Targeting DCAF5 suppresses SMARCB1-mutant cancer by stabilizing SWI/SNF

Whereas oncogenes can potentially be inhibited with small molecules, the loss of tumour suppressors is more common and is problematic because the tumour-suppressor proteins are no longer present to be targeted. Notable examples include SMARCB1-mutant cancers, which are highly lethal malignancies driven by the inactivation of a subunit of SWI/SNF (also known as BAF) chromatin-remodelling complexes. Here, to generate mechanistic insights into the consequences of SMARCB1 mutation and to identify vulnerabilities, we contributed 14 SMARCB1-mutant cell lines to a near genome-wide CRISPR screen as part of the Cancer Dependency Map Project1-3. We report that the little-studied gene DDB1-CUL4-associated factor 5 (DCAF5) is required for the survival of SMARCB1-mutant cancers. We show that DCAF5 has a quality-control function for SWI/SNF complexes and promotes the degradation of incompletely assembled SWI/SNF complexes in the absence of SMARCB1. After depletion of DCAF5, SMARCB1-deficient SWI/SNF complexes reaccumulate, bind to target loci and restore SWI/SNF-mediated gene expression to levels that are sufficient to reverse the cancer state, including in vivo. Consequently, cancer results not from the loss of SMARCB1 function per se, but rather from DCAF5-mediated degradation of SWI/SNF complexes. These data indicate that therapeutic targeting of ubiquitin-mediated quality-control factors may effectively reverse the malignant state of some cancers driven by disruption of tumour suppressor complexes.

Measurements of All-Particle Energy Spectrum and Mean Logarithmic Mass of Cosmic Rays from 0.3 to 30 PeV with LHAASO-KM2A

We present the measurements of all-particle energy spectrum and mean logarithmic mass of cosmic rays in the energy range of 0.3-30 PeV using data collected from LHAASO-KM2A between September 2021 and December 2022, which is based on a nearly composition-independent energy reconstruction method, achieving unprecedented accuracy. Our analysis reveals the position of the knee at 3.67±0.05±0.15  PeV. Below the knee, the spectral index is found to be -2.7413±0.0004±0.0050, while above the knee, it is -3.128±0.005±0.027, with the sharpness of the transition measured with a statistical error of 2%. The mean logarithmic mass of cosmic rays is almost heavier than helium in the whole measured energy range. It decreases from 1.7 at 0.3 PeV to 1.3 at 3 PeV, representing a 24% decline following a power law with an index of -0.1200±0.0003±0.0341. This is equivalent to an increase in abundance of light components. Above the knee, the mean logarithmic mass exhibits a power law trend towards heavier components, which is reversal to the behavior observed in the all-particle energy spectrum. Additionally, the knee position and the change in power-law index are approximately the same. These findings suggest that the knee observed in the all-particle spectrum corresponds to the knee of the light component, rather than the medium-heavy components.

Host genotype-specific rhizosphere fungus enhances drought resistance in wheat

BACKGROUND

The severity and frequency of drought are expected to increase substantially in the coming century and dramatically reduce crop yields. Manipulation of rhizosphere microbiomes is an emerging strategy for mitigating drought stress in agroecosystems. However, little is known about the mechanisms underlying how drought-resistant plant recruitment of specific rhizosphere fungi enhances drought adaptation of drought-sensitive wheats. Here, we investigated microbial community assembly features and functional profiles of rhizosphere microbiomes related to drought-resistant and drought-sensitive wheats by amplicon and shotgun metagenome sequencing techniques. We then established evident linkages between root morphology traits and putative keystone taxa based on microbial inoculation experiments. Furthermore, root RNA sequencing and RT-qPCR were employed to explore the mechanisms how rhizosphere microbes modify plant response traits to drought stresses.

RESULTS

Our results indicated that host plant signature, plant niche compartment, and planting site jointly contribute to the variation of soil microbiome assembly and functional adaptation, with a relatively greater effect of host plant signature observed for the rhizosphere fungi community. Importantly, drought-resistant wheat (Yunhan 618) possessed more diverse bacterial and fungal taxa than that of the drought-sensitive wheat (Chinese Spring), particularly for specific fungal species. In terms of microbial interkingdom association networks, the drought-resistant variety possessed more complex microbial networks. Metagenomics analyses further suggested that the enriched rhizosphere microbiomes belonging to the drought-resistant cultivar had a higher investment in energy metabolism, particularly in carbon cycling, that shaped their distinctive drought tolerance via the mediation of drought-induced feedback functional pathways. Furthermore, we observed that host plant signature drives the differentiation in the ecological role of the cultivable fungal species Mortierella alpine (M. alpina) and Epicoccum nigrum (E. nigrum). The successful colonization of M. alpina on the root surface enhanced the resistance of wheats in response to drought stresses via activation of drought-responsive genes (e.g., CIPK9 and PP2C30). Notably, we found that lateral roots and root hairs were significantly suppressed by co-colonization of a drought-enriched fungus (M. alpina) and a drought-depleted fungus (E. nigrum).

CONCLUSIONS

Collectively, our findings revealed host genotypes profoundly influence rhizosphere microbiome assembly and functional adaptation, as well as it provides evidence that drought-resistant plant recruitment of specific rhizosphere fungi enhances drought tolerance of drought-sensitive wheats. These findings significantly underpin our understanding of the complex feedbacks between plants and microbes during drought, and lay a foundation for steering "beneficial keystone biome" to develop more resilient and productive crops under climate change. Video Abstract.

Prognostic Significance of Uric Acid Levels in Intracerebral Hemorrhage Patients

Background and Purpose

The role of serum uric acid (UA) level in patients suffering from stroke remains controversial. Our aim was to investigate the effect of UA level on clinical outcomes in patients with intracerebral hemorrhage (ICH).

Methods

In the retrospective cohort study, we analyzed data from 250 patients with intracerebral hemorrhage (85 women and 165 men) to investigate the difference in UA levels between patients with a good prognosis and those with a poor prognosis. Additionally, we analyzed the impact of UA levels on the risk of short-time prognosis of ICH patients.

Results

Patients with a good prognosis presented with significantly lower levels of UA (348.71 ± 84.97 μmol/L) than those with poor prognosis (393.06 ± 148.46 μmol/L). Furthermore, multivariate logistic regression model demonstrated that a high UA level was a likely risk factor for worse prognosis among patients suffering in ICH (odds ratio [95% confidence interval], 1.006 [1.0012, 1.0108]; P = 0.015). Additionally, UA has a threshold effect value of 363.9 μmol/L and was presented in levels that were in a nonlinear relationship with incidence rate of short-time prognosis outcome of ICH patients.

Conclusion

Our findings indicate that higher UA levels can increase the risk of poor clinical prognosis in patients with ICH and high UA levels are not conductive to the clinical prognosis of patients with ICH. These findings provide a new perspective on the treatment and prevention of ICH.

Thymidine Phosphorylase Promotes the Formation of Abdominal Aortic Aneurysm in Mice Fed a Western Diet

Aims

The precise molecular drivers of abdominal aortic aneurysm (AAA) remain unclear. Thymidine phosphorylase (TYMP) contributes to increased platelet activation, thrombosis, and inflammation, all of which are key factors in AAA development. Additionally, TYMP suppresses the proliferation of vascular smooth muscle cells (VSMCs), which are central to the development and progression of AAA. We hypothesize that TYMP plays a key role in AAA development.

Methods and Results

We conducted a histological study using human AAA samples and normal abdominal aortas, revealing heightened levels of TYMP in human AAA vessel walls. To validate this observation, we utilized an Ang II perfusion-induced AAA model in wild-type C57BL/6J (WT) and Tymp-/- mice, feeding them a Western diet (TD.88137) starting from 4 weeks of age. We found that Tymp-/- mice were protected from Ang II perfusion-induced AAA formation. Furthermore, by using TYMP-expressing VSMCs as well as primarily cultured VSMCs from WT and Tymp-/- mice, we elucidated the essential role of TYMP in regulating MMP2 expression and activation. TYMP deficiency or inhibition by tipiracil, a selective TYMP inhibitor, led to reduced MMP2 production, release, and activation in VSMCs. Additionally, TYMP was found to promote pro-inflammatory cytokine expression systemically, and its absence attenuates TNF-α-stimulated activation of MMP2 and AKT. By co-culturing VSMCs and platelets, we observed that TYMP-deficient platelets had a reduced inhibitory effect on VSMC proliferation compared to WT platelets. Moreover, TYMP appeared to enhance the expression of activated TGFβ1 in cultured VSMCs in vitro and in human AAA vessel walls in vivo. TYMP also boosted the activation of thrombospondin-1 type 1 repeat domain-enhanced TGFβ1 signaling, resulting in increased connective tissue growth factor production.

