CI: 0.801, 0.810). The final radiomic signature for PD-L1 status was consisted of three PET radiomic features.

CONCLUSION

This study showed that an 18F-FDG PET/CT-based radiomic signature could be used as a non-invasive biomarker to discriminate PD-L1-positive from PD-L1-negative in patients with NSCLC.

Analysis of soluble programmed death-1 ligand-1 of lung cancer patients with different characteristics

OBJECTIVE

To analyze the association of soluble programmed death-1 ligand-1 (sPD-L1) levels with clinicopathological characteristics, therapy efficacy, and survival outcomes in lung cancer patients.

PATIENTS AND METHODS

The study included two hundred treatment-naive patients with small cell lung cancer (SCLC) (n=12), and non-small cell lung cancer (NSCLC) (n=188). Plasma samples from 96 healthy individuals and 13 patients with benign tumors served as controls. Enzyme-linked immunosorbent assay (ELISA) was used to evaluate sPD-L1 expression. Blood samples of 67 NSCLC patients before and after therapy were collected.

RESULTS

sPD-L1 expression was significantly higher in lung cancer patients compared to the control groups (p=0.002). Moreover, patients with lower performance status had significantly higher sPD-L1 levels (p=0.005). NSCLC patients at later stages of the disease had greater sPD-L1 levels than those at the early stages (p<0.001). The presence of epidermal growth factor receptor (EGFR) mutation was not significantly different with higher sPD-L1 expression (p=0.334). Although sPD-L1 levels and progression-free survival (PFS) were linked with excellent response to therapy and advancing disease (p=0.307), no correlation was seen between sPD-L1 decrease and progression free survival (PFS).

CONCLUSIONS

Elevated sPD-L1 expression in NSCLC patients was associated with more advanced disease and worse overall health of the patients, suggesting a possible association with a negative clinical response and prognosis. sPD-L1 expression may be influenced by the mutation in EGFR.

[Clinical characteristics of children with IgE-mediated cow's milk protein allergy]

Objective: To analyze the clinical characteristics of children with IgE-mediated cow's milk protein allergy (CMPA) and provide a basis for disease management and prevention. Methods: A cross-sectional study was conducted to analyze 142 children aged 0-12 years who were diagnosed with IgE-mediated CMPA in Capital Institute of Pediatrics Affiliated Children's Hospital from 2020 to 2022. There were 79 males (55.6%) and 63 females (44.4%), with an average age of 14 (8, 27) months. 61 cases (43.0%) were in the <1-year-old group, 54 cases (38.0%) in the 1-3-year-old group, and 27 cases (19.0%) in the >3-year-old group. Data on demographic data, clinical manifestations, mean wheel diameter of skin prick test and serum specific IgE level were collected. The serum cow's milk protein sIgE and component sIgE were measured by ImmunoCAP fully automated system of fluorescence enzyme-linked immunosorbent assay, and statistically analyzed using chi-square test, nonparametric tests, correlation. Results: Cutaneous symptoms were the first and most frequent in 142 children (97.9%, 139/142 cases), followed by digestive (29.6%, 42/142 cases) and respiratory symptoms (27.5%, 39/142 cases).The proportion of children with respiratory symptoms after consuming cow's milk was significantly higher in the>3 years age group than those in the infant and toddler groups(66.7% vs 19.7%,χ2=18.396,P<0.01;66.7% vs 16.7%,χ2=20.250,P<0.01), and the symptoms involving ≥3 systems were also significantly higher than those in the other two groups(37.0% vs 13.1%,χ2=6.597,P<0.05;37.0% vs 7.4%,χ2=12.120,P<0.01). The average cow's milk SPT diameter and serum sIgE levels in the>3 years age group were significantly higher than those in the infant and toddler groups (Z=-4.682, P<0.01; Z=-3.498, P<0.01); (Z=-4.463, P<0.01; Z=-6.463, P<0.01). The most common cow's milk component protein were β-lactoglobulin(65.1%,56/86 cases) and casein (57.0%, 49/86 cases). Multiple-sensitization rate of the patients were 54.9%. Egg white (43.7%, 62/142 cases) was the most common co-sensitization food allergen while mold (12.7%, 18/142 cases) and weed pollen (12.7%, 18/142 cases) were the main co-sensitization aeroallergens. The proportion of multiple-sensitization to aeroallergens in the children group was the highest (51.9%, 14/27 cases), followed by the toddler group (29.6%, 16/54 cases), and the infant group was the least (3.3%, 2/61 cases). There was a significant difference among these three groups (χ2=7.476, P<0.05). Conclusion: Skin and mucosal symptoms are the most common in CMPA patients. The proportion of respiratory symptoms and multisystem involvement increased with age as well as the wheal diameter in skin test and serum sIgE level elevated. CMPA patients older than 3 years had the highest proportion of aeroallergen sensitization and airway allergic diseases.

