Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation

Transcription factor (TF)-cofactor (COF) interactions define dynamic, cell-specific networks that govern gene expression; however, these networks are understudied due to a lack of methods for high-throughput profiling of DNA-bound TF-COF complexes. Here we describe the Cofactor Recruitment (CoRec) method for rapid profiling of cell-specific TF-COF complexes. We define a lysine acetyltransferase (KAT)-TF network in resting and stimulated T cells. We find promiscuous recruitment of KATs for many TFs and that 35% of KAT-TF interactions are condition specific. KAT-TF interactions identify NF-κB as a primary regulator of acutely induced H3K27ac. Finally, we find that heterotypic clustering of CBP/P300-recruiting TFs is a strong predictor of total promoter H3K27ac. Our data supports clustering of TF sites that broadly recruit KATs as a mechanism for widespread co-occurring histone acetylation marks. CoRec can be readily applied to different cell systems and provides a powerful approach to define TF-COF networks impacting chromatin state and gene regulation.

Forb stability, dwarf shrub stability and species asynchrony regulate ecosystem stability along an experimental precipitation gradient in a semi-arid desert grassland

Precipitation pattern changes may affect plant biodiversity, which could impact ecosystem stability. However, the effects of changes in precipitation regime on ecosystem stability and their potential mechanisms are still unclear. We conducted a 3-year field manipulation experiment with five precipitation treatments (-40%, -20%, 0% (CK), +20% and +40% of ambient growing season precipitation) in a semi-arid desert grassland to examine the effects of precipitation alterations on functional group stability, species asynchrony, and diversity, and the underlying mchanisms of ecosystem stability using structural equation modelling. Alterations in precipitation had different effects on community biomass and functional group biomass. Moreover, ecosystem stability was mainly driven by forb stability (path coefficient = 0.79). Changes in precipitation had significant effects on soil dissolved inorganic N (P < 0.01) further affecting ecosystem stability through species asynchrony (path coefficient = 0.25). Dwarf shrubs had a stabilizing effect on ecosystem stability (path coefficient = 0.32), mainly via deep roots. Ecosystem stability tended to be lower in the -40% (4.72) and +40% (2.74) precipitation treatments. The common reduction in species asynchrony and stability of forb and dwarf shrub functional groups resulted in lower ecosystem stability under the -40% treatment. The lower stability under the +40% treatment might be ascribed to unimproved dwarf shrub stability. Higher dwarf shrub and forb stability contributed to higher ecosystem stability under normal precipitation changes (±20% treatments) and CK. Species diversity was not a crucial driver of ecosystem stability. Our results indicate that precipitation alteration can regulate ecosystem stability via functional group stability (e.g. forb stability, dwarf shrub stability) and species asynchrony in a semiarid desert grassland.

[Analysis of clinical data of necrotizing fasciitis secondary to intestinal fistulas and screening the mortality risk factors]

Objective: To analyze the clinical data and to screen the mortality risk factors of necrotizing fasciitis (NF) secondary to intestinal fistulas (NFsIF). Methods: This study was a retrospective observational study. The data of all NFsIF cases who met the inclusion criteria and were admitted into Shandong Provincial Hospital Affiliated to Shandong First Medical University (hereinafter referred to as our unit) from January 2000 to October 2023, and in PubMed, Web of Science, Scopus, China National Knowledge Infrastructure, and Chinese Medical Journal Network databases from its establishment to October 2023 were retrieved and screened. Based on clinical outcomes, the cases were divided into survival group (47 males and 24 females) and death group (16 males and 7 females), and the mortality rate was calculated. Clinical data of patients in the two groups including age, underlying diseases (most related to NF), symptom duration before presentation, white blood cell count, causes of NF, signs of peritonitis, scope of NF involvement, and intestinal management and wound management measures were compared and analyzed to screen the risk factors of death in 94 patients with NFsIF. Results: A total of 94 valid cases were collected, including 90 patients reported in the literature and 4 patients admitted to our unit, with the mortality rate of patients being 24.5% (23/94). Univariate analysis showed that there were no statistically significant differences in age, underlying diseases, symptom duration before presentation, white blood cell count, causes of NF, signs of peritonitis, scope of NF involvement between patients in the two groups (P>0.05); there were statistically significant differences in intestinal treatment and wound treatment between the two groups (with χ2 values of 17.97 and 8.33, respectively, P<0.05). Multivariate logistic regression analysis showed that both intestinal treatment measures and wound treatments measures were independent risk factors for death in 94 NFsIF patients, among which first-stage colostomy+late-stage reconstruction and negative presssure therapy had higher protective effects (with odds ratios of 0.05 and 0.27, respectively, 95% confidence intervals of 0.01-0.33 and 0.08-0.88, respectively, P<0.05). Conclusions: The mortality risk of patients with NFsIF is high. Based on comprehensive treatments, active intestinal and wound treatment may be the key to avoid death, with first-stage colostomy+late-stage reconstruction and negative pressure therapy having higher protective effects.