Conclusion

Our findings collectively demonstrated that TYMP serves as a novel regulatory force in vascular biology, exerting influence over VSMC functionality and inflammatory responses that promote the development of AAA.

Measurement of Ultra-High-Energy Diffuse Gamma-Ray Emission of the Galactic Plane from 10 TeV to 1 PeV with LHAASO-KM2A

The diffuse Galactic γ-ray emission, mainly produced via interactions between cosmic rays and the interstellar medium and/or radiation field, is a very important probe of the distribution, propagation, and interaction of cosmic rays in the Milky Way. In this Letter, we report the measurements of diffuse γ rays from the Galactic plane between 10 TeV and 1 PeV energies, with the square kilometer array of the Large High Altitude Air Shower Observatory (LHAASO). Diffuse emissions from the inner (15°10  TeV). The energy spectrum in the inner Galaxy regions can be described by a power-law function with an index of -2.99±0.04, which is different from the curved spectrum as expected from hadronic interactions between locally measured cosmic rays and the line-of-sight integrated gas content. Furthermore, the measured flux is higher by a factor of ∼3 than the prediction. A similar spectrum with an index of -2.99±0.07 is found in the outer Galaxy region, and the absolute flux for 10≲E≲60  TeV is again higher than the prediction for hadronic cosmic ray interactions. The latitude distributions of the diffuse emission are consistent with the gas distribution, while the longitude distributions show clear deviation from the gas distribution. The LHAASO measurements imply that either additional emission sources exist or cosmic ray intensities have spatial variations.

[Genome sequence analysis of two SARS-CoV-2 virus infections in Inner Mongolia, 2022]

The target gene sequences of the novel coronaviruses obtained by sequencing were compared with the reference sequences to analyze the genetic variation of the two cases of the novel coronaviruses from Inner Mongolia Autonomous Region in 2022 and to explore the sources of infection. The results showed that the two sequences belonged to different evolutionary branches, Delta (AY.122) and Omicron (BA.1.1), respectively. hCoV-19/Inner Mongolia/IVDC-591/2022 had 48 single nucleotide polymorphisms on the genome sequences, sharing 40 nucleotide mutation sites with a Mongolian strain; hCoV-19/Inner Mongolia/IVDC-592/2022 genome shared 57 nucleotide mutation sites with a UK strain, and the nucleotide mutation site identity was 100% (57/57). Phylogenetic analysis showed that the target gene sequences were not directly related to domestic novel coronavirus sequences during the same period, but were related to isolates from Europe and Mongolia.

Develop a Deep Radiomics Model for Predicting the Response to Neoadjuvant Chemoradiotherapy (nCRT) in Patients with Locally Advanced Esophageal Cancer Using Three-Stage Longitudinal CT Images

PURPOSE/OBJECTIVE(S)

To develop a deep radiomics model for predicting the response to neoadjuvant chemoradiotherapy (nCRT) of patients with locally advanced esophageal cancer using three stage longitudinal CT images.

MATERIALS/METHODS

In this study, 189 patients were used to train our model, 80 patients were used to test the performance of the trained model. All patients enrolled in this study underwent nCRT followed by esophagectomy, and all patients underwent three stage longitudinal CT scans (before nCRT, after nCRT and before esophagectomy). The number of radiomics features for each CT images was 2153, the number of longitudinal radiomic features for each patient was 6459. Then, we used the least absolute shrinkage and selection operator regression for feature importance analysis. After this, the selected features of each stage were feed to the disentangled representation network to explore the relationship between the dynamic changes of tumors before and after nCRT and the pathological complete response (pCR). In addition, in order to further evaluate the effect of the time interval between nCRT and esophagectomy on the response to nCRT, we conducted subgroup analysis on different time frames. The performance of our model was evaluated by area under curve (AUC), accuracy, sensitivity and specificity.

RESULTS

Compared with only using single-stage CT images (the AUC of only using before nCRT CT images, after nCRT CT images, before esophagectomy CT images were 73.27%, 74.21%, and 74.95%, respectively), effectively exploring the dynamic changes of the tumor can achieve better performance in predicting the response to nCRT in the testing cohort (the AUC was 84.29%, 95% CI, 81.14%-87.44%). In addition, the performance of our proposed method outperforms any combinations of two stage CT images (the AUC using the CT images of before nCRT and after nCRT was 77.92%, the AUC using the CT images of before nCRT and before esophagectomy was 79.31%, the AUC using the CT images of after nCRT and before esophagectomy was 80.01%). Finally, the results showed that exploring the dynamic changes of the tumor using the three-stage CT images outperformed using single-stage CT images and any combinations of two-stage CT images in predicting the response to nCRT. The study also found that the time interval between nCRT and esophagectomy had some influence on the accuracy of pCR prediction, with the prediction accuracy tending to increase from 1 to 6 weeks and stabilizing after 6 weeks.

CONCLUSION

By exploring the dynamic changes of tumors, the designed disentangled representation network can effectively predict the response to nCRT of patients with esophageal cancer. In addition, the time interval between nCRT and esophagectomy also has a certain impact on the response to nCRT.

Development and validation of a novel clinical prediction model to predict the 90-day functional outcome of spontaneous intracerebral hemorrhage

Background

Spontaneous intracerebral hemorrhage (SICH) is associated with high mortality and disability. Accurately predicting adverse prognostic risks of SICH is helpful in developing risk stratification and precision medicine strategies for this phenomenon.

Methods

We analyzed 413 patients with SICH admitted to Hefei Second People's Hospital as a training cohort, considering 74 patients from the First Affiliated Hospital of Anhui Medical University for external validation. Univariate and multivariate logistic regression analyses were used to select risk factors for 90-day functional outcomes, and a nomogram was developed to predict their incidence in patients. Discrimination, fitting performance, and clinical utility of the resulting nomogram were evaluated through receiver operating characteristic (ROC) curves, accuracy, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), calibration plots, and decision curves analysis (DCA), respectively.

Results

Of the 413 patients, 180 had a poor prognosis. Univariate analysis showed significant variance of age, systolic pressure, intraventricular hemorrhage (IVH), Glasgow Coma Scale (GCS) scores, National Institute of Health Stroke Scale (NIHSS) scores, and hematoma volume between the groups (p < 0.05). Logistic multivariate regression analysis showed that age, IVH, NIHSS, and hematoma volume were associated with unfavorable outcomes. Based on the results, a nomogram model was developed with an area under the ROC curve of 0.91 (95% CI; 0.88-0.94) and 0.89 (95% CI; 0.80-0.95) in the training and validation sets, respectively. In the validation set, the accuracy, sensitivity, specificity, PPV, and NPV of the model were 0.851, 0.923, 0.812, 0.727, and 0.951, respectively. The calibration plot demonstrates the goodness of fit between the nomogram predictions and actual observations. Finally, DCA indicated significant clinical adaptability.

Conclusion

We developed and validated a short-term prognostic nomogram model for patients with SICH including NIHSS scores, age, hematoma volume, and IVH. This model has valuable potential in predicting the prognosis of patients with SICH.

Serum β2-microglobulin is closely associated with 3-month outcome of acute intracerebral hemorrhage: a retrospective cohort study

BACKGROUND

Intracerebral hemorrhage (ICH) is a frequent type of hemorrhagic stroke. Numerous studies have suggested that inflammation plays an important role in the injury and recovery of ICH. β2-microglobulin (β2M) is an inflammatory indicator with an unclear association with ICH development. This study aimed to explore the role of β2M in the outcome of patients with ICH after 3 months of ICH onset.

METHODS

The β2M and other baseline information of 231 patients with ICH were assessed (83 females and 148 males). We followed up with all patients 3 months after ICH onset, and severe disability or a worse outcome was our main focus. We collected the serum β2M levels, National Institutes of Health Stroke Scale (NIHSS) and modified Rankin scale (mRS) scores, and other relevant baseline information of each patient. We used multiple regression analysis to explore the association between β2M levels and follow-up outcomes.

RESULTS

Our results indicated that the β2M level of the good outcome (2.35 ± 0.84 mg/l) group was significantly lower than that of the poor outcome group (3.06 ± 1.71 mg/l) (P < 0.001). Further multiple regression analysis showed that β2M was regarded as a risk factor that was closely associated with the poor outcome 3 months after ICH onset (odds ratio = 2.26, 95% confidence interval = 1.22-4.19, P = 0.009). Further correlation analysis revealed that β2M was significantly correlated with NIHSS scores (r = 0.187, P = 0.004) and follow-up mRS scores (r = 0.25, P < 0.001).