The OsSGS3-tasiRNA-OsARF3 module orchestrates abiotic-biotic stress response trade-off in rice

Recurrent heat stress and pathogen invasion seriously threaten crop production, and abiotic stress often antagonizes biotic stress response against pathogens. However, the molecular mechanisms of trade-offs between thermotolerance and defense remain obscure. Here, we identify a rice thermo-sensitive mutant that displays a defect in floret development under high temperature with a mutation in SUPPRESSOR OF GENE SILENCING 3a (OsSGS3a). OsSGS3a interacts with its homolog OsSGS3b and modulates the biogenesis of trans-acting small interfering RNA (tasiRNA) targeting AUXIN RESPONSE FACTORS (ARFs). We find that OsSGS3a/b positively, while OsARF3a/b and OsARF3la/lb negatively modulate thermotolerance. Moreover, OsSGS3a negatively, while OsARF3a/b and OsARF3la/lb positively regulate disease resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo) and the fungal pathogen Magnaporthe oryzae (M. oryzae). Taken together, our study uncovers a previously unknown trade-off mechanism that regulates distinct immunity and thermotolerance through the OsSGS3-tasiRNA-OsARF3 module, highlighting the regulation of abiotic-biotic stress response trade-off in plants.

[Acetylcorynoline inhibits microglia activation by regulating EGFR/MAPK signaling to promote functional recovery of injured mouse spinal cord]

OBJECTIVE

To investigate the effect of acetylcorynoline (Ace) for promoting functional recovery of injured spinal cord in rats and explore the underlying mechanism.

METHODS

Rat models of spinal cord injury (SCI) were treated with intraperitoneal injection of different concentrations of Ace, with the sham-operated rats as the control group. After the treatment, the changes in motor function of the rats and the area of spinal cord injury were assessed with BBB score and HE staining, and the changes in pro-inflammatory cytokine levels and microglial activation were determined using PCR, ELISA and immunofluorescence staining. In a lipopolysaccharide (LPS)-treated BV2 cell model, the effects of different concentrations of Ace or DMSO on microglial activation and inflammatory cytokine production were observed. Network pharmacology analysis was performed to predict the target protein and signaling mechanism that mediated the inhibitory effect of Ace on microglia activation, and AutoDock software was used for molecular docking between Ace and the target protein. A signaling pathway blocker (Osimertinib) was used to verify the signaling mechanism in rat models of SCI and LPS-treated BV2 cell model.

RESULTS

In rat models of SCI, Ace treatment significantly increased the BBB score, reduced the area of spinal cord injury, and lowered the number of activated microglia cells and the levels of pro-inflammatory cytokines (P < 0.05). The cell experiments showed that Ace treatment significantly lower the level of cell activation and the production of inflammatory cytokines in LPS-treated BV2 cells (P < 0.05). Network pharmacology analysis suggested that EGFR was the main target of Ace, and they bound to each other via hydrogen bonds as shown by molecular docking. Western blotting confirmed that Ace inhibited the activation of the EGFR/MAPK signaling pathway in injured mouse spinal cord tissue and in LPS-treated BV2 cells, and its inhibitory effect was comparable to that of Osimertinib.

CONCLUSION

In rat models of SCI, treatment with Ace can inhibit microglia-mediated inflammatory response by regulating the EGFR/MAPK pathway, thus promoting tissue repair and motor function recovery.

