Molecular characterization and pathogenicity of a novel monopartite geminivirus infecting tobacco in China.

The occurrence of geminiviruses causes significant economic losses in many economically important crops. In this study, a novel geminivirus isolated from tobacco in Sichuan province of China, named tomato leaf curl Chuxiong virus (TLCCxV), was characterized by small RNA-based deep sequencing. The full-length of TLCCxV genome was determined to be 2744 nucleotides (nt) encoding six open reading frames. Phylogenetic and genome-wide pairwise identity analysis revealed that TLCCxV shared less than 91% identities with reported geminiviruses. A TLCCxV infectious clone was constructed and successfully infected Nicotiana benthamiana, N. tabacum, N. glutinosa, Solanum lycopersicum and Petunia hybrida plants. Furthermore, expression of the V2, C1 and C4 proteins through a potato virus X vector caused severe chlorosis or necrosis symptom in N. benthamiana. Taken together, we identified a new geminivirus in tobacco plants, and found that V2, C1 and C4 contribute to symptom development.

Integration of transcriptomics and metabolomics identify biomarkers of aberrant lipid metabolism in ulcerative colitis.

BACKGROUND: The incidence of ulcerative colitis (UC) continues to rise globally, but effective therapeutic targets are still lacking. In recent years, numerous studies have indicated that lipid therapies could offer a novel perspective for UC treatment. Given the absence of prior research utilizing high-throughput data to identify target genes associated with lipid metabolism, we conducted this work. METHODS: The training set for this study was derived from four datasets within the Gene Expression Omnibus (GEO), encompassing a total of 357 UC patients. We employed four machine learning methods (LASSO, SVM, RF, and Boruta) to jointly identify core biomarkers in these patients, whose aberrant expression needed to be validated in independent datasets and in dextrose sulfate sodium salt (DSS)-induced UC mouse models. Regarding metabolomics, we detected abnormal oxidized lipids in the serum of UC mouse using liquid chromatography-tandem mass spectrometry (LC-MS/MS) in conjunction with orthogonal partial least squares-discriminant analysis (OPLS-DA). RESULTS: Phospholipase A2 Group IIA (PLA2G2A) was first identified as a possible biomarker for UC, with AUC values of 0.810 and 1.000 in the two validation sets, while in animal models the gene showed similarly significant up-regulation in damaged intestinal mucosa. Further analysis of this gene showed that it was positively correlated with 17 immune cell types and histological severity. Additionally, we pioneered the development of a lipid metabolism score in UC research, which outperformed all individual genes in terms of disease diagnostic efficacy (AUC values of 0.980 and 1.000 for the two validation sets, respectively). Finally, the metabolomics study also identified 31 significantly abnormal oxidized lipids, including 12-HHT and DHA. CONCLUSIONS: PLA2G2A is a key therapeutic target for UC, and oxidized lipids such as 12-HHT can serve as potential serologic indicators for diagnosis.

The HSP90-MYC-CDK9 network drives therapeutic resistance in mantle cell lymphoma.

Brexucabtagene autoleucel CAR-T therapy is highly efficacious in overcoming resistance to Bruton's tyrosine kinase inhibitors (BTKi) in mantle cell lymphoma. However, many patients relapse post CAR-T therapy with dismal outcomes. To dissect the underlying mechanisms of sequential resistance to BTKi and CAR-T therapy, we performed single-cell RNA sequencing analysis for 66 samples from 25 patients treated with BTKi and/or CAR-T therapy and conducted in-depth bioinformatics™ analysis. Our analysis revealed that MYC activity progressively increased with sequential resistance. HSP90AB1 (Heat shock protein 90 alpha family class B member 1), a MYC target, was identified as early driver of CAR-T resistance. CDK9 (Cyclin-dependent kinase 9), another MYC target, was significantly upregulated in Dual-R samples. Both HSP90AB1 and CDK9 expression were correlated with MYC activity levels. Pharmaceutical co-targeting of HSP90 and CDK9 synergistically diminished MYC activity, leading to potent anti-MCL activity. Collectively, our study revealed that HSP90-MYC-CDK9 network is the primary driving force of therapeutic resistance.

Single-cell multiomics decodes regulatory programs for mouse secondary palate development.