CONCLUSION

β2M was a risk factor for early outcome after ICH onset, and high β2M level was associated with short-time poor prognosis of ICH patients.

A tera-electron volt afterglow from a narrow jet in an extremely bright gamma-ray burst

Some gamma-ray bursts (GRBs) have a tera-electron volt (TeV) afterglow, but the early onset of this has not been observed. We report observations with the Large High Altitude Air Shower Observatory of the bright GRB 221009A, which serendipitously occurred within the instrument field of view. More than 64,000 photons >0.2 TeV were detected within the first 3000 seconds. The TeV flux began several minutes after the GRB trigger, then rose to a peak about 10 seconds later. This was followed by a decay phase, which became more rapid ~650 seconds after the peak. We interpret the emission using a model of a relativistic jet with half-opening angle ~0.8°. This is consistent with the core of a structured jet and could explain the high isotropic energy of this GRB.

Targeting the Dark Lipid Kinase PIP4K2C with a Potent and Selective Binder and Degrader

Phosphatidylinositol 5-phosphate 4-kinase, type II, gamma (PIP4K2C) remains a poorly understood lipid kinase with minimal enzymatic activity but potential scaffolding roles in immune modulation and autophagy-dependent catabolism. Achieving potent and selective agents for PIP4K2C while sparing other lipid and non-lipid kinases has been challenging. Here, we report the discovery of the highly potent PIP4K2C binder TMX-4102, which shows exclusive binding selectivity for PIP4K2C. Furthermore, we elaborated the PIP4K2C binder into TMX-4153, a bivalent degrader capable of rapidly and selectively degrading endogenous PIP4K2C. Collectively, our work demonstrates that PIP4K2C is a tractable and degradable target, and that TMX-4102 and TMX-4153 are useful leads to further interrogate the biological roles and therapeutic potential of PIP4K2C.

Cetuximab or nimotuzumab in combination with chemotherapy for treating recurrent/metastatic nasopharyngeal carcinoma: A meta‑analysis and systemic review

The present study aimed to evaluate the effectiveness and safety of cetuximab (CTX) or nimotuzumab (NTZ) in combination with chemotherapy for patients with recurrent and/or metastatic nasopharyngeal carcinoma (RM-NPC), and for this purpose, a single-group rate meta-analysis was performed. A systematic search of the Cochrane library, Pubmed, EMBASE, Chwina National Knowledge Infrastructure and WanFang databases for studies published until February 15, 2022 was performed. The 1-, 2-, 3- and 5-year overall survival (OS) rates were the primary endpoints. Complete response, partial response, stable disease, objective response rate, disease control rate and grade ≥3 toxicities were considered secondary endpoints. Cochran Q test and I² statistics were performed to assess the heterogeneity among studies. A total of nine studies comprising 435 patients were included in the analysis. The pooled 1-, 2-, 3- and 5-year OS rates were 81.0% [95% confidence interval (CI): 65.0-90.7%], 49.9% (95% CI: 35.3-64.5%), 46.3% (95% CI: 31.4-61.8%) and 31.0% (95% CI: 20.8-43.4%), respectively. The pooled disease control rate and objective response rate were 88.7% (95% CI: 78.4-94.5%) and 55.6% (95% CI: 39.9-70.1%), respectively. In addition, all grade 3-4 adverse events from the included studies were gathered. In conclusion, the use of CTX or NTZ in combination with chemotherapy may be a feasible and safe option for treating RM-NPC.

Thymidine Phosphorylase Deficiency or Inhibition Preserves Cardiac Function in Mice With Acute Myocardial Infarction

Background Ischemic cardiovascular disease is the leading cause of death worldwide. Current pharmacologic therapy has multiple limitations, and patients remain symptomatic despite maximal medical therapies. Deficiency or inhibition of thymidine phosphorylase (TYMP) in mice reduces thrombosis, suggesting that TYMP could be a novel therapeutic target for patients with acute myocardial infarction (AMI). Methods and Results A mouse AMI model was established by ligation of the left anterior descending coronary artery in C57BL/6J wild-type and TYMP-deficient (Tymp-/-) mice. Cardiac function was monitored by echocardiography or Langendorff assay. TYMP-deficient hearts had lower baseline contractility. However, cardiac function, systolic left ventricle anterior wall thickness, and diastolic wall strain were significantly greater 4 weeks after AMI compared with wild-type hearts. TYMP deficiency reduced microthrombus formation after AMI. TYMP deficiency did not affect angiogenesis in either normal or infarcted myocardium but increased arteriogenesis post-AMI. TYMP deficiency enhanced the mobilization of bone marrow stem cells and promoted mesenchymal stem cell (MSC) proliferation, migration, and resistance to inflammation and hypoxia. TYMP deficiency increased the number of larger MSCs and decreased matrix metalloproteinase-2 expression, resulting in a high homing capability. TYMP deficiency induced constitutive AKT phosphorylation in MSCs but reduced expression of genes associated with retinoid-interferon-induced mortality-19, a molecule that enhances cell death. Inhibition of TYMP with its selective inhibitor, tipiracil, phenocopied TYMP deficiency, improved post-AMI cardiac function and systolic left ventricle anterior wall thickness, attenuated diastolic stiffness, and reduced infarct size. Conclusions This study demonstrated that TYMP plays an adverse role after AMI. Targeting TYMP may be a novel therapy for patients with AMI.

Plant domestication shapes rhizosphere microbiome assembly and metabolic functions

BACKGROUND

The rhizosphere microbiome, which is shaped by host genotypes, root exudates, and plant domestication, is crucial for sustaining agricultural plant growth. Despite its importance, how plant domestication builds up specific rhizosphere microbiomes and metabolic functions, as well as the importance of these affected rhizobiomes and relevant root exudates in maintaining plant growth, is not well understood. Here, we firstly investigated the rhizosphere bacterial and fungal communities of domestication and wild accessions of tetraploid wheat using amplicon sequencing (16S and ITS) after 9 years of domestication process at the main production sites in China. We then explored the ecological roles of root exudation in shaping rhizosphere microbiome functions by integrating metagenomics and metabolic genomics approaches. Furthermore, we established evident linkages between root morphology traits and keystone taxa based on microbial culture and plant inoculation experiments.

RESULTS

Our results suggested that plant rhizosphere microbiomes were co-shaped by both host genotypes and domestication status. The wheat genomes contributed more variation in the microbial diversity and composition of rhizosphere bacterial communities than fungal communities, whereas plant domestication status exerted much stronger influences on the fungal communities. In terms of microbial interkingdom association networks, domestication destabilized microbial network and depleted the abundance of keystone fungal taxa. Moreover, we found that domestication shifted the rhizosphere microbiome from slow growing and fungi dominated to fast growing and bacteria dominated, thereby resulting in a shift from fungi-dominated membership with enrichment of carbon fixation genes to bacteria-dominated membership with enrichment of carbon degradation genes. Metagenomics analyses further indicated that wild cultivars of wheat possess higher microbial function diversity than domesticated cultivars. Notably, we found that wild cultivar is able to harness rhizosphere microorganism carrying N transformation (i.e., nitrification, denitrification) and P mineralization pathway, whereas rhizobiomes carrying inorganic N fixation, organic N ammonification, and inorganic P solubilization genes are recruited by the releasing of root exudates from domesticated wheat. More importantly, our metabolite-wide association study indicated that the contrasting functional roles of root exudates and the harnessed keystone microbial taxa with different nutrient acquisition strategies jointly determined the aboveground plant phenotypes. Furthermore, we observed that although domesticated and wild wheats recruited distinct microbial taxa and relevant functions, domestication-induced recruitment of keystone taxa led to a consistent growth regulation of root regardless of wheat domestication status.

CONCLUSIONS

Our results indicate that plant domestication profoundly influences rhizosphere microbiome assembly and metabolic functions and provide evidence that host plants are able to harness a differentiated ecological role of root-associated keystone microbiomes through the release of root exudates to sustain belowground multi-nutrient cycles and plant growth. These findings provide valuable insights into the mechanisms underlying plant-microbiome interactions and how to harness the rhizosphere microbiome for crop improvement in sustainable agriculture. Video Abstract.

