A Prion-like Domain in Transcription Factor EBF1 Promotes Phase Separation and Enables B Cell Programming of Progenitor Chromatin.

Establishment of B-lineage-specific gene expression requires the binding of transcription factors to inaccessible chromatin of progenitors. The transcription factor EBF1 can bind genomic regions prior to the detection of chromatin accessibility in a manner dependent on EBF1's C-terminal domain (CTD) and independent of cooperating transcription factors. Here, we studied the mechanism whereby the CTD enables this pioneering function. The CTD of EBF1 was dispensable for initial chromatin targeting but stabilized occupancy via recruitment of the chromatin remodeler Brg1. We found that the CTD harbors a prion-like domain (PLD) with an ability of liquid-liquid phase separation, which was enhanced by interaction of EBF1 with the RNA-binding protein FUS. Brg1 also partitioned into phase-separated FUS condensates and coincided with EBF1 and FUS foci in pro-B cells. Heterologous PLDs conferred pioneering function on EBF1ΔCTD. Thus, the phase separation ability of EBF1 facilitates Brg1-mediated chromatin opening and the transition of naive progenitor chromatin to B-lineage-committed chromatin.

FusionNW, a potential clinical impact assessment of kinases in pan-cancer fusion gene network.

Kinase fusion genes are the most active fusion gene group in human cancer fusion genes. To help choose the clinically significant kinase so that the cancer patients that have fusion genes can be better diagnosed, we need a metric to infer the assessment of kinases in pan-cancer fusion genes rather than relying on the sample frequency expressed fusion genes. Most of all, multiple studies assessed human kinases as the drug targets using multiple types of genomic and clinical information, but none used the kinase fusion genes in their study. The assessment studies of kinase without kinase fusion gene events can miss the effect of one of the mechanisms that enhance the kinase function in cancer. To fill this gap, in this study, we suggest a novel way of assessing genes using a network propagation approach to infer how likely individual kinases influence the kinase fusion gene network composed of ~5K kinase fusion gene pairs. To select a better seed of propagation, we chose the top genes via dimensionality reduction like a principal component or latent layer information of six features of individual genes in pan-cancer fusion genes. Our approach may provide a novel way to assess of human kinases in cancer.

FusionPDB: a knowledgebase of human fusion proteins.

Tumorigenic functions due to the formation of fusion genes have been targeted for cancer therapeutics (i.e. kinase inhibitors). However, many fusion proteins involved in various cellular processes have not been studied for targeted therapeutics. This is because the lack of complete fusion protein sequences and their whole 3D structures has made it challenging to develop new therapeutic strategies. To fill these critical gaps, we developed a computational pipeline and a resource of human fusion proteins named FusionPDB, available at https://compbio.uth.edu/FusionPDB. FusionPDB is organized into four levels: 43K fusion protein sequences (14.7K in-frame fusion genes, Level 1), over 2300 + 1267 fusion protein 3D structures (from 2300 recurrent and 266 manually curated in-frame fusion genes, Level 2), pLDDT score analysis for the 1267 fusion proteins from 266 manually curated fusion genes (Level 3), and virtual screening outcomes for 68 selected fusion proteins from 266 manually curated fusion genes (Level 4). FusionPDB is the only resource providing whole 3D structures of fusion proteins and comprehensive knowledge of human fusion proteins. It will be regularly updated until it covers all human fusion proteins in the future.

FusionNeoAntigen: a resource of fusion gene-specific neoantigens.

Among the diverse sources of neoantigens (i.e. single-nucleotide variants (SNVs), insertions or deletions (Indels) and fusion genes), fusion gene-derived neoantigens are generally more immunogenic, have multiple targets per mutation and are more widely distributed across various cancer types. Therefore, fusion gene-derived neoantigens are a potential source of highly immunogenic neoantigens and hold great promise for cancer immunotherapy. However, the lack of fusion protein sequence resources and knowledge prevents this application. We introduce 'FusionNeoAntigen', a dedicated resource for fusion-specific neoantigens, accessible at https://compbio.uth.edu/FusionNeoAntigen. In this resource, we provide fusion gene breakpoint crossing neoantigens focused on ∼43K fusion proteins of ∼16K in-frame fusion genes from FusionGDB2.0. FusionNeoAntigen provides fusion gene information, corresponding fusion protein sequences, fusion breakpoint peptide sequences, fusion gene-derived neoantigen prediction, virtual screening between fusion breakpoint peptides having potential fusion neoantigens and human leucocyte antigens (HLAs), fusion breakpoint RNA/protein sequences for developing vaccines, information on samples with fusion-specific neoantigen, potential CAR-T targetable cell-surface fusion proteins and literature curation. FusionNeoAntigen will help to develop fusion gene-based immunotherapies. We will report all potential fusion-specific neoantigens from all possible open reading frames of ∼120K human fusion genes in future versions.