Changes in brain susceptibility in Wilson's disease patients: a quantitative susceptibility mapping study

AIM

To assess changes in the susceptibility of the caudate nucleus (CN), putamen, and globus pallidus (GP) in patients with neurological and hepatic Wilson's disease (WD) by quantitative susceptibility mapping (QSM).

MATERIAL AND METHODS

The brain MRI images of 33 patients diagnosed with WD and 20 age-matched controls were analysed retrospectively. All participants underwent brain T1-weighted, T2-weighted, and QSM imaging using a 1.5 T magnetic resonance imaging (MRI) machine. QSM maps were evaluated with the STISuite toolbox. The quantitative susceptibility levels of the CN, putamen, and GP were analysed using region of interest analysis on QSM maps. Differences among neurological WD patients, hepatic patients, and controls were determined.

RESULTS

Susceptibility levels were significantly higher for all examined structures (CN, putamen and GP) in patients with neurological WD compared with controls (all p<0.05) and hepatic WD patients (all p<0.05). No statistically significant differences were found in susceptibility levels between patients with hepatic WD and controls (all p>0.05).

CONCLUSION

The QSM technique is a valuable tool for detecting changes in brain susceptibility in WD patients, indicating abnormal metal deposition. Notably, the current findings suggest that neurological WD patients exhibit more severe susceptibility changes compared with hepatic WD patients. Therefore, QSM can be utilised as a complementary method to detect brain injury in WD patients.

Photonic spin Hall effect driven broadband multi-focus dielectric metalens

The multi-focus metalens can couple the light into multiple channels in optical interconnections, which is beneficial to the development of planar, miniaturized, and integrated components. We propose broadband photonic spin Hall effect (PSHE) driven multi-focus metalenses, in which each nanobrick plays a positive role for all focal points. Three PSHE driven metalenses with four, six, and eight focal points have been designed and investigated, respectively. Under the incidences of left-/right-handed circularly polarized (LCP/RCP) light, these metalenses can generate regularly distributed two, three, and four RCP/LCP focal points, respectively. The uniformity of the focusing intensity has been investigated in detail by designing an additional four six-focus metalenses with different focus distributions. The uniqueness of these metalenses makes this design philosophy very attractive for applications in spin photonics, compact polarization detection, multi-imaging systems, and information processing systems.

The Role of Radiotherapy in Patients with Refractory Hodgkin Lymphoma after Brentuximab Vedotin and -/or Immune Checkpoint Inhibitors

PURPOSE/OBJECTIVE(S)

Brentuximab vedotin (BV) and immune checkpoint inhibitors (ICIs) had important roles in the treatment of relapse or refractory (R/R) Hodgkin lymphoma (HL). Treatment of refractory disease after BV and -/or ICIs remains a challenge. This study was conducted to evaluate the efficacy and safety of radiotherapy for R/R HL after failure to BV or ICIs.

MATERIALS/METHODS

We retrospectively analyzed patients in two institutions with R/R HL who had failed after first-line therapy, and were refractory to BV or ICIs, and received radiotherapy (RT) thereafter. The overall response rate (ORR), duration of response (DOR), progression-free survival (PFS) and overall survival (OS) were analyzed.