Diagnostic TR-FRET assays for detection of antibodies in patient samples

Serological assays are important diagnostic tools for surveying exposure to the pathogen, monitoring immune response post vaccination, and managing spread of the infectious agent among the population. Current serological laboratory assays are often limited because they require the use of specialized laboratory technology and/or work with a limited number of sample types. Here, we evaluate an alternative by developing time-resolved Förster resonance energy transfer (TR-FRET) homogeneous assays that exhibited exceptional versatility, scalability, and sensitivity and outperformed or matched currently used strategies in terms of sensitivity, specificity, and precision. We validated the performance of the assays measuring total immunoglobulin G (IgG) levels; antibodies against severe acute respiratory syndrome coronavirus (SARS-CoV) or Middle Eastern respiratory syndrome (MERS)-CoV spike (S) protein; and SARS-CoV-2 S and nucleocapsid (N) proteins and applied it to several large sample sets and real-world applications. We further established a TR-FRET-based ACE2-S competition assay to assess the neutralization propensity of the antibodies. Overall, these TR-FRET-based serological assays can be rapidly extended to other antigens and are compatible with commonly used plate readers.

E3-Specific Degrader Discovery by Dynamic Tracing of Substrate Receptor Abundance

Targeted protein degradation (TPD) is a new pharmacology based on small-molecule degraders that induce proximity between a protein of interest (POI) and an E3 ubiquitin ligase. Of the approximately 600 E3s encoded in the human genome, only around 2% can be co-opted with degraders. This underrepresentation is caused by a paucity of discovery approaches to identify degraders for defined E3s. This hampers a rational expansion of the druggable proteome and stymies critical advancements in the field, such as tissue- and cell-specific degradation. Here, we focus on dynamic NEDD8 conjugation, a post-translational, regulatory circuit that controls the activity of 250 cullin RING E3 ligases (CRLs). Leveraging this regulatory layer enabled us to develop a scalable assay to identify compounds that alter the interactome of an E3 of interest by tracing their abundance after pharmacologically induced auto-degradation. Initial validation studies are performed for CRBN and VHL, but proteomics studies indicate broad applicability for many CRLs. Among amenable ligases, we select CRLDCAF15 for a proof-of-concept screen, leading to the identification of a novel DCAF15-dependent molecular glue degrader inducing the degradation of RBM23 and RBM39. Together, this strategy empowers the scalable identification of degraders specific to a ligase of interest.

Structural basis of regulated m7G tRNA modification by METTL1-WDR4

Chemical modifications of RNA have key roles in many biological processes1-3. N7-methylguanosine (m7G) is required for integrity and stability of a large subset of tRNAs4-7. The methyltransferase 1-WD repeat-containing protein 4 (METTL1-WDR4) complex is the methyltransferase that modifies G46 in the variable loop of certain tRNAs, and its dysregulation drives tumorigenesis in numerous cancer types8-14. Mutations in WDR4 cause human developmental phenotypes including microcephaly15-17. How METTL1-WDR4 modifies tRNA substrates and is regulated remains elusive18. Here we show,  through structural, biochemical and cellular studies of human METTL1-WDR4, that WDR4 serves as a scaffold for METTL1 and the tRNA T-arm. Upon tRNA binding, the αC region of METTL1 transforms into a helix, which together with the α6 helix secures both ends of the tRNA variable loop. Unexpectedly, we find that the predicted disordered N-terminal region of METTL1 is part of the catalytic pocket and essential for methyltransferase activity. Furthermore, we reveal that S27 phosphorylation in the METTL1 N-terminal region inhibits methyltransferase activity by locally disrupting the catalytic centre. Our results provide a molecular understanding of tRNA substrate recognition and phosphorylation-mediated regulation of METTL1-WDR4, and reveal the presumed disordered N-terminal region of METTL1 as a nexus of methyltransferase activity.

Constraints on Heavy Decaying Dark Matter from 570 Days of LHAASO Observations

The kilometer square array (KM2A) of the large high altitude air shower observatory (LHAASO) aims at surveying the northern γ-ray sky at energies above 10 TeV with unprecedented sensitivity. γ-ray observations have long been one of the most powerful tools for dark matter searches, as, e.g., high-energy γ rays could be produced by the decays of heavy dark matter particles. In this Letter, we present the first dark matter analysis with LHAASO-KM2A, using the first 340 days of data from 1/2-KM2A and 230 days of data from 3/4-KM2A. Several regions of interest are used to search for a signal and account for the residual cosmic-ray background after γ/hadron separation. We find no excess of dark matter signals, and thus place some of the strongest γ-ray constraints on the lifetime of heavy dark matter particles with mass between 10^{5} and 10^{9}  GeV. Our results with LHAASO are robust, and have important implications for dark matter interpretations of the diffuse astrophysical high-energy neutrino emission.

Whole exome sequencing in Brugada and long QT syndromes revealed novel rare and potential pathogenic mutations related to the dysfunction of the cardiac sodium channel

Background

Brugada syndrome (Brs) and long QT syndrome (LQTs) are the most observed “inherited primary arrhythmia syndromes” and “channelopathies”, which lead to sudden cardiac death.

Methods

Detailed clinical information of Brs and LQTs patients was collected. Genomic DNA samples of peripheral blood were conducted for whole-exome sequencing on the Illumina HiSeq 2000 platform. Then, we performed bioinformatics analysis for 200 genes susceptible to arrhythmias and cardiomyopathies. Protein interaction and transcriptomic co-expression were analyzed using the online website and GTEx database.

Results

All sixteen cases of Brs and six cases of LQTs were enrolled in the current study. Four Brs carried known pathogenic or likely pathogenic of single-point mutations, including SCN5A p.R661W, SCN5A p.R965C, and KCNH2 p.R692Q. One Brs carried the heterozygous compound mutations of DSG2 p.F531C and SCN5A p.A1374S. Two Brs carried the novel heterozygous truncated mutations (MAF < 0.001) of NEBL (p.R882X) and NPPA (p.R107X), respectively. Except for the indirect interaction between NEBL and SCN5A, NPPA directly interacts with SCN5A. These gene expressions had a specific and significant positive correlation in myocardial tissue, with high degrees of co-expression and synergy. Two Brs carried MYH7 p.E1902Q and MYH6 p.R1820Q, which were predicted as "damaging/possibly damaging" and "damaging/damaging" by Polyphen and SIFT algorithm. Two LQTs elicited the pathogenic single splicing mutation of KCNQ1 (c.922-1G > C). Three LQTs carried a single pathogenic mutation of SCN5A p.R1880H, KCNH2 p.D161N, and KCNQ1 p.R243S, respectively. One patient of LQTs carried a frameshift mutation of KCNH2 p. A188Gfs*143.

Conclusions

The truncated mutations of NEBL (p.R882X) and NPPA (p.R107X) may induce Brugada syndrome by abnormally affecting cardiac sodium channel. SCN5A (p.R661W, p.R965C and p.A1374S) and KCNH2 (p.R692Q) may cause Brugada syndrome, while SCN5A (p.R1880H), KCNQ1 (c.922-1G > C and p.R243S) and KCNH2 (p.D161N and p.A188Gfs*143) may lead to long QT syndrome.

Exploring the target scope of KEAP1 E3 ligase-based PROTACs

Targeted protein degradation (TPD) uses small molecules to recruit E3 ubiquitin ligases into the proximity of proteins of interest, inducing ubiquitination-dependent degradation. A major bottleneck in the TPD field is the lack of accessible E3 ligase ligands for developing degraders. To expand the E3 ligase toolbox, we sought to convert the Kelch-like ECH-associated protein 1 (KEAP1) inhibitor KI696 into a recruitment handle for several targets. While we were able to generate KEAP1-recruiting degraders of BET family and murine focal adhesion kinase (FAK), we discovered that the target scope of KEAP1 was narrow, as targets easily degraded using a cereblon (CRBN)-recruiting degrader were refractory to KEAP1-mediated degradation. Linking the KEAP1-binding ligand to a CRBN-binding ligand resulted in a molecule that induced degradation of KEAP1 but not CRBN. In sum, we characterize tool compounds to explore KEAP1-mediated ubiquitination and delineate the challenges of exploiting new E3 ligases for generating bivalent degraders.