Systematic investigation of the homology sequences around the human fusion gene breakpoints in pan-cancer - bioinformatics study for a potential link to MMEJ.

Microhomology-mediated end joining (MMEJ), an error-prone DNA damage repair mechanism, frequently leads to chromosomal rearrangements due to its ability to engage in promiscuous end joining of genomic instability and also leads to increasing mutational load at the sequences flanking the breakpoints (BPs). In this study, we systematically investigated the homology sequences around the genomic breakpoint area of human fusion genes, which were formed by the chromosomal rearrangements initiated by DNA double-strand breakage. Since the RNA-seq data is the typical data set to check the fusion genes, for the known exon junction fusion breakpoints identified from RNA-seq data, we have to infer the high chance of genomic breakpoint regions. For this, we utilized the high feature importance score area calculated from our recently developed fusion BP prediction model, FusionAI and identified 151 K microhomologies among ~24 K fusion BPs in 20 K fusion genes. From our multiple bioinformatics studies, we found a relationship between sequence homologies and the immune system. This in-silico study will provide novel knowledge on the sequence homologies around the coded structural variants.

Real-time single-proton counting with transmissive perovskite nanocrystal scintillators.

High-sensitivity radiation detectors for energetic particles are essential for advanced applications in particle physics, astronomy and cancer therapy. Current particle detectors use bulk crystals, and thin-film organic scintillators have low light yields and limited radiation tolerance. Here we present transmissive thin scintillators made from CsPbBr3 nanocrystals, designed for real-time single-proton counting. These perovskite scintillators exhibit exceptional sensitivity, with a high light yield (~100,000 photons per MeV) when subjected to proton beams. This enhanced sensitivity is attributed to radiative emission from biexcitons generated through proton-induced upconversion and impact ionization. These scintillators can detect as few as seven protons per second, a sensitivity level far below the rates encountered in clinical settings. The combination of rapid response (~336 ps) and pronounced ionostability enables diverse applications, including single-proton tracing, patterned irradiation and super-resolution proton imaging. These advancements have the potential to improve proton dosimetry in proton therapy and radiography.

Interaction of CCR4-NOT with EBF1 regulates gene-specific transcription and mRNA stability in B lymphopoiesis.

Transcription factor EBF1 (early B-cell factor 1) regulates early B-cell differentiation by poising or activating lineage-specific genes and repressing genes associated with alternative cell fates. To identify proteins that regulate the diverse functions of EBF1, we used SILAC (stable isotope labeling by amino acids in cell culture)-based mass spectrometry of proteins associated with endogenous EBF1 in pro-B cells. This analysis identified most components of the multifunctional CCR4-NOT complex, which regulates transcription and mRNA degradation. CNOT3 interacts with EBF1, and we identified histidine 240 in EBF1 as a critical residue for this interaction. Complementation of Ebf1-/- progenitors with EBF1H240A revealed a partial block of pro-B-cell differentiation and altered expression of specific EBF1 target genes that show either reduced transcription or increased mRNA stability. Most deregulated EBF1 target genes show normal occupancy by EBF1H240A, but we also detected genes with altered occupancy, suggesting that the CCR4-NOT complex affects multiple activities of EBF1. Mice with conditional Cnot3 inactivation recapitulate the block of early B-cell differentiation, which we found to be associated with an impaired autoregulation of Ebf1 and reduced expression of pre-B-cell receptor components. Thus, the interaction of the CCR4-NOT complex with EBF1 diversifies the function of EBF1 in a context-dependent manner and may coordinate transcriptional and post-transcriptional gene regulation.

Nature-Derived Hollow Micron-Tubular Signal Tracers Conquering the Size Limitations for Multimodal Immunochromatographic Detection of Antibiotics.

Developing signal tracers (STAs) with large size, multifunctionality, and high retention bioaffinity is believed to be a potential solution for achieving high-performance immunochromatographic assays (ICAs). However, the size limitations of STAs on strips are always a challenge because of the serious steric hindrance. Here, based on metal-quinone coordination and further metal etching, hollow micron-tubular STAs formed by natural alizarin and Fe3+ ions (named ALIFe) are produced to break through size limitations, provide more active sites, and achieve three-mode ICAs (ALIFe STAs-ICAs). Thanks to the special tubular morphology, ALIFe can successfully pass through the strip and provide an ideal signal intensity within 7 min at low mAb and probe dosages to achieve stable ICA analysis. Importantly, ALIFe shows excellent antibody enrichment and bioaffinity retention capability. With a proof-of-concept for streptomycin, the ALIFe STAs-ICAs showed the limit of detection (LOD) at 0.39 ng mL-1 for colorimetric mode, 0.32 ng mL-1 for catalytic mode, and 0.016 ng mL-1 for photothermal mode with total recoveries ranging from 80.46 to 121.59% in mike and honey samples. We anticipate that our study will help expand the ideas for the design of high-performance STAs with large size and broaden the practical application of ICA.