Perturbations in gene regulation during palatogenesis can lead to cleft palate, which is among the most common congenital birth defects. Here, we perform single-cell multiome sequencing and profile chromatin accessibility and gene expression simultaneously within the same cells (n = 36,154) isolated from mouse secondary palate across embryonic days (E) 12.5, E13.5, E14.0, and E14.5. We construct five trajectories representing continuous differentiation of cranial neural crest-derived multipotent cells into distinct lineages. By linking open chromatin signals to gene expression changes, we characterize the underlying lineage-determining transcription factors. In silico perturbation analysis identifies transcription factors SHOX2 and MEOX2 as important regulators of the development of the anterior and posterior palate, respectively. In conclusion, our study charts epigenetic and transcriptional dynamics in palatogenesis, serving as a valuable resource for further cleft palate research.

A newly isolated intestinal bacterium involved in the C-ring cleavage of flavan-3-ol monomers and the antioxidant activity of the metabolites.

Flavan-3-ols are an important class of secondary metabolites in many plants. Their bioavailability and bioactivity are largely determined by the metabolism of intestinal microbiota. However, little is known about the intestinal bacteria involved in the metabolism of flavan-3-ols and the activities of the metabolites. C-ring cleavage is the initial and key step in the metabolism of flavan-3-ol monomers. Here, we isolated a strain from porcine cecum content, which is capable of cleaving the heterocyclic C-ring to form 1-(3',4'-dihydroxyphenyl)-3-(2'',4'',6''-trihydroxyphenyl)propan-2-ol from (+)-catechin and (-)-epicatechin, and 1-(3',4',5'-trihydroxyphenyl)-3-(2'',4'',6''-trihydroxyphenyl) propan-2-ol from (-)-epigallocatechin. The strain was identified as Streptococcus pasteurianus (Streptococcus gallolyticus subsp. Pasteurianus, designated as F32-1) based on 16S rDNA similarity and MALDI-TOF-MS identification. The formation of the C-ring cleavage structural unit by the F32-1 strain enhanced the chemical antioxidant ability and altered the cellular antioxidant activity of (+)-catechin, (-)-epicatechin and (-)-epigallocatechin. Overall, in this study we isolated a new intestinal bacterium involved in the C-ring cleavage of flavan-3-ol monomers and elucidated the bioactivity of their metabolites.

The Gene Expression Profiles Associated with Maternal Nicotine Exposure in the Liver of Offspring Mice.

This study aims to investigate the effect of maternal nicotine exposure on the gene expression profiles in the liver of offspring mice. Pregnant mice were subcutaneously injected with either saline vehicle or nicotine twice a day on gestational days 11-21. Total RNA from the liver samples which collected from the offspring mice of postnatal day 7 and 21 was subjected to RNA sequencing. Gene Ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway enrichment analysis were conducted to identify the functions of differentially expressed genes (DEGs). Four genes were selected for further validation by quantitative reverse transcription polymerase chain reaction (qRT-PCR). A total of 448 DEGs and 186 DEGs were identified on postnatal day 7 and 21, respectively. GO analysis revealed that the DEGs on postnatal day 7 mainly participated in the biological functions of cell growth and proliferation, and the DEGs on postnatal day 21 mainly participated in ion transport/activity. KEGG enrichment analysis showed that the DEGs on postnatal day 7 were mainly enriched in the cell cycle, cytokine-cytokine receptor interactions, hypertrophic cardiomyopathy, and the p53 signaling pathway, while the DEGs on postnatal day 21 were mainly enriched in neuroactive ligand-receptor interactions, the calcium signaling pathway, retinol metabolism, and axon guidance. The qRT-PCR results were consistent with the RNA sequencing data. The DEGs may affect the growth of liver in early postnatal period while may affect ion transport/activity in late postnatal period.

Fhb7-GST catalyzed glutathionylation effectively detoxifies the trichothecene family.