[Based on CT radiomics model for predicting the response to first-line chemotherapy of diffuse large B-cell lymphoma]

Objective: To investigate the potential value of CT Radiomics model in predicting the response to first-line chemotherapy in diffuse large B-cell lymphoma (DLBCL). Methods: Pre-treatment CT images and clinical data of DLBCL patients treated at Shanxi Cancer Hospital from January 2013 to May 2018 were retrospectively analyzed and divided into refractory patients (73 cases) and non-refractory patients (57 cases) according to the Lugano 2014 efficacy evaluation criteria. The least absolute shrinkage and selection operator (LASSO) regression algorithm, univariate and multivariate logistic regression analyses were used to screen out clinical factors and CT radiomics features associated with efficacy response, followed by radiomics model and nomogram model. Receiver operating characteristic (ROC) curve, calibration curve and clinical decision curve were used to evaluate the models in terms of the diagnostic efficacy, calibration and clinical value in predicting chemotherapy response. Results: Based on pre-chemotherapy CT images, 850 CT texture features were extracted from each patient, and 6 features highly correlated with the first-line chemotherapy effect of DLBCL were selected, including 1 first order feature, 1 gray level co-occurence matrix, 3 grey level dependence matrix, 1 neighboring grey tone difference matrix. Then, the corresponding radiomics model was established, whose ROC curves showed AUC values of 0.82 (95% CI: 0.76-0.89) and 0.73 (95% CI: 0.60-0.86) in the training and validation groups, respectively. The nomogram model, built by combining validated clinical factors (Ann Arbor stage, serum LDH level) and CT radiomics features, showed an AUC of 0.95 (95% CI: 0.90-0.99) and 0.91 (95% CI: 0.82-1.00) in the training group and the validation group, respectively, with significantly better diagnostic efficacy than that of the radiomics model. In addition, the calibration curve and clinical decision curve showed that the nomogram model had good consistency and high clinical value in the assessment of DLBCL efficacy. Conclusion: The nomogram model based on clinical factors and radiomics features shows potential clinical value in predicting the response to first-line chemotherapy of DLBCL patients.

[A cohort study of incidence of club drug abuse in men who have sex with men in Qingdao]

Objective: To understand and analyze the incidence of club drug abuse and influencing factors in men who have sex with men (MSM) in Qingdao, and provide reference for the AIDS prevention and intervention in this population. Methods: From March 2017 to July 31, 2022, MSM who did not abuse club drug were recruited by snowball sampling of MSM social organizations in Qingdao, a prospective cohort was established, and a follow-up survey was conducted every 6 months. The survey collected the information about the MSM's demographic characteristics, sexual characteristics, club drug abuse and others. The incidence of club drug abuse was the outcome dependent variable and the interval between the recruitment into the cohort and the incidence of club drug abuse was the time dependent variable. Cox regression analysis was conducted to identify the influencing factors for club drug abuse. Results: A total of 509 MSM were recruited at baseline survey, and 369 eligible MSM were enrolled in this cohort. A total of 62 MSM began to abuse club drug during the study period, and the cumulative follow-up time was 911.54 person-years, the incidence of club drug abuse was 6.80/100 person-years. All the club drug abusers shared drugs with others in the first club drug abuse, and 16.13% (10/62) had mix-use of club drugs. The multivariate Cox proportional risk regression analysis showed that being students (aHR=2.17, 95%CI: 1.15-4.10), receiving no HIV testing or receiving 1 HIV testing during past 6 months (aHR=4.57, 95%CI:1.80-11.60; aHR=5.15, 95%CI: 2.83-9.36), having sex only with regular sexual partners during past 6 months (aHR=4.75,95%CI:2.32-9.75), having more than 4 homosexual partners (aHR=1.70, 95%CI:1.01-2.87) and abuse of club drug of sexual partners during past 6 months (aHR=12.78, 95%CI:3.06-53.35) were significantly associated with club drug abuse in the MSM. Conclusions: The incidence of club drug abuse was at a high level in the MSM cohort in Qingdao, indicating a high risk for HIV infection. Being student, receiving less HIV testing, having sex only with regular sexual partners, having more homosexual partners and abuse of club drug of sexual partners during past 6 months were risk factors for the incidence of club drug abuse in the MSM. Targeted surveillance and intervention measures should be strengthened to reduce the risk of club drug abuse in MSM.

Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation

Legumes form symbiosis with rhizobium leading to the development of nitrogen-fixing nodules. By integrating single-nucleus and spatial transcriptomics, we established a cell atlas of soybean nodules and roots. In central infected zones of nodules, we found that uninfected cells specialize into functionally distinct subgroups during nodule development, and revealed a transitional subtype of infected cells with enriched nodulation-related genes. Overall, our results provide a single-cell perspective for understanding rhizobium-legume symbiosis.