RESULTS

A total of 19 patients were enrolled. First-line systemic therapy consisted of ABVD (84.2%), AVD + ICIs (10.5%) and BEACOPP (5.3%), respectively. After first-line therapy, 15 patients (78.9%) were refractory, and 4 patients (21.1%) relapsed. After diagnosis of R/R HL, 8 patients (42.1%) received BV, and 17 patients (89.5%) received ICIs. RT was delivered in all 19 patients who failed after BV or ICIs. In 16 efficacy-evaluable patients, the ORR and CR rate were 100% and 100%. The median DOR was 17.2 months (range, 7.9 to 46.7 months). 3 patients progressed at outside of the radiation field. The in-field-response rate was 100%. The 12-month PFS and OS were 84.4% and 100%, respectively. No patients were reported with sever adverse events.

CONCLUSION

This study concluded that radiotherapy was effective and safe for refractory HL after BV or ICIs. Further prospective studies were warranted.

[Efficacy of arteriovenous argatroban versus heparin flush anticoagulation after cardiovascular surgery]

Objective: To compare the effects of arteriovenous argatroban and heparin flushes on platelet count and assess the occurrence of heparin-induced thrombocytopenia (HIT) and other complications in patients undergoing cardiovascular surgeries. Methods: A single-center, prospective randomized control study was conducted. Patients who underwent cardiovascular surgery at Fuwai Hospital, Chinese Academy of Medical Sciences from March to December 2019 were randomly divided into the argatroban group (250 ml normal saline plus 2.5 mg of argatroban) and the heparin group (250 ml normal saline plus 10 mg of heparin). Platelet count, hemorrhage, and thrombosis were assessed. The 4T scores of HIT, the incidences of HIT and other complications were also evaluated. Results: A total of 491 patients (307 males and 184 females) were included in the study, with a mean age of (52.3±13.7) years. There were 245 cases in the argatroban group and 246 cases in the heparin group, respectively. There was no statistically significant difference in the preoperative platelet count between the argatroban and heparin groups [198.0 (161.0, 248.0)×10⁹/L vs 194.0 (157.2, 243.8)×10⁹/L, P=0.498]. Likewise, there were no statistically significant differences in the platelet count between the argatroban and heparin groups at 12 h, 1 day, and 5 days after operation [127.0 (100.0, 154.0)×10⁹/L vs 121.5 (90.2, 149.0)×10⁹/L, 126.0 (97.0, 162.0)×10⁹/L vs 123.5 (88.0, 151.0)×10⁹/L, 168.0 (130.0, 215.0) ×10⁹/L vs 161.0 (101.0, 210.5)×10⁹/L] (repeated measures ANOVA between groups: F=3.327, P=0.069; time comparison: F=532.523, P<0.001; time interaction between groups: F=0.675, P=0.512). The proportion of 4T scores of medium and high scores (≥4)[9.8% (24/245) vs 10.6% (26/246), P=0.777] and incidence of HIT antibody positive [1.63% (4/245) vs 1.63% (4/246), P=0.726] were similar between argatroban group and the heparin group. Mechanical ventilation time was shorter in the argatroban group than that in the heparin group [13.0 (11.0, 21.0) vs 15.5 (12.0, 21.0) h, P=0.020]. Conclusion: Compared with heparin, routine management with argatroban for arteriovenous flush in patients undergoing cardiovascular surgery does not affect the HIT incidence.

Abstract 1785: Multi-step engineering of gene-edited CAR T cells using RNA lipid nanoparticles

Autologous chimeric antigen receptor (CAR) T therapies utilize patient cells and can be limited by cell quality, and the high manufacturing burden of viral vectors. As such, there is a need for allogeneic, “off-the-shelf” CAR T cells to make these transformative treatments widely available. However, allogeneic therapies require multiple genetic engineering steps to express CAR and to delete proteins responsible for graft-versus-host disease. Messenger RNA (mRNA) is a promising approach for expression of therapeutic proteins and gene editing nucleases. In this work, we demonstrate a new method for multi-step engineering of gene-edited CAR T cells using RNA lipid nanoparticles (LNPs).