Trichothecene (TCN) contamination in food and feed is a serious challenge due to the negative health and economic impacts. Here, we confirmed that the glutathione S-transferase (GST) Fhb7-GST could broadly catalyze type A, type B and type D TCNs into glutathione epoxide adducts (TCN-13-GSHs). To evaluate the toxicity of TCN-13-GSH adducts, we performed cell proliferation assays in vitro, which demonstrated decreased cytotoxicity of the adducts. Moreover, in vivo assays (repeated-dose treatment in mice) confirmed that TCN-13-GSH adducts were dramatically less toxic than the corresponding TCNs. To establish whether TCN-13-GSH was metabolized back to free toxin during digestion, single-dose metabolic tests were performed in rats; DON-13-GSH was not hydrolyzed in vivo, but rather was quickly metabolized to another low-toxicity compound, DON-13-N-acetylcysteine. These results demonstrate the promise of Fhb7-GST as a candidate of detoxification enzyme potentially applied in TCN-contaminated agricultural samples, minimizing the detrimental effects of the mycotoxin.

Potentiation of apoptosis in drug-resistant mantle cell lymphoma cells by MCL-1 inhibitor involves downregulation of inhibitor of apoptosis proteins.

Bruton's tyrosine kinase inhibitors (BTKi) and CAR T-cell therapy have demonstrated tremendous clinical benefits in mantle cell lymphoma (MCL) patients, but intrinsic or acquired resistance inevitably develops. In this study, we assessed the efficacy of the highly potent and selective MCL-1 inhibitor AZD5991 in various therapy-resistant MCL cell models. AZD5991 markedly induced apoptosis in these cells. In addition to liberating BAK from the antiapoptotic MCL-1/BAK complex for the subsequent apoptosis cascade, AZD5991 downregulated inhibitor of apoptosis proteins (IAPs) through a BAK-dependent mechanism to amplify the apoptotic signal. The combination of AZD5991 with venetoclax enhanced apoptosis and reduced mitochondrial oxygen consumption capacity in MCL cell lines irrespective of their BTKi or venetoclax sensitivity. This combination also dramatically inhibited tumor growth and prolonged mouse survival in two aggressive MCL patient-derived xenograft models. Mechanistically, the augmented cell lethality was accompanied by the synergistic suppression of IAPs. Supporting this notion, the IAP antagonist BV6 induced dramatic apoptosis in resistant MCL cells and sensitized the resistant MCL cells to venetoclax. Our study uncovered another unique route for MCL-1 inhibitor to trigger apoptosis, implying that the pro-apoptotic combination of IAP antagonists and apoptosis inducers could be further exploited for MCL patients with multiple therapeutic resistance.

Pyroptosis is involved in maternal nicotine exposure-induced metabolic associated fatty liver disease progression in offspring mice.

We have investigated whether inflammasomes and pyroptosis are activated in maternal nicotine exposure (MNE) offspring mice and whether they are involved in MNE-promoted metabolic associated fatty liver disease (MAFLD) in adult offspring. We injected pregnant mice subcutaneously with saline vehicle or nicotine twice a day on gestational days 11-21. Offspring mice from both groups were fed with a normal diet (ND) or a high-fat diet (HFD) for 6 months at postnatal day 21 to develop the MAFLD model. Serum biochemical indices were analyzed, and liver histology was performed. The expression levels of inflammasome and pyroptosis proteins were detected by western blot. We found MNE significantly aggravated the injury of MAFLD in adult offspring mice. MNE activated inflammasomes and pyroptosis in both infant and adult offspring mice. HFD treatment activated inflammasomes but not pyroptosis at 3 months, while it showed no effect at 6 months. However, pyroptosis was more severe in MNE-HFD mice than in MNE-ND mice at 6 months. Taken together, our data suggest MNE promotes MAFLD progression in adult offspring mice. MNE also induces NLRP3 and NLRP6 inflammasome activation and pyroptosis in both infant and adult offspring mice, which may be involved in MNE-promoted progression of MAFLD.

Cortical Reorganization After Optical Alignment in Strabismic Patients Outside of Critical Period.