Mobile ARGONAUTE 1d binds 22-nt miRNAs to generate phasiRNAs important for low-temperature male fertility in rice

Phased small interfering RNAs (phasiRNAs) are abundantly expressed in anthers and linked to environment-related male fertility in grasses, yet how they function under different environmental conditions remains unclear. Here, we identified a rice (Oryza sativa) low temperature-induced Argonaute (AGO) protein, OsAGO1d, that is responsible for generating phasiRNAs and preserving male fertility at low temperature. Loss of OsAGO1d function causes low-temperature male sterility associated with delayed programmed cell death of tapetal cells during anther development. OsAGO1d binds miR2118 and miR2275 family members and triggers phasiRNA biogenesis; it also binds 21-nt phasiRNAs with a 5' terminal U. In total, phasiRNAs from 972 loci are OsAGO1d-dependent. OsAGO1d protein moves from anther wall cells into meiocytes, where it loads miR2275 to produce 24-nt phasiRNAs. Together, our results show that OsAGO1d acts as a mobile signal to fine-tune phasiRNA production and this function is important for male fertility at low temperature.

Pseudouridylation of chloroplast ribosomal RNA contributes to low temperature acclimation in rice

Ribosomal RNAs (rRNAs) undergo many modifications during transcription and maturation; homeostasis of rRNA modifications is essential for chloroplast biogenesis in plants. The chloroplast acts as a hub to sense environmental signals, such as cold temperature. However, how RNA modifications contribute to low temperature responses remains unknown. Here we reveal that pseudouridine (Ψ) modification of rice chloroplast rRNAs mediated by the pseudouridine synthase (OsPUS1) contributes to cold tolerance at seedling stage. Loss-function of OsPUS1 leads to abnormal chloroplast development and albino seedling phenotype at low temperature. We find that OsPUS1 is accumulated upon cold and binds to chloroplast precursor rRNAs (pre-rRNAs) to catalyse the pseudouridylation on rRNA. These modifications on chloroplast rRNAs could be required for their processing, as the reduction of mature chloroplast rRNAs and accumulation of pre-rRNAs are observed in ospus1-1 at low temperature. Therefore, the ribosome activity and translation in chloroplasts is disturbed in ospus1-1. Furthermore, transcriptome and translatome analysis reveals that OsPUS1 balances growth and stress-responsive state, preventing excess reactive oxygen species accumulation. Taken together, our findings unveil a crucial function of Ψ in chloroplast ribosome biogenesis and cold tolerance in rice, with potential applications in crop improvement.

Single cell sequencing unveils endothelial alterations after cisplatin treatment

Introduction

Cisplatin, one of the most potent anti-cancer chemotherapy drugs, is still broadly used in first-line chemotherapy regimens, which are subscribed to about 10 to 20% of total cancer patients. Nephrotoxicity is a particularly limiting factor for cancer patients to remain in the effective treatment due to the acute kidney injury. It has been reported that as early as 24 hours post treatment, testicular cancer patients receiving cisplatin developed endothelial dysfunction and vascular injury. A cross-sectional follow-up study published in 2008 suggested that testicular cancer survivors continued to experience endothelial dysfunction and vascular injury. A recent 30-year follow-up study on testicular cancer survivors suggested that testicular cancer survivors experienced worse diastolic function.

Purpose

This study is focused on identifying the specific genes altered in cardiac endothelial cells after the cisplatin treatment to unveil the molecular mechanisms of injury for potential new therapeutic development.

Methods

Cisplatin induced AKI mouse model was generated by i.p. injecting 25 mg/kg cisplatin to C57BL/6 mice. Saline injection was served as control. To evaluate blood vessel damage induced by cisplatin, mice were sacrificed 48 hours post injection. Hearts were collected and single cell suspensions were produced by using Multi Tissue Dissociation Kit 2. Freshly prepared single cell suspensions were used to created libraries by using 10X genomics kits, before sequencing. The CellRanger (10X genomics) was used for processing Single cell RNASeq outputs, before secondary Seurat and DE pathway analysis.

Results

The GO enrichment analysis suggested that, in endothelial cells, cisplatin treatment significantly altered cellular anatomical entity, intracellular anatomical structure, apical part of the cell, cell junction, and anchoring junction. Consequently, increased vascular permeability, signaling regulating monocyte differentiation, macrophage cytokine production, and cardiac muscle cell apoptosis were observed. At molecular level, cisplatin treatment significantly upregulated DNA damage (Ddit4, Acer2), hypoxia (Phlda3, Mt1, Slc3a2, Ier3, Klf9, Adipor2, UCP2), inflammatory responses (Timp4, Tns1, Gdf15, Neat1), cellular senescence (Cdkn1a), Cell cycle arrest (Trp53inpl), intrinsic and extrinsic apoptosis (Fas, Bax, Ei24, Tgm2), blood vessel remodeling (Pim-3), and angiogenesis (Timp3, Flt1). These results indicated that cisplatin treatment likely not only result in acute endothelial dysfunction, injury, and death, but also accelerated aging, which could contribute the cardiovascular complications in the cancer survivors.