Fertilizing-induced changes in the nitrifying microbiota associated with soil nitrification and crop yield

Ammonia oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira (CMX) play pivotal roles in global nitrogen-cycling network. Despite its importance, the driving forces for niche specialization of these nitrifiers, as well as their relative contributions to nitrification and crop yield have not been fully understood. Here, we investigated the niche specialization and environmental prevalence of nitrifying communities, and their importance for the nitrification rate and crop yield across a gradient of nitrogen inputs in a two-decade old field experiment. The results of ¹⁵N-tracer and quantitative PCR revealed that AOB and NOB jointly determined the gross nitrification rates across mineral fertilizer treatments, whereas AOA and AOB contributed more than other nitrifiers to nitrification under with organic fertilizer amendments. Linear regression model revealed that crop yield could be linked with AOB and NOB under inorganic farming but closely associated with CMX under organic management. Amplicon sequencing of these functional genes further demonstrated that mineral and organic fertilizers have distinct influences on the β-diversity and niche breadth of these nitrifying communities, indicating that fertilization triggered niche specialization of nitrifying guilds in agricultural soils. Notably, organic fertilization enhanced the network complexity of these nitrifiers by harboring keystone taxa. Random forest analysis provide robustly evidence for the hypothesis that abundance of functional genes contributed more than a- and β-diversity of these nitrifiers for driving nitrification rates and crop yields. Collectively, these findings provide the empirical evidence for the environmental adaptation and niche specialization of nitrifying communities, and their contributions in nitrification and crop yield when confronted with long-term nitrogen inputs.

Redirecting the Neo-Substrate Specificity of Cereblon-Targeting PROTACs to Helios

Immunomodulatory imide drugs (IMiDs), such as thalidomide and its analogues, are some of the most commonly utilized E3 ligase ligands for the development of proteolysis targeting chimeras (PROTACs). While the canonical neo-substrates of IMiDs (i.e., Ikaros and Aiolos) are often considered to be unwanted targets of PROTACs, maintaining the degradation of these neo-substrates also provides the opportunity to synergistically degrade multiple proteins with a single compound. Here, we report the development of ALV-07-082-03, a CDK4/CDK6/Helios triple degrader that consists of palbociclib, an FDA-approved CDK4/6 inhibitor, conjugated to DKY709, a novel IMiD-based Helios degrader. Pharmacological codegradation of CDK4/6 and Helios resulted in potent suppression of downstream signaling and proliferation in cancer cells, as well as enhanced derepression of IL-2 secretion. Thus, not only do we demonstrate the possibility of rationally redirecting the neo-substrate specificity of PROTACs by incorporating alternative molecular glue molecules as E3 ligase ligands but our findings also suggest that cotargeting CDK4/6 and Helios may have synergistic effects.

The effect of driving pressure-guided ventilation strategy on the patients with mechanical ventilation: a meta-analysis of randomized controlled trials

OBJECTIVE

The aim of this study was to evaluate the effect of driving pressure (DP) guided ventilation strategy on the patients with mechanical ventilation in the hospital.

MATERIALS AND METHODS

The articles published in PubMed, the Cochrane Library, the China National Knowledge Information (CNKI), Wei Pu, Wan Fang database and Web of Science from inception to September 2021 were retrieved. The Q test and the I² statistic were used to assess statistical heterogeneity. Risks ratios (RR) with 95% confidence intervals (CI) were calculated for mortality.

RESULTS

Seven studies (n=1,405 patients) were included. Five studies reported an adjusted Risk Ratio (RR) of mortality. Compared with the control group, the DP guided ventilation group was associated with a decreased mortality (RR 0.56; 95% confidence interval [CI], 0.39-0.79; p=0.001; I2 = 23%) using a fixed-effects model without significant heterogeneity. The control group had significantly higher driving pressure level than DP guided group (MD -3.03, 95%CI, -5.72 - -0.34, I2=100%, p=0.03); PaO2/FiO2 was significantly higher in DP guided group than in control group (MD 43.37; 95%CI, 12.58-74.15; I2=97%, p=0.006). There was no statistically significant difference in respiratory compliance, complications, platform pressure, duration of mechanical ventilation and the length of hospital stay between the DP guided group and the control group.

CONCLUSIONS

The results suggested that the driving pressure guided ventilation strategy could decrease the mortality and increase oxygenation index (OI). However, further high-quality randomized controlled trials (RCTs) are needed to verify the impact of driving pressure on mechanically ventilated patients.

Abstract 5277: Humoral SARS-CoV-2 response in asymptomatic precursor plasma cell dyscrasia patients: IMPACT study results

Introduction: Patients with hematologic malignancies, including multiple myeloma (MM), experience worse SARS-CoV-2 infection outcomes and sub-optimal vaccine responses. Monoclonal gammopathy of undetermined significance (MGUS) and smoldering multiple myeloma (SMM) precede MM and affect ~5% of individuals age &gt;=50. We previously showed that individuals with MGUS and SMM exhibit immune dysregulation. Here, we investigate the immune response to SARS-CoV-2 vaccination in these asymptomatic but potentially immunocompromised individuals.

Methods: The IMPACT study (IRB #20-332) is a prospective study at Dana-Farber Cancer Institute in collaboration with MMRF, which enrolled individuals nationwide with a diagnosed plasma cell dyscrasia and healthy individuals. As of October 2021, 3,005 individuals completed a questionnaire regarding prior infection or vaccination. We obtained 1,350 blood samples from 628 participants and analyzed anti-SARS-CoV-2 IgG antibody titer by ELISA.

Results: 2,771 (92%) participants were fully vaccinated (2 doses BNT162b2 or mRNA-1273; 1 dose Ad26.COV2.s), 269 (9%) had received a 3rd mRNA vaccine dose, and 234 (8%) were unvaccinated. 1,387 (46%) and 1,093 (36%) participants received mRNA vaccines (BNT162b2 and mRNA-1273), and 139 (5%) participants received an adenovirus vector vaccine (Ad26.COV2.S). 34 (1%) individuals reported SARS-CoV-2 infection after full vaccination.

We measured antibody titers in 201 MGUS, 223 SMM, 40 smoldering Waldenstrom macroglobulinemia (SWM), 64 MM, and 100 healthy controls. Multiple linear regression model estimated the association between various clinical variables and post-vaccination antibody titers. As previously reported, having MM was associated with low antibody titer (p &lt; 0.001). Of note, having SMM, regardless of risk stratification by 2/20/20 criteria, was also associated with low antibody titers, indicating that even low-risk SMM patients have a poor response to vaccination. MGUS and SWM diagnoses were not significantly associated with antibody titers. Additionally, male sex (p &lt; 0.010), elapsed time after vaccination (p &lt; 0.001), and BNT162b2 vaccine (p &lt; 0.001) were associated with low antibody titers. SARS-CoV-2 infection prior to vaccination was associated with high antibody titers.

We identified 25 patients (6 MGUS, 10 SMM, 2 SWM, 7 MM) who submitted blood samples after both the 2nd and 3rd dose. In these patients we observed a significant increase in antibody titer after a 3rd dose (p = 0.002). We also observed that antibody titers of patients after a 3rd dose (13 MGUS, 12 SMM, 2 SWM, 31 MM) were comparable to that of healthy individuals after a 2nd dose (p = 0.833).

Conclusion: Our data indicates that suboptimal response to SARS-CoV-2 does not only occur with MM and cancer patients receiving therapy but also in precursor asymptomatic patients including low-risk SMM.

Citation Format: Yoshinobu Konishi, Romanos Sklavenitis-Pistofidis, Hong Yue, Federico Ferrari, Massimiliano Russo, Robert A. Redd, Jacqueline Perry, Erica Horowitz, Anna V. Justis, Nader A. Shayegh, Elizabeth D. Lightbody, Shohreh Varmeh, Radoslaw P. Nowak, Mark Hamilton, Daniel Auclair, Catherine R. Marinac, Lorenzo Trippa, Eric S. Fischer, Irene M. Ghobrial. Humoral SARS-CoV-2 response in asymptomatic precursor plasma cell dyscrasia patients: IMPACT study results [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5277.

POS0833 DIFFERENCES BETWEEN AVACOPAN AND PREDNISONE FOR THE TREATMENT OF ANCA-ASSOCIATED VASCULITIS AT DIFFERENT THRESHOLDS OF GLUCOCORTICOID TOXICITY

Background

Treatment with glucocorticoids (GCs) for ANCA-associated vasculitis (AAV) is associated with substantial toxicity. The Glucocorticoid Toxicity Index (GTI) was developed to measure change in GC toxicity over time.1 Data from the composite GTI domains provide both an Aggregate Improvement Score (AIS) and a Cumulative Worsening Score (CWS) of GC toxicity, permitting the instrument to compare both improvement and worsening of GC toxicity across treatment groups. The GTI was a pre-specified secondary outcome in ADVOCATE, a randomized, double-blind, placebo-controlled trial in patients with AAV that aimed to replace a GC taper with avacopan, a complement C5a receptor inhibitor. Patients were randomized to either avacopan or a prednisone taper on a background of either cyclophosphamide or rituximab.2 In ADVOCATE, the median GC exposure was 400 mg vs. 2939 mg in the avacopan and prednisone groups, respectively, which is an 86% median reduction in GC exposure from all sources. Remission rates were comparable in the two groups at 26 weeks (72.3% vs. 70.1%, respectively), and avacopan was superior at 52 weeks (sustained remission in 65.7% vs. 54.9%).2

Objectives

To compare GC toxicity between the treatment groups at three different thresholds of GC toxicity, beginning with the minimum detectable difference (MDD) of the GTI.