Purpose: To measure visual crowding, an essential bottleneck on object recognition and reliable psychophysical index of cortex organization, in older children and adults with horizontal concomitant strabismus before and after strabismus surgery. Methods: Using real-time eye tracking to ensure gaze-contingent display, we examined the peripheral visual crowding effects in older children and adults with horizontal concomitant strabismus but without amblyopia before and after strabismus surgery. Patients were asked to discriminate the orientation of the central tumbling E target letter with flankers arranged along the radial or tangential axis in the nasal or temporal hemifield at different eccentricities (5° or 10°). The critical spacing value, which is the minimum space between the target and the flankers required for correct discrimination, was obtained for comparisons before and after strabismus surgery. Results: Twelve individuals with exotropia (6 males, 21.75 ± 7.29 years, mean ± SD) and 15 individuals with esotropia (6 males, 24.13 ± 5.96 years) participated in this study. We found that strabismic individuals showed significantly larger critical spacing with nasotemporal asymmetry along the radial axis that related to the strabismus pattern, with exotropes exhibiting stronger temporal field crowding and esotropes exhibiting stronger nasal field crowding before surgical alignment. After surgery, the critical spacing was reduced and rebalanced between the nasal and temporal hemifields. Furthermore, the postoperative recovery of stereopsis was associated with the extent of nasotemporal balance of critical spacing. Conclusions: We find that optical realignment (i.e., strabismus surgery) can normalize the enlarged visual crowding effects, a reliable psychophysical index of cortical organization, in the peripheral visual field of older children and adults with strabismus and rebalance the nasotemporal asymmetry of crowding, promoting the recovery of postoperative stereopsis. Our results indicated a potential of experience-dependent cortical organization after axial alignment even for individuals who are out of the critical period of visual development, illuminating the capacity and limitations of optics on sensory plasticity and emphasizing the importance of ocular correction for clinical practice.

Synergistic biocontrol of Bacillus subtilis and Pseudomonas fluorescens against early blight disease in tomato.

Early blight of tomato caused by Alternaria solani results in significant crop losses. In this study, Bacillus subtilis J3 and Pseudomonas fluorescens J8 were co-cultured as a synthetic microbial community (BCA) for synergistic biocontrol of A. solani, and the inhibition mechanism was investigated. BCA presented an inhibition ration against A. solani at 94.91%, which lowered the disease incidence by 38.26-42.87%; reduced peroxidase, catalase, superoxide dismutase activity of tomatoes by 73.11-90.22%; and promoted the biomass by 66.91-489.21%. With BCA protection, the relative expression of tomato resistance genes (including gPAL2, SWRKY, PR-10, and CHI) in roots and leaves was 12.83-90.70% lower than without protection. BCA also significantly altered the rhizosphere and phyllosphere microbial community. The abundance of potentially beneficial bacteria, including Bacillus, Pseudomonas, Arthrobacter, Lysobacter, and Rhizobium, elevated by 6.58-192.77%. They were negatively correlated with resistance gene expression, indicating their vital involvement in disease control. These results provided essential information on the synergistic biocontrol mechanism of bacteria against pathogens, which could contribute to developing novel biocontrol strategies. KEY POINTS: • Bacillus and Pseudomonas present a synergistic biocontrol effect against A. solani. • Biocontrol prevents pathogen damage and improves tomato growth and systemic resistance. • Beneficial bacteria thrive in the rhizosphere is the key to microbial regulation.

Panax quinquefolius saponin inhibits vascular smooth muscle cell calcification via activation of nuclear factor-erythroid 2-related factor 2.

BACKGROUND: Panax quinquefolius saponin (PQS) is the main active component of Panax quinquefolius. Emerging evidence suggests that PQS exerts beneficial effects against cardiovascular diseases. However, the role and mechanism of PQS in vascular calcification are not unclear. The present study investigated the effects of PQS on the calcification of vascular smooth muscle cell (VSMCs). METHODS: The present study used calcification medium containing 3 mM inorganic phosphate (Pi) to induce rat VSMCs calcification. We investigated the effects of PQS on VSMCs calcification using alizarin red staining and alkaline phosphatase (ALP) activity assays. The intracellular reactive oxygen species (ROS) levels and the transcriptional activity of nuclear factor-erythroid 2-related factor 2 (Nrf2) were determined. The mRNA and protein expression levels of Nrf2, the antioxidant gene heme oxygenase-1 (HO-1), osteogenic markers, including runt-related transcription factor 2 (Runx2) and bone morphogenetic protein 2 (BMP2), and Kelch-like ECH-associated protein 1 (Keap1) were also measured. RESULTS: Treatment with Pi significantly increased intracellular calcium deposition and ALP activity, which were suppressed by PQS in a concentration-dependent manner. During VSMCs calcification, PQS inhibited the mRNA and protein expression of Runx2 and BMP2. PQS treatment reduced intracellular ROS production and significantly upregulated Nrf2 transcriptional activity and the expression of Nrf2 and its target antioxidant gene HO-1. PQS suppressed the Pi-induced protein expression of Keap1, which is an endogenous inhibitor of Nrf2. Keap1 siRNA treatment induced Nrf2 expression and downregulated Runx2 expression in the presence of Pi and PQS. CONCLUSION: Taken together, these findings suggest that PQS could effectively inhibit VSMCs calcification by ameliorating oxidative stress and regulating osteogenic genes via the promotion of Nrf2 expression.