Conclusions

Protecting endothelial cells from oxidative stress and inflammation caused by cisplatin treatment might prevent their irreversible injury and entering into premature cellular senescence, consequently, mitigating anti-cancer treatment induced cardiovascular complications in cancer survivors.

Funding Acknowledgement

Type of funding sources: Other. Main funding source(s): NIH

[Centromere protein U is highly expressed in colorectal cancer and associated with a poor long-term prognosis]

OBJECTIVE

To analyze the expression of centromere protein U (CENPU) in colorectal cancer and its predictive value for long-term prognosis of the patients.

METHODS

We retrospectively analyzed the data of 102 patients with colorectal cancer undergoing radical resection in our hospital between January, 2005 and December, 2011. The expression level of CENPU in colorectal cancer tissue was detected immunohistochemically, and its association with clinicopathological characteristics of the patients were analyzed. The patients were divided into low expression group (n=51) and high expression group (n=51) based on the median CENPU expression level for analysis the value of CENPU for predicting long-term prognosis of the patients after radical resection of the tumors. In the in vitro study, we constructed colorectal cancer cell lines with CENPU interference and CENPU overexpression by lentiviral transfection and assessed the changes in the proliferation, migration and invasion of the cells using CCK-8 assay and Transwell assay.

RESULTS

The protein expression level of CENPU was significantly higher in colorectal cancer tissues than in the adjacent tissues (P < 0.05) and was positively correlated with the expressions levels of Ki67 (r=0.569, P < 0.05) and VEGF-C (r=0.629, P < 0.05). CENPU expression level in colorectal cancer tissue was closely related with tumor progression and clinicopathological stage of the tumor (P < 0.05). Kaplan-Meier survival analysis showed that the patients with high CENPU expression had significantly decreased postoperative overall survival (χ²=11.155, P < 0.05); Cox multivariate regression analysis suggested that CENPU expression level was an independent risk factor affecting the overall survival of the patients after radical resection (HR=1.848, P < 0.05). The results of cell experiments demonstrated that high CENPU expression significantly promoted the proliferation, migration and invasion of the tumor cells.

CONCLUSION

CENPU is highly expressed in colorectal cancer tissues in closely correlation with tumor progression and may serve as a potential biomarker for evaluating the long-term prognosis of colorectal cancer patients.

[Construction of an adenovirus vector expressing engineered splicing factor for regulating alternative splicing of YAP1 in neonatal rat cardiomyocytes]

OBJECTIVE

To construct an adenovirus vector expressing artificial splicing factor capable of regulating alternative splicing of Yap1 in cardiomyocytes.

METHODS

The splicing factors with different sequences were constructed against Exon6 of YAP1 based on the sequence specificity of Pumilio1. The PCR fragment of the artificially synthesized PUF-SR or wild-type PUFSR was cloned into pAd-Track plasmid, and the recombinant plasmids were transformed into E. coli DH5α for plasmid amplification. The amplified plasmids were digested with Pac I and transfected into 293A cells for packaging to obtain the adenovirus vectors. Cultured neonatal rat cardiomyocytes were transfected with the adenoviral vectors, and alternative splicing of YAP1 was detected using quantitative and semi-quantitative PCR; Western blotting was performed to detect the signal of the fusion protein Flag.

RESULTS

The transfection efficiency of the adenovirus vectors was close to 100% in rat cardiomyocytes, and no fluorescent protein was detected in the cells with plasmid transfection. The results of Western blotting showed that both the negative control and Flag-SR-NLS-PUF targeting the YAPExon6XULIE sequence were capable of detecting the expression of the protein fused to Flag. The results of reverse transcription-PCR and PCR demonstrated that the artificial splicing factor constructed based on the 4th target sequence of YAP1 effectively regulated the splicing of YAP1 Exon6 in the cardiomyocytes (P < 0.05).