Methods

The MDD for the GTI (10 points) was calculated in the initial validation phase of the instrument. Thus, any GTI score > 10 points may be considered to represent a true change in GC toxicity. We compared the two groups at GTI thresholds of 10, 20, and 30 points for both the CWS and AIS. The CWS comprises a total of all GC-related toxicities that have occurred in the GTI between baseline and 26 weeks (time of primary outcome). The AIS, in contrast, allows toxicities to be added if they are new or subtracted if they improve. Higher CWS and AIS values indicate greater severity of GC toxicity. The two scores together capture the nuances of longitudinal GC toxicity across multiple domains. We compared the percentages of those in the two treatment groups who exceeded GTI threshold values of 10, 20, and 30 points in the CWS or AIS.

Results

The percentages of patients exceeding the specified AIS thresholds differentiated the avacopan group from the prednisone group (48.2% vs. 60.4%, respectively, at the 10-point threshold, p=0.02; 29.5% vs. 45.1% at the 20-point threshold, p=0.003; and 18.1% vs. 33.5% at the 30-point threshold, p=0.001) (Table 1). The CWS differentiated avacopan from prednisone at the 20- and 30-point thresholds (57.8% vs 73.2%, respectively, at 20 points, p=0.002; 41.0% vs 55.5% at 30 points, p=0.007).

Table 1.

Percentages of Patients in ADVOCATE Exceeding Selected GTI Thresholds at Week 26

GTI threshold/study groupn (%) exceeding CWS thresholdp-valuen (%) exceeding AIS thresholdp-valueGTI worsening > 10 points Avacopan (N = 164)138 (83.1%)0.14780 (48.2%)0.022 Prednisone (N = 166)144 (87.8%)99 (60.4%)GTI worsening > 20 points Avacopan (N = 164)96 (57.8%)0.00249 (29.5%)0.003 Prednisone (N = 166)120 (73.2%)74 (45.1%)GTI worsening > 30 points Avacopan (N = 164)68 (41.0%)0.00730 (18.1%)0.001 Prednisone (N = 166)91 (55.5%)55 (33.5%)

AIS, Aggregate Improvement Score; CWS, Cumulative Worsening Score; GTI, Glucocorticoid Toxicity Index

Conclusion

Among patients with AAV, treatment with avacopan was associated with lower GC toxicity across multiple GTI thresholds compared to treatment with prednisone, consistent with the substantial reduction in total GC exposure associated with avacopan. The GTI scores differentiated the two treatment groups effectively through a composite of GC toxicity domains.

References

[1]McDowell PJ, Stone JH, Zhang Y, et al. Quantification of Glucocorticoid-Associated Morbidity in Severe Asthma Using the Glucocorticoid Toxicity Index. J Allergy Clin Immunol Pract. 2021; 9:365-72.

[2]Jayne DRW, Merkel PA, Schall TJ, et al. Avacopan for the Treatment of ANCA-Associated Vasculitis. N Engl J Med. 2021;384:599-609.

Disclosure of Interests

Naomi Patel: None declared, Yuqing Zhang: None declared, David Jayne Speakers bureau: Amgen, Vifor, Consultant of: Astra-Zeneca, BMS, Boehringer-Ingelheim, Chemocentryx, GSK, Novartis, Otsuka, Roche/Genentech, Takeda, UCB & Vifor, Grant/research support from: GSK, Roche/Genentech, Peter A Merkel Consultant of: AbbVie, AstraZeneca, Boeringher-Ingelheim, Bristol-Myers Squibb, ChemoCentryx, Forbius, Genentech/Roche, Genzyme/Sanofi, GlaxoSmithKline, Immagene, InflaRx, Jannsen, Kiniksa, Kyverna, Magenta, MiroBio, Novartis, Pfizer, Regeneron, Sparrow, Takeda, Talaris, Grant/research support from: AbbVie, AstraZeneca, Boeringher-Ingelheim, Bristol-Myers Squibb, ChemoCentryx, Forbius, Genentech/Roche, Genzyme/Sanofi, GlaxoSmithKline, InflaRx, Sanofi, Takeda, Huibin Yue Shareholder of: ChemoCentryx, Employee of: ChemoCentryx, Pirow Bekker Shareholder of: ChemoCentryx, Consultant of: ChemoCentryx, Employee of: ChemoCentryx, John H. Stone Shareholder of: Steritas, Consultant of: ChemoCentryx, Roche/Genentech, Sanofi, Bristol-Myers Squib, AbbVie, InflaRx, Kyverna, Novartis, Q32Bio, Zenas, Horizon, Grant/research support from: Roche/Genentech, Horizon, Sanofi, Bristol-Myers Squib

OP0180 EFFECT OF AVACOPAN ON RELAPSE RATES AND RELAPSE-FREE TIME IN PATIENTS WITH ANCA-ASSOCIATED VASCULITIS, RESULTS OF THE PHASE 3 ADVOCATE STUDY

Background

For patients with ANCA-associated vasculitis, both failure to achieve remission and relapse after achieving remission are associated with worse long-term outcomes. Avacopan, an oral selective inhibitor of the C5a receptor, is approved for the treatment of ANCA-associated vasculitis. The phase 3 ADVOCATE study tested daily avacopan as a substitute for a standard oral glucocorticoid taper regimen. At week 26, the avacopan group achieved a remission rate (72.3%) comparable to the prednisone group (70.1%) and superior sustained remission at Week 52 (65.7% avacopan vs. 54.9% prednisone groups, respectively [1]). The median (mean) total glucocorticoid dose from all sources was 400 mg (1349 mg) in the avacopan group versus 2939 mg (3655 mg) in the prednisone group, representing 86% (63%) lower glucocorticoid exposure in the avacopan group. Compared with the prednisone group, the avacopan group showed a reduction in the proportion of patients who relapsed after achieving remission and, among patients who achieved remission, a longer time to relapse (1).

Objectives

To further characterize efficacy, additional post-hoc analyses compared the avacopan and prednisone groups regarding i) failure to achieve remission and ii) relapse after achieving remission.

Methods

ADVOCATE, a phase 3, randomized, double-blind, controlled trial in 330 patients, evaluated the efficacy and safety of avacopan. Patients with ANCA-associated vasculitis (new-onset or relapsing disease) were randomized to receive avacopan 30 mg twice daily, or a standard 20-week oral prednisone taper, plus matching placebos, in addition to background immunosuppressant therapy. For the purpose of these analyses, remission was defined as the first timepoint when a BVAS of 0 was achieved. Relapse was defined as worsening of disease, after having previously achieved remission, that involved one or more major or three or more minor items in the BVAS, or one or two minor items in the BVAS recorded at two consecutive study visits.

Two post-hoc sensitivity analyses of patients in the intent-to-treat population examined: i) the proportion of patients who failed to achieve remission, or achieved remission and subsequently relapsed after achieving that remission, and ii) relapse-free time. For patients who achieved remission, relapse-free time was calculated as the number of days from the initial remission achieved to relapse. For patients who failed to achieve remission, relapse-free time was imputed as one day (remission and relapse on the same day). Patients who did not relapse were censored at the time of the last BVAS assessment.

Results

Baseline characteristics and time to achieve initial remission were similar between groups, and the incidence of BVAS 0 at any point in the study occurred approximately equally in both groups (158 avacopan vs. 157 prednisone). In the first sensitivity analysis, the avacopan group showed a reduction in the proportion of patients who failed to achieve remission, or relapsed after remission, compared with the prednisone group (24 [14.5% vs 40 [24.4%], p=0.011). In the second sensitivity analysis that included all patients in the trial, the hazard ratio of relapse-free time for avacopan vs prednisone was 0.57, 95% CI (0.35, 0.96), p=0.029 (log-rank test) (Figure 1).

Figure 1.

Relapse-free time among patients with ANCA-associated vasculitis in ADVOCATE (intention-to-treat population).