Acrylamide in food: Occurrence, metabolism, molecular toxicity mechanism and detoxification by phytochemicals.

Acrylamide (ACR) is a common pollutant formed during food thermal processing such as frying, baking and roasting. ACR and its metabolites can cause various negative effects on organisms. To date, there have been some reviews summarizing the formation, absorption, detection and prevention of ACR, but there is no systematic summary on the mechanism of ACR-induced toxicity. In the past five years, the molecular mechanism for ACR-induced toxicity has been further explored and the detoxification of ACR by phytochemicals has been partly achieved. This review summarizes the ACR level in foods and its metabolic pathways, as well as highlights the mechanisms underlying ACR-induced toxicity and ACR detoxification by phytochemicals. It appears that oxidative stress, inflammation, apoptosis, autophagy, biochemical metabolism and gut microbiota disturbance are involved in various ACR-induced toxicities. In addition, the effects and possible action mechanisms of phytochemicals, including polyphenols, quinones, alkaloids, terpenoids, as well as vitamins and their analogs on ACR-induced toxicities are also discussed. This review provides potential therapeutic targets and strategies for addressing various ACR-induced toxicities in the future.

Exploiting PRMT5 as a target for combination therapy in mantle cell lymphoma characterized by frequent ATM and TP53 mutations.

Constant challenges for the treatment of mantle cell lymphoma (MCL) remain to be recurrent relapses and therapy resistance, especially in patients harboring somatic mutations in the tumor suppressors ATM and TP53, which are accumulated as therapy resistance emerges and the disease progresses, consistent with our OncoPrint results that ATM and TP53 alterations were most frequent in relapsed/refractory (R/R) MCL. We demonstrated that protein arginine methyltransferase-5 (PRMT5) was upregulated in R/R MCL, which predicted a poor prognosis. PRMT5 inhibitors displayed profound antitumor effects in the mouse models of MCL with mutated ATM and/or TP53, or refractory to CD19-targeted CAR T-cell therapy. Genetic knockout of PRMT5 robustly inhibited tumor growth in vivo. Co-targeting PRMT5, and ATR or CDK4 by using their inhibitors showed synergistic antitumor effects both in vitro and in vivo. Our results have provided a rational combination therapeutic strategy targeting multiple PRMT5-coordinated tumor-promoting processes for the treatment of R/R MCL with high mutation burdens.

Imaging findings and clinical function after combined surgery for recurrent patella dislocation: a comparative study.

Background: Limited research has evaluated imaging results following a combination of operations for recurrent patella dislocation (RPD) based on medial patellofemoral ligament (MPFL) reconstruction. Therefore, this study aimed to retrospectively compare the imaging and clinical results of RPD following 2 types of combined surgical techniques. Methods: Patients who underwent combined surgery for RPD from January 2008 to December 2019 were enrolled in the study and allocated into 2 groups. MPFL reconstruction combined with lateral retinacular release (LRR) was performed in groups A and B, and an additional tibial tuberosity transfer (TTT) was performed in group B only. Patients in group A with a tibial tuberosity trochlear groove (TT-TG) distance greater than 15 mm were included in subgroup A*. Congruence angle (CA), patellar tilt angle (PTA), lateral patellofemoral angle (LPA), lateral patellar displacement (LPD), TT-TG, Insall-Salvati Index (ISI), the Dejour type of trochlear dysplasia, and knee function were assessed. All groups were followed up in the short-term (1-2 years), and group B was also followed up in the mid-term (over 5 years). Results: A total of 40 knees (36 patients) were included in group A, 26 knees (24 patients) in subgroup A*, and 27 knees (26 patients) in group B. In group A, CA, PTA, and LPD had increased at the short-term follow-up, yet LPA had decreased compared to the results 3 days after surgery. In group B, at the mid-term follow-up, PTA (12.54±6.88 vs. 15.23±6.10; P=0.002) increased while LPD (7.08±6.48 vs. 4.69±6.28; P=0.049) decreased compared with the short-term outcomes. The more severe the femoral trochlear dysplasia, the lower the mid-term Kujala scores in group B (P=0.007). The short-term TT-TG (17.32±4.288 vs. 12.84±3.758; P<0.001) and ISI [1.25 (1.1075, 1.300) vs. 1.06 (1.00, 1.16); P<0.001] in group B were lower than those in group A, who had a higher Kujala score (P<0.001). The CA, LPD, ISI, TT-TG, and Kujala score in subgroup A* were higher than those in group B at the short-term follow-up (P<0.05). Conclusions: Both types of combination treatments were successful in altering the patellofemoral joint in a satisfactory manner, and the knee function improved in both groups. A TTT might not be necessary for patients with a TT-TG distance greater than 15 mm.