CONCLUSION

We successfully constructed adenovirus vectors capable of regulating YAP1 alternative splicing rat cardiomyocytes.

[Characteristics and changes of sensitization patterns of major allergens in children from 2010 to 2020 in a hospital of pediatric in Beijing]

Objective: To analyze the sensitization characteristics and change of major allergens in children from 2010 to 2020 in Beijing, so as to provide basis for diagnosis, treatment and prevention of allergic diseases in children. Methods: A retrospective study was conducted to analyze the children who were suspected of allergic diseases and tested for serum immunoglobulin E (total IgE and specific IgE) in the children's Hospital Affiliated to the Capital Institute of Pediatrics from January 2010 to December 2020. A total of 45 746 children aged 0-17 years in Beijing were enrolled with a median (interquartile range) of 3.8 (2.5, 5.3) years. There were 28 918 boys (63.2%) and 16 828 girls (36.8%) and 14 984 cases (32.8%) in the infant group (<3 years old), 22 049 cases (48.2%) in the preschool group (3-6 years old), and 8 713 cases (19.0%) in the school-age group (6 years old and above). Immunocap allergen detection system (fluorescence enzyme-linked immunosorbent assay) was used to detect and the characteristics and change trend of allergens during 11 years were statistically analyzed by Chi square test. Results: The top three positive rates of single food allergens sIgE were egg white 42.6% (2 788/6 577 tests), milk 38.4% (2 606/6 782 tests) and wheat 31.8% (1 417/4 449 tests), and the sequence of single inhaled allergens were Ragweed 42.6% (440/1 034 tests), Artemisia 38.4% (1 045/3 191 tests) and Alternaria alternata 31.3% (3 358/10 725 tests). The positive detection rates of egg white 47.0%(1 904/4 048 tests), milk 41.9%(1 769/4 226 tests) and wheat 33.9%(973/2 870 tests) in the infant group were the highest, and there have statistically significant(χ²=91.495, 73.907, 16.966, P<0.05). The positive rates of fx1 (22.5%, 121/537 tests), peanut (24.9%, 111/446 tests), soybean (20.0%, 74/370 tests) and shrimp (7.48%, 44/588 tests) were the highest in the school-age group(χ²=14.436, 10.751, 11.569, 13.703, P<0.05). The most common inhaled allergens were Alternaria alternata (14.8%, 422/2 859 tests) in the infant group, Ambrosia (34.5%, 143/415 tests) and Alternaria alternata (33.5%, 1 762/5 254 tests) in the preschool group, while in the school-age group were Ambrosia (56.4%, 282/500 tests) and Artemisia (48.2%, 573/1 189 tests). The positive rates of egg white, milk, wheat, sesame seed and peanut varied from 2010 to 2020, showing a trend of falling first and then rising(χ²=10.293,χ²=12.066,χ²=7.402,χ²=32.458,χ²=31.747,P<0.05).The positive detection rates of soybean showed a significant downward trend (21.4%, 173/809 tests in 2010, 15.4%, 70/455 tests in 2020, χ²=6.751,P=0.009), while that of shrimp and crab were at a stable low level(χ²=0.263, 1.346;P>0.05). From 2010 to 2020, mold (26.7%, 1 066/3 998 tests in 2010, 40.2% 1 705/4 243 tests in 2020), grass pollen (19.8%, 259/1 308 tests in 2010, 39.3%, 1 472/3 746 tests in 2020), tree pollen(17%, 180/1 058 tests in 2010, 29.8%, 916/3 075 tests in 2020) and animal dander (18.5%, 111/601 tests in 2010, 26.6%, 672/2 522 tests in 2020) were all showed significant upward trend (χ²=168.600, 163.601, 65.931 and 17.271 respectively, P<0.001) but dust mites (30.7%, 1 270/4 132 tests in 2010, 26.7%, 1 126/4 221 tests in 2020) showed a significant downward trend(χ²=16.822,P<0.001).In 2010, the most common inhaled allergen was dust mite 30.7% (1 270/4 132 tests), followed by mold 26.7% (1 066/3 998 tests), while they were mold 40.2% (1 705/1 243 tests), and grass pollen 39.3% (1 472/3 746 texts) respectively in 2020. Conclusion: In the past 11 years, the main food allergens in children were still egg white and milk, wheat, but the mold and pollen gradually replaced dust mite as the most common inhaled allergen.