LNPs encapsulating Spy-Cas9 mRNA, TCR and CD52 guide RNA (sgRNA), and CAR mRNA were produced using microfluidics. The CAR construct contained an anti-CD19 scFv binding domain and CD3ζ/4-1BB co-stimulatory domains. Microgram quantities of RNA LNPs were produced to optimize LNP packaging, cargo ratios, and sgRNA combinations. Lead candidates were scaled to milligrams. Purified human primary T cells were cultured, activated, and expanded in serum-free media in plates, flasks and bioreactors. CAR+, TCR− or CD52− cells were generated by addition of the corresponding LNP to activated cells. Cytotoxic killing was determined by co-culture assays with leukemia cells. Gene knockout, CAR expression, viability and cell killing were measured using flow-cytometry.

CD19 CAR was selected as a relevant protein for expression, with TCR and CD52 proteins as gene knockout targets. Single-step addition of CAR LNPs to T cells resulted in transfection efficiencies of 95.0 ± 2.1% and high protein expression. Upon TCR or CD52 LNP addition to T cells, the onset of gene editing was within 48 hours, reaching single target knockout efficiencies of 92.3 ± 3.0% (TCR−), and double knockouts (TCR−/CD52−) of 74.5 ± 6.1%. Similar results were obtained when comparing different LNP batch sizes (microgram to milligram RNA) and cell culture vessels (125,000 to 45 million cells), demonstrating scalability of both the LNP production and cell treatment. Cell viabilities above 90% were maintained at all steps and for all RNA LNPs. Finally, as proof-of-concept for multi-step engineering, sequential addition of TCR LNPs and CAR LNPs resulted in simultaneous CAR expression and TCR gene knockout. These “off-the-shelf” gene-edited CAR T cells were functionally equivalent to non-edited cells in a B cell killing assay, efficiently clearing over 80% of leukemia target cells at a 1:1 ratio.

Our findings demonstrate the advantages of LNPs for RNA delivery to T cells. The simple and gentle nature of LNP cell treatment allows for multiple genetic engineering steps for simultaneous expression and deletion of proteins. Furthermore, LNPs can be easily manufactured using microfluidics, enabling small-scale screening of RNA libraries and rapid scale-up of lead candidates for clinical translation.

Citation Format: Samuel Clarke, R Geczy, A Balgi, S Park, R Zhao, M Swaminathan, R Tieu, N Hoang, C Webb, E Watt, M Wong, M Fujisawa, N Jain, Angela Zhang, Anitha Thomas. Multi-step engineering of gene-edited CAR T cells using RNA lipid nanoparticles [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1785.

ROS generation and p-38 activation contribute to montmorillonite-induced corneal toxicity in vitro and in vivo

BACKGROUND

Montmorillonite (Mt) and its derivatives are now widely used in industrial and biomedical fields. Therefore, safety assessments of these materials are critical to protect human health after exposure; however, studies on the ocular toxicity of Mt are lacking. In particular, varying physicochemical characteristics of Mt may greatly alter their toxicological potential. To explore the effects of such characteristics on the eyes, five types of Mt were investigated in vitro and in vivo for the first time, and their underlying mechanisms studied.

RESULTS

The different types of Mt caused cytotoxicity in human HCEC-B4G12 corneal cells based on analyses of ATP content, lactate dehydrogenase (LDH) leakage, cell morphology, and the distribution of Mt in cells. Among the five Mt types, Na-Mt exhibited the highest cytotoxicity. Notably, Na-Mt and chitosan-modified acidic Na-Mt (C-H-Na-Mt) induced ocular toxicity in vivo, as demonstrated by increases corneal injury area and the number of apoptotic cells. Na-Mt and C-H-Na-Mt also induced reactive oxygen species (ROS) generation in vitro and in vivo, as indicated by 2',7'-dichlorofluorescin diacetate and dihydroethidium staining. In addition, Na-Mt activated the mitogen-activated protein kinase signaling pathway. The pretreatment of HCEC-B4G12 cells with N-acetylcysteine, an ROS scavenger, attenuated the Na-Mt-induced cytotoxicity and suppressed p38 activation, while inhibiting p38 activation with a p38-specific inhibitor decreased Na-Mt-induced cytotoxicity.

CONCLUSIONS

The results indicate that Mt induces corneal toxicity in vitro and in vivo. The physicochemical properties of Mt greatly affect its toxicological potential. Furthermore, ROS generation and p38 activation contribute at least in part to Na-Mt-induced toxicity.