Visual Crowding Reveals Field- and Axis-Specific Cortical Miswiring After Long-Term Axial Misalignment in Strabismic Patients Without Amblyopia.

Purpose: Inspired by physiological and neuroimaging findings that revealed squint-induced modification of cortical volume and visual receptive field in early visual areas, we hypothesized that strabismic eyes without amblyopia manifest an increase in critical spacing of visual crowding, an essential bottleneck on object recognition and reliable psychophysical index of cortical organization. Methods: We used real-time eye tracking to ensure gaze-contingent display and examined visual crowding in patients with horizontal concomitant strabismus (both esotropia and exotropia) but without amblyopia and age-matched normal controls. Results: Nineteen patients with exotropia (12 men, mean ± SD = 22.89 ± 7.82 years), 21 patients with esotropia (10 men, mean ± SD = 23.48 ± 6.95 years), and 14 age-matched normal controls (7 men, mean ± SD = 23.07 ± 1.07 years) participated in this study. We found that patients with strabismus without amblyopia showed significantly larger critical spacing with nasotemporal asymmetry in only the radial axis that related to the strabismus pattern, with exotropia exhibiting stronger temporal hemifield crowding and esotropia exhibiting stronger nasal hemifield crowding, in both the deviated and fixating eyes. Moreover, the magnitude of crowding change was related to the duration and degree of strabismic deviation. Conclusions: Using visual crowding as a psychophysical index of cortical organization, our study demonstrated significantly greater peripheral visual crowding with nasotemporal asymmetry in only the radial axis in patients with strabismus without amblyopia, indicating the existence of hemifield- and axis-specific miswiring of cortical processing in object recognition induced by long-term adaptation to ocular misalignment.

Cotargeting of BTK and MALT1 overcomes resistance to BTK inhibitors in mantle cell lymphoma.

Bruton's tyrosine kinase (BTK) is a proven target in mantle cell lymphoma (MCL), an aggressive subtype of non-Hodgkin lymphoma. However, resistance to BTK inhibitors is a major clinical challenge. We here report that MALT1 is one of the top overexpressed genes in ibrutinib-resistant MCL cells, while expression of CARD11, which is upstream of MALT1, is decreased. MALT1 genetic knockout or inhibition produced dramatic defects in MCL cell growth regardless of ibrutinib sensitivity. Conversely, CARD11-knockout cells showed antitumor effects only in ibrutinib-sensitive cells, suggesting that MALT1 overexpression could drive ibrutinib resistance via bypassing BTK/CARD11 signaling. Additionally, BTK knockdown and MALT1 knockout markedly impaired MCL tumor migration and dissemination, and MALT1 pharmacological inhibition decreased MCL cell viability, adhesion, and migration by suppressing NF-κB, PI3K/AKT/mTOR, and integrin signaling. Importantly, cotargeting MALT1 with safimaltib and BTK with pirtobrutinib induced potent anti-MCL activity in ibrutinib-resistant MCL cell lines and patient-derived xenografts. Therefore, we conclude that MALT1 overexpression associates with resistance to BTK inhibitors in MCL, targeting abnormal MALT1 activity could be a promising therapeutic strategy to overcome BTK inhibitor resistance, and cotargeting of MALT1 and BTK should improve MCL treatment efficacy and durability as well as patient outcomes.