Conclusion

In the phase 3 ADVOCATE study of ANCA-associated vasculitis, more patients in the avacopan group compared to the prednisone group achieved remission, and fewer in the avacopan group relapsed after achieving remission. Patients receiving avacopan had a longer relapse-free time compared to the prednisone group. These post-hoc sensitivity analyses provide additional evidence of the efficacy of avacopan for the treatment of ANCA-associated vasculitis.

References

[1]Jayne D et al., Avacopan for the Treatment of ANCA-Associated Vasculitis. N Engl J Med 2021 384(7):599-609.

Disclosure of Interests

Peter A. Merkel Consultant of: AbbVie, AstraZeneca, Boeringher-Ingelheim, Bristol-Myers Squibb, ChemoCentryx, CSL Behring, Dynacure, EMDSerono, Forbius, Genentech/Roche, Genzyme/Sanofi, GlaxoSmithKline, Immagene, InflaRx, Jannsen, Kiniksa, Kyverna, Magenta, MiroBio, Neutrolis, Novartis, Pfizer, Regeneron, Sparrow, Takeda, Talaris.

Royalties: UpToDate., Grant/research support from: AbbVie, AstraZeneca, Boeringher-Ingelheim, Bristol-Myers Squibb, ChemoCentryx, Eicos, Forbius, Genentech/Roche, Genzyme/Sanofi, GlaxoSmithKline, InflaRx, Sanofi, Takeda, Huibin Yue Shareholder of: ChemoCentryx, Employee of: ChemoCentryx, Emil deGoma Shareholder of: ChemoCentryx, Employee of: ChemoCentryx, Pirow Bekker Shareholder of: ChemoCentryx, Consultant of: ChemoCentryx, David Jayne Paid instructor for: Lecture Fees: Amgen, Vifor, Consultant of: Astra-Zeneca, BMS, Boehringer-Ingelheim, Chemocentryx, GSK, NICE, Novartis, Otsuka, Roche/Genentech, Takeda, UCB & Vifor. Board Member: Aurinia., Grant/research support from: Commercial: GSK, Roche/Genentech; Non-commercial: EU, MRC, NIHR, Versus Arthritis

Overexpression of MdASMT9, an N-acetylserotonin methyltransferase gene, increases melatonin biosynthesis and improves water-use efficiency in transgenic apple

Improving apple water-use efficiency (WUE) is increasingly desirable in the face of global climate change. Melatonin is a pleiotropic molecule that functions in plant development and stress tolerance. In apple, exogenous application of melatonin has been largely investigated, but melatonin biosynthesis and its physiological roles remain elusive. In the plant biosynthetic pathway of melatonin, the last and key step is that N-acetylserotonin methyltransferase (ASMT) converts N-acetylserotonin into melatonin. Here, we identified an apple ASMT gene, MdASMT9, using homology-based cloning and in vitro enzyme assays. Overexpression of MdASMT9 significantly increased melatonin accumulation in transgenic apple lines. Moreover, an enhanced WUE was observed in the MdASMT9-overexpressing apple lines. Under well-watered conditions, this increase in WUE was attributed to an enhancement of photosynthetic rate and stomatal aperture via a reduction in abscisic acid biosynthesis. By contrast, under long-term moderate water deficit conditions, regulations in photoprotective mechanisms, stomatal behavior, osmotic adjustment and antioxidant activity enhanced the WUE in transgenic apple lines. Taken together, our findings shed light on the positive effect of MdASMT9 on improving WUE of apple by modulating melatonin biosynthesis.

Abstract 130: Thymidine Phosphorylase Enhances Abdominal Aortic Aneurysm Formation In Mice

Abdominal aortic aneurysm (AAA) is affected by multiple factors, including vessel wall cells, extracellular matrix, genetic disorders, etc.; however, the pathophysiology of AAA remains unclear. We recently found that thymidine phosphorylase (TYMP) is a signaling protein, and an increase of TYMP inhibits the proliferation of VSMCs, the major cell population that affects AAA progression. TYMP enhances platelet activity, thrombosis, and inflammation. These data suggest that TYMP may play a role in AAA formation. By using human AAA samples, we found that TYMP expression was significantly increased in AAA vessel walls than in healthy aortas. We thus further examined the role of TYMP in AAA formation using a mouse model. WT C57BL/6J and Tymp -/- mice were fed a western diet (TD.88137), started at 4 weeks (wks) old for 8 wks, and then received implantation of Ang II mini pump, which delivers Ang II to mice at a dose of 1 μg/kg/min for 4 wks. By echography, we found that Ang II perfusion dramatically increased inner aorta diameter at the diastolic phase in WT, but not Tymp -/- mice. Mice were sacrificed 4 wks after Ang II perfusion. AAA was confirmed in 3 of the 12 WT mice, but no AAA was found in all 11 Tymp -/- mice used. The AAA was mainly formed at the suprarenal artery level. Histological examination confirmed the presence of freshly formed or fibrotic hematoma. By using TYMP overexpressing rat VSMC cell line, C2, and its control cells, PC, we found that TYMP increased MMP2 production, secretion, and activation, which was diminished by tipiracil, a selective TYMP inhibitor. Ang II did not affect extracellular MMP2 activity in both PC and C2. TYMP facilitated TNF-α induced MMP2 activation. TYMP induced constitutive AKT phosphorylation, which was further enhanced by TNF-α. TYMP increased expression of active TGFβ1. Consequently, TYMP significantly enhanced thrombospondin-1 type 1 repeat domain (TSR) stimulated TGFβ1 signaling activation and expression of CTGF, which is correlated with severe fibrotic disorders and AAA. In summary, our study, for the first time, demonstrated that TYMP, a pyrimidine salvage pathway enzyme, plays an important role in regulating vascular biology, especially, VSMC function. TYMP-mediated microenvironment changes enhance the development of AAA.

Serological testing for SARS-CoV-2 antibodies of employees shows low transmission working in a cancer center

BACKGROUND

The COVID-19 pandemic led to emergency measures to continue patient care and research at a comprehensive cancer center while protecting both employees and patients. Determining exposure and infection rates with SARS-CoV-2 were important to adjust workplace policies over time.

METHODS

Dana-Farber Cancer Institute (DFCI) has over 7,000 employees. Participation was voluntary. After consent, participants completed questionnaire of demographics, exposures and risk factors for COVID-19 illness at each time point (baseline, 3, 6, and 12 months) along with blood draws for SARS-CoV-2 antibody testing. Primary measure was determination of titers of SARS-CoV-2 spike protein IgG over time.

RESULTS

In total, 745 employees enrolled from May 2020 to February 2021 (mean [SD] age, 40[14] years; 572[80%] women). From May to July 2020, 47 of 519 employees (9.2%, 95% confidence interval [CI] 6.7-12.0%) tested positive for SARS-CoV-2 spike protein IgG antibodies. Three months later, 40 of 428 employees had positive antibodies (8.5%, 95% CI 6.0-11.0%) with 17 newly positive. At month 6, 78.5% of participants reported having received at least one dose of vaccine and the positivity rate for those vaccinated was 98% (95% CI, 95-100%). Spike protein IgG titers for those vaccinated were 7.9 times higher than participants not vaccinated (median IgG titer = 0.28 for positive antibody but not vaccinated versus 2.2 for vaccinated) but demonstrate evidence of waning over time.

CONCLUSIONS

SARS-CoV-2 antibody positivity remained less than 10% at a single comprehensive cancer center prior to vaccination and there is evidence of waning IgG titers over time after vaccination.

The functions of phospholipases and their hydrolysis products in plant growth, development and stress responses

Cell membranes are the initial site of stimulus perception from environment and phospholipids are the basic and important components of cell membranes. Phospholipases hydrolyze membrane lipids to generate various cellular mediators. These phospholipase-derived products, such as diacylglycerol, phosphatidic acid, inositol phosphates, lysophopsholipids, and free fatty acids, act as second messengers, playing vital roles in signal transduction during plant growth, development, and stress responses. This review focuses on the structure, substrate specificities, reaction requirements, and acting mechanism of several phospholipase families. It will discuss their functional significance in plant growth, development, and stress responses. In addition, it will highlight some critical knowledge gaps in the action mechanism, metabolic and signaling roles of these phospholipases and their products in the context of plant growth, development and stress responses.