Liquid-like atoms in dense-packed solid glasses

Revealing the microscopic structural and dynamic pictures of glasses is a long-standing challenge for scientists^1,2. Extensive studies on the structure and relaxation dynamics of glasses have constructed the current classical picture^3-5: glasses consist of some 'soft zones' of loosely bound atoms embedded in a tightly bound atomic matrix. Recent experiments have found an additional fast process in the relaxation spectra^6-9, but the underlying physics of this process remains unclear. Here, combining extensive dynamic experiments and computer simulations, we reveal that this fast relaxation is associated with string-like diffusion of liquid-like atoms, which are inherited from the high-temperature liquids. Even at room temperature, some atoms in dense-packed metallic glasses can diffuse just as easily as they would in liquid states, with an experimentally determined viscosity as low as 10⁷ Pa·s. This finding extends our current microscopic picture of glass solids and might help establish the dynamics-property relationship of glasses⁴.

[P2X7R promotes migration and invasion of Lewis lung cancer cells by activating the AKT signaling pathway]

OBJECTIVE

To explore the role of P2X7 receptor (P2X7R) in migration and invasion of mouse Lewis lung cancer (LLC) cells and examine the tumorigenic ability of LLC cells in P2X7R-knockout mice.

METHODS

RT-PCR was used to examine P2X7R mRNA expression in LLC cells. LLC cells were treated with ATP (as a P2X7R agonist) or 2'- 3'- O- (4-benzoyl- benzoyl)-ATP (BzATP) (a P2X7R agonist) with or without pretreatment with P2X7R antagonist oxATP or A438079. The changes in migration and invasive abilities of the cells were evaluated using wound healing assay and Transwell assay; Western blotting was performed to determine the activation level of the key proteins in the AKT signaling pathway. The effects of BzATP, A438079, and LY294002 (a inhibitor of the PI3K/AKT pathway) on migration and invasion of LLC cells were also examined. In wild-type (WT) and P2X7R knockout (P2X7^-/-) C57BL/6 mice, the growth of subcutaneous LLC cell xenografts were observed by measuring tumor volume and weight.

RESULTS

P2X7R expression was detected in LLC cells. Treatment with P2X7R agonist significantly enhanced migration and invasion abilities of LLC cells, and this effect was inhibited by application of P2X7R antagonists (P < 0.001). Western blotting showed that BzATP treatment of LLC cells significantly increased the expression level of p-AKT protein, which was obviously lowered by treatment with P2X7R antagonist (P < 0.01). P2X7R antagonist strongly inhibited BzATP-induced enhancement of LLC cell migration and invasion (P < 0.001). In the tumor- bearing mice, the tumor volume and weight were significantly lower in P2X7^-/- mice than in WT mice (P < 0.05).

CONCLUSION

P2X7R promotes migration and invasion of LLC cells by activating the AKT signaling pathway, and LLC cells show lowered tumorigenic capacity in P2X7^-/- mice.

Waste Cooking Oil-Modified Epoxy Asphalt Rubber Binders with Improved Compatibility and Extended Allowable Construction Time

The application of crumb rubber from end-of-life tires and waste cooking oil (WCO) in road pavements is of significant importance from an economic and environmental viewpoint. However, the incorporation of crumb rubber greatly shortens the allowable construction time of epoxy asphalt binders due to the high viscosity of the epoxy asphalt rubber (EAR) binder and poor compatibility between crumb rubber and asphalt binder. To lower the viscosity of asphalt rubber, extend the allowable construction time and improve the compatibility of EAR binder, waste cooking oil (WCO) was introduced. The effect of WCO on the viscosity–time behavior, thermal stability, dynamic modulus, glass transitions, crosslink density, damping ability, compatibility, mechanical properties and phase separation of WCO-modified EAR binders was investigated by using the Brookfield viscometer, thermogravimetric analysis, dynamic mechanical analysis, universal testing machine and laser confocal microscopy. The test results demonstrated that the incorporation of WCO declined the viscosity and extended the allowable construction time of the unmodified EAR binder. The inclusion of WCO improved the compatibility between asphalt and crumb rubber and the damping ability and elongation at the break of the unmodified EAR binder. The presence of WCO had a marginal effect on the thermal stability of the unmodified EAR binder. Confocal microscopy observation revealed that asphalt rubber particles aggregated in the epoxy phase of the unmodified EAR binder. With the inclusion of WCO, co-continuous asphalt rubber particles became more spherical.