Control of OsARF3a by OsKANADI1 contributes to lemma development in rice

In rice (Oryza sativa), the lemma and palea protect the internal organs of the floret，provide nutrients for seed development, and determine grain size. We previously revealed that a trans-acting small interfering RNA targeting AUXIN RESPONSE FACTORS (tasiR-ARF) regulates lemma polarity establishment via post-transcriptional repression of AUXIN RESPONSE FACTORS (ARFs) in rice. TasiR-ARF formation requires RNA-DEPENDENT RNA POLYMERASE 6 (RDR6). However, the underlying molecular mechanism of the tasiR-ARF-ARF regulon in lemma development remains unclear. Here, by genetic screening for suppressors of the thermosensitive mutant osrdr6-1, we identified three suppressors, huifu 1 (hf1), hf9, and hf17. Mapping-by-sequencing revealed that HF1 encodes a MYB transcription factor belonging to the KANADI1 family. The hf1 mutation partially rescued the osrdr6-1 lemma defect but not the defect in tasiR-ARF levels. DNA affinity purification sequencing analysis identified 17 725 OsKANADI1-associated sites, most of which contain the SPBP-box binding motif (RGAATAWW) and are located in the promoter, protein-coding, intron, and intergenic regions. Moreover, we found that OsKANADI1 could directly bind to the intron of OsARF3a in vitro and in vivo and promote OsARF3a expression at the transcriptional level. In addition, hf9 and hf17 are intragenic suppressors containing mutations in OsRDR6 that partially rescue tasiR-ARF levels by restoring OsRDR6 protein levels. Collectively, our results demonstrate that OsKANADI1 and tasiR-ARFs synergistically maintain the proper expression of OsARF3a and thus contribute to rice lemma development.

[ALDH3B1 expression is correlated with histopathology and long-term prognosis of gastric cancer]

OBJECTIVE

To investigate the expression of aldehyde dehydrogenase 3B1 (ALDH3B1) in gastric cancer and explore its correlation with the pathological parameters and long-term prognosis of the patients.

METHODS

We analyzed the clinical data of 101 patients who underwent radical gastrectomy for gastric cancer in our hospital between January, 2013 and November, 2016, and examined the expression of ALDH3B1 in paraffin-embedded samples of gastric cancer tissues and adjacent tissues from these cases by immunohistochemical staining. We evaluated the correlation between ALDH3B1 expressions and histopathological parameters and assessed the predictive value of ALDH3B1 expression for long-term survival of the patients. We also examined the effect of lentivirus-mediated interference and overexpression of ALDH3B1 on the malignant behaviors of MGC-803 gastric cancer cells.

RESULTS

The expressions of ALDH3B1 and Ki67 were significantly higher in gastric cancer tissues than in adjacent tissues (P < 0.05). In gastric cancer patients, ALDH3B1 expression was positively correlated with peripheral blood CEA and CA19-9 levels (P < 0.01). The proportion of patients with CEA ≥5 μg/L, CA19-9 ≥37 kU/L, T stage of 3- 4, and N stage of 2-3 was significantly greater in high ALDH3B1 expression group than in low expression group. Kaplan-Meier survival analysis showed that the 5-year survival rate was significantly lower in gastric cancer patients with high ALDH3B1 expressions (P < 0.01). Univariate and Cox multiple regression analyses identified a high expression of ALDH3B1 (P < 0.05, HR= 0.231, 95% CI: 0.064-0.826), CEA≥5 μg/L (P < 0.01, HR=4.478, 95% CI: 1.530-13.110), CA19-9≥37 kU/L (P < 0.01, HR=3.877, 95% CI: 1.625-9.247), T stage of 3-4 (P < 0.01, HR=4.953, 95% CI: 1.768-13.880), and N stage of 2-3 (P < 0.05, HR=2.152, 95% CI: 1.152-4.022) as independent risk factors affecting 5-year survival after radical gastrectomy. The relative ALDH3B1 expression level, at the cut-off point of 4.66, showed a sensitivity of 76.47% and a specificity of 76% for predicting 5-year postoperative death (P < 0.01). In the cell experiment, overexpression of ALDH3B1 obviously promoted the proliferation, migration and invasion of MGC-803 cells.

CONCLUSION

As an independent risk factor affecting 5-year survival after radical gastrectomy, ALDH3B1 is highly expressed in gastric cancer and correlated with pathological parameters of the tumor, and a high ALDH3B1 expression may promote proliferation, invasion and metastasis of gastric cancer cells.