MdUGT88F1-mediated phloridzin biosynthesis coordinates carbon and nitrogen accumulation in apple

The high accumulation of phloridzin makes apple (Malus domestica) unique in the plant kingdom, which suggests a vital role of its biosynthesis in physiological processes. In our previous study, silencing MdUGT88F1 (a key UDP-GLUCOSE: PHLORETIN 2'-O-GLUCOSYLTRANSFERASE gene) revealed the importance of phloridzin biosynthesis in apple development and Valsa canker resistance. Here, results from MdUGT88F1-silenced lines showed that phloridzin biosynthesis was indispensable for normal chloroplast development and photosynthetic carbon fixation by maintaining MdGLK1/2 (GOLDEN2-like1/2) expression. Interestingly, increased phloridzin biosynthesis did not affect plant (or chloroplast) development, but reduced nitrogen accumulation, leading to chlorophyll deficiency, light sensitivity, and sugar accumulation in MdUGT88F1-overexpressing apple lines. Further analysis revealed that MdUGT88F1-mediated phloridzin biosynthesis negatively regulated the cytosolic glutamine synthetase1-asparagine synthetase-asparaginase (GS1-AS-ASPG) pathway of ammonium assimilation and limited chlorophyll synthesis in apple shoots. The interference of phloridzin biosynthesis in the GS1-AS-ASPG pathway was also assumed to be associated with its limitation of the carbon skeleton of ammonium assimilation through metabolic competition with the tricarboxylic acid cycle. Taken together, our findings shed light on the role of MdUGT88F1-mediated phloridzin biosynthesis in the coordination between carbon and nitrogen accumulation in apple trees.

Chemo-proteomics exploration of HDAC degradability by small molecule degraders

Targeted protein degradation refers to the use of small molecules that recruit a ubiquitin ligase to a target protein for ubiquitination and subsequent proteasome-dependent degradation. While degraders have been developed for many targets, key questions regarding degrader development and the consequences of acute pharmacological degradation remain, specifically for targets that exist in obligate multi-protein complexes. Here, we synthesize a pan-histone deacetylase (HDAC) degrader library for the chemo-proteomic exploration of acute degradation of a key class of chromatin-modifying enzymes. Using chemo-proteomics, we not only map the degradability of the zinc-dependent HDAC family identifying leads for targeting HDACs 1-8 and 10 but also explore important aspects of degrading epigenetic enzymes. We discover cell line-driven target specificity and that HDAC degradation often results in collateral loss of HDAC-containing repressive complexes. These findings potentially offer a new mechanism toward controlling chromatin structure, and our resource will facilitate accelerated degrader design and development for HDACs.

Fluid-structure interaction analysis on motion control of a self-propelled flexible plate near a rigid body utilizing PD control

Inspired by a previous experimental study of fish swimming near a cylinder, we numerically investigate the swimming and station-holding behavior of a flexible plate ahead of a circular cylinder whose motion is controlled by a proportional-derivative (PD) controller. Specifically, the deformation of this two-dimensional plate is actuated by a periodically varying external force applied on the body surface, which mimics the fish muscle force to produce propulsive thrust. The actuation force amplitude is dynamically adjusted by a feedback controller to instruct the plate to swim the desired distance from an initial position to a target location and then hold the station there. Instead of directly using the instantaneous position signal, an average speed measured over one force actuation period is proposed with the inclusion of instantaneous position information to form the tracking error for the PD control. Our results show that the motion control of swimming and station holding has been achieved by this simple but effective feedback control without large overshoot when approaching the target at different flow conditions and actuation force formulas. Although the swimming distance remains the same, a plate whose initial position is closer to the cylinder requires less energy expenditure to swim to the target location and hold the station there. This is because the low-pressure zone near the trailing edge of the plate is reduced in size, which provides drag reduction, contributing to reduced swimming energy. A higher Reynolds number also leads to energy savings. Under the same control strategy, the swimming performance is more affected by the force-frequency while the phase shift of the actuation force has a less significant impact.

Preoperative anxiety in children aged 2-7 years old: a cross-sectional analysis of the associated risk factors

BACKGROUND

Preoperative anxiety in children is harmful. Despite this, there is a scarcity of studies examining the incidence of preoperative anxiety and its related effects in China. This study investigated preoperative anxiety in children aged 2 to 7 in the pediatric surgery department of a tertiary hospital in China. The factors influencing preoperative anxiety in these children were identified.

METHODS

The researchers used the Chinese version of the modified Yale Preoperative Anxiety Scale (CmYPAS) and the Short Form of CmYPAS (CmYPAS-SF) to assess the preoperative anxiety state of children aged 2 to 7 who underwent elective surgery in the pediatric department of a tertiary hospital in China from July 1, 2020 to September 30, 2020 were enrolled in this study. The generalized estimating equation model was used to analyze the factors influencing preoperative anxiety in children.

RESULTS

The preoperative anxiety rate of 220 children in the tertiary hospital was 67.6%. Multivariate analysis revealed that children who attended elementary school had a lower risk of preoperative anxiety compared to children who did not attend school [odd ratio (OR) =0.39, 95% confidence interval (CI), 0.19 to 0.79, P=0.010]. Children whose caregivers felt very worried experienced an increased risk of preoperative anxiety compared to children whose caregivers were not worried about the surgery at all (OR =3.40, 95% CI, 1.35 to 8.56, P=0.009). Children who were very resistant, cried violently, twisted their bodies during puncturing the needle were 5.8 times more likely to experience preoperative anxiety compared to children who were very cooperative. The risk of preoperative anxiety in children who cooperated with a staff member was about 1.5 times higher than that of children who were very cooperative.

CONCLUSIONS

The incidence of preoperative anxiety in children aged 2 to 7 in the tertiary hospital in China was similar to the children in other countries. The caregivers' degree of concern priored to the operation and the degree of cooperation from the children during puncturing the indwelling needle were the main factors influencing the occurrence of preoperative anxiety.

Discovery of a Potent Degrader for Fibroblast Growth Factor Receptor 1/2

Aberrant activation of FGFR signaling occurs in many cancers, and ATP-competitive FGFR inhibitors have received regulatory approval. Despite demonstrating clinical efficacy, these inhibitors exhibit dose-limiting toxicity, potentially due to a lack of selectivity amongst the FGFR family and are poorly tolerated. Here, we report the discovery and characterization of DGY-09-192, a bivalent degrader that couples the pan-FGFR inhibitor BGJ398 to a CRL2^VHL E3 ligase recruiting ligand, which preferentially induces FGFR1&2 degradation while largely sparing FGFR3&4. DGY-09-192 exhibited two-digit nanomolar DC₅₀ s for both wildtype FGFR2 and several FGFR2-fusions, resulting in degradation-dependent antiproliferative activity in representative gastric cancer and cholangiocarcinoma cells. Importantly, DGY-09-192 induced degradation of a clinically relevant FGFR2 fusion protein in a xenograft model. Taken together, we demonstrate that DGY-09-192 has potential as a prototype FGFR degrader.

Acute pharmacological degradation of Helios destabilizes regulatory T cells

The zinc-finger transcription factor Helios is critical for maintaining the identity, anergic phenotype and suppressive activity of regulatory T (T_reg) cells. While it is an attractive target to enhance the efficacy of currently approved immunotherapies, no existing approaches can directly modulate Helios activity or abundance. Here, we report the structure-guided development of small molecules that recruit the E3 ubiquitin ligase substrate receptor cereblon to Helios, thereby promoting its degradation. Pharmacological Helios degradation destabilized the anergic phenotype and reduced the suppressive activity of T_reg cells, establishing a route towards Helios-targeting therapeutics. More generally, this study provides a framework for the development of small-molecule degraders for previously unligandable targets by reprogramming E3 ligase substrate specificity.

Genome-Wide Identification of PRP Genes in Apple Genome and the Role of MdPRP6 in Response to Heat Stress

Plant proline-rich proteins (PRPs) are cell wall proteins that occur in the plant kingdom and are involved in plant development and stress response. In this study, 9 PRP genes were identified from the apple genome and a comprehensive analysis of the PRP family was conducted, including gene structures, phylogenetic analysis, chromosome mapping, and so on. The expression of MdPRPs varied among tissues and in response to different types of stresses. MdPRP4 and MdPRP7 were induced by five detected stress treatments, including heat, drought, abscisic acid, cold, and salt; the expression patterns of the others varied under different types of stress. Subcellular localization showed that MdPRPs mainly functioned in the cytoplasm, except for MdPRP1 and MdPRP5, which also functioned in the nucleus. When MdPRP6 was overexpressed in tobacco, the transgenic plants showed higher tolerance to high temperature (48 °C) compared with wild-type (WT) plants. The transgenic plants showed milder wilting, a lower accumulation of electrolyte leakage, MDA and ROS, and a higher level of chlorophyll and SOD and POD activity, indicating that MdPRP6 may be an important gene in apples for heat stress tolerance. Overall, this study suggested that MdPRPs are critically important for the ability of apple responses to stresses.