Graphene Oxide-Modified Epoxy Asphalt Bond Coats with Enhanced Bonding Properties

The bonding strength of the bond coat plays an important role in the composite action between the wearing surface and the deck plate of the orthotropic steel deck system. Poor bonding results in the delamination of the wearing surface from the deck plate. Graphene oxide (GO) possesses outstanding mechanical and thermal properties, as well as impressive multifunctional groups, which makes it an ideal reinforcement candidate for polymer matrices. In this study, graphene oxide was used to improve the bonding strength and toughness of the epoxy asphalt bond coat (EABC). The dispersion, hydrophobicity, viscosity-time behavior, phase-separated morphology, dynamic mechanical properties, pull-off strength, shear strength and mechanical performance of GO-modified EABCs were investigated using various techniques. The inclusion of GO improved the hydrophobicity of the unmodified EABC. The viscosity of the unmodified EABC was lowered with the addition of GO during curing. Moreover, the allowable construction time for the modified EABCs was extended with the GO loading. The incorporation of GO enhanced the stiffness of the unmodified EABC in the glassy and rubbery states. However, graphene oxide lowered the glass transition temperature of the asphalt of the unmodified EABC. Confocal microscopy observations revealed that GO was invisible in both the asphalt and epoxy phases of the EABC. The inclusion of GO improved the bonding strength, particularly at 60 °C, and mechanical properties of the unmodified EABC.

Influence of the Epoxy/Acid Stoichiometry on the Cure Behavior and Mechanical Properties of Epoxy Vitrimers

Bisphenol A epoxy resin cured with a mixture of dimerized and trimerized fatty acids is the first epoxy vitrimer and has been extensively studied. However, the cure behavior and thermal and mechanical properties of this epoxy vitrimer depend on the epoxy/acid stoichiometry. To address these issues, epoxy vitrimers with three epoxy/acid stoichiometries (9:11, 1:1 and 11:9) were prepared and recycled four times. Differential scanning calorimetry (DSC) was used to study the cure behavior of the original epoxy vitrimers. The dynamic mechanical properties and mechanical performance of the original and recycled epoxy vitrimers were investigated by using dynamic mechanical analysis (DMA) and a universal testing machine. Furthermore, the reaction mechanism of epoxy vitrimer with different epoxy/acid stoichiometry was interpreted. With an increase in the epoxy/acid ratio, the reaction rate, swelling ratio, glass transition temperature and mechanical properties of the original epoxy vitrimers decreased, whereas the gel content increased. The recycling decreased the swelling ratio and elongation at break of the original epoxy vitrimers. Moreover, the elongation at break of the recycled epoxy vitrimers decreased with the epoxy/acid ratio at the same recycling time. However, the gel content, tensile strength and toughness of the original epoxy vitrimers increased after the recycling. The mechanical properties of epoxy vitrimers can be tuned with the variation in the epoxy/acid stoichiometry.

Silica nanoparticles: Biomedical applications and toxicity

Silica nanoparticles (SiNPs) are composed of silicon dioxide, the most abundant compound on Earth, and are used widely in many applications including the food industry, synthetic processes, medical diagnosis, and drug delivery due to their controllable particle size, large surface area, and great biocompatibility. Building on basic synthetic methods, convenient and economical strategies have been developed for the synthesis of SiNPs. Numerous studies have assessed the biomedical applications of SiNPs, including the surface and structural modification of SiNPs to target various cancers and diagnose diseases. However, studies on the in vitro and in vivo toxicity of SiNPs remain in the exploratory stage, and the toxicity mechanisms of SiNPs are poorly understood. This review covers recent studies on the biomedical applications of SiNPs, including their uses in drug delivery systems to diagnose and treat various diseases in the human body. SiNP toxicity is discussed in terms of the different systems of the human body and the individual organs in those systems. This comprehensive review includes both fundamental discoveries and exploratory progress in SiNP research that may lead to practical developments in the future.