Validation of the Canadian TIA Score to Predict Subsequent Stroke Risk in Chinese TIA Patients.

BACKGROUND AND OBJECTIVES: The Canadian TIA Score has been verified as a good predictive tool for subsequent stroke risk in Caucasian patients; however, it had insufficient external verification of other races. We aimed to validate the Canadian TIA Score in Chinese patients and compared it with ABCD2 for subsequent stroke risk after transient ischemic attack (TIA). METHODS: The Third China National Stroke Registry (CNSR-III) was a nationwide, multicenter prospective registry recruiting consecutive patients with acute ischemic stroke or TIA within 7 days of the onset from August 2015 to March 2018. The Canadian TIA Score was verified in patients diagnosed with TIA from the CNSR-III (N = 1,184). The outcomes were subsequent stroke at 7 days, 14 days/discharge, 3 months, and 1 year. Outcomes were recorded by face-to-face assessment or telephone interview. The prognostic performance of the scoring system was assessed by the area under the receiver operator characteristic curve (AUC). RESULTS: Of 1,184 TIA patients (mean [IQR] age, 61.00 [53.00-69.00] years; 413 women [34.88%]), there were 40 patients (3.38%) having subsequent stroke within 7 days, 45 (3·80%) within 14 days/hospitalization, 66 (5·57%) within 3 months, and 100 (8·45%) within 1 year. The Canadian TIA Score (AUC 0 63-0·68) seemed to be a better prognostic score of stroke risk than the ABCD2 score (AUC 0·61-0·62), although no significant differences were noted. In the subgroup of atypical TIA, the Canadian TIA Score showed significantly stronger predictivity than the ABCD2 score within 7 days (0.80 [0.62-0.98] vs. 0.52 [0.30-0.73]; difference in AUC, 0.28 [0.03-0.53]; p, 0.026), and marginal significantly stronger predictivity within 1 year (0.71 [0.61-0.80] vs. 0.58 [0.48-0.68]; difference in AUC, 0.12 [-0.01 to 0.25]; p, 0.06). CONCLUSION: The Canadian TIA Score might be a better prognostic score than the ABCD2 score for post-TIA stroke risk, especially in patients with atypical TIA.

NH2-MIL-53(Al) Metal-Organic Framework as the Smart Platform for Simultaneous High-Performance Detection and Removal of Hg2.

The worsening pollution due to mercury species makes it inevitable to explore prospective versatile materials, which not only can detect mercury ions (Hg2+) with high sensitivity but also possesses efficient capture and removal ability. In this study, a series of classic organic ligand-based luminescence MOFs materials with high oxidation state central metals (Al3+, Zr4+, Cr3+, Fe3+, and Ti4+) were synthesized and were screened to achieve simultaneously Hg2+ detection and removal through the strong coordination of amino groups or nitrogen centers with Hg2+ and the intrinsic fluorescence intensity of MOFs regulated by the ligand-to-metal charge transfer (LMCT) effect. Among these checked materials, NH2-MIL-53(Al) exhibited the excellent ability for Hg2+ detection with wide response interval (1-17.3 µM), low detection limit (0.15 µM), good selectivity, wide pH adaptation (4.0-10.0), and strong anti-interference ability. Meanwhile, the resultant NH2-MIL-53(Al) possessed an efficient removal capability toward Hg2+, accompanied by a fast uptake kinetics (within 60 min) and large loading capacity (153.85 mg g-1). Furthermore, NH2-MIL-53(Al) also displayed satisfactory stability before and after Hg2+ treatment because of the formation of strong coordination bonds between high oxidation state aluminum (Al3+) and organic carboxylate ligands. Notably, the prepared NH2-MIL-53(Al) had no significant loss of adsorption performance even after being reused four times. All of these superior properties render the smart NH2-MIL-53(Al) nanohexahedron a great potential for simultaneous Hg2+ detection and removal from water.

Rapid and selective fluorometric determination of tannic acid using MoO3-x quantum dots.

The authors describe a fluorometric method for the quantification of tannic acid (TA). MoO3-x quantum dots (QDs) can selectively capture TA via the formation of an organic molybdate complex. This causes an electron transfer effect and an inner filter effect to result in synergistic quenching of the fluorescence of the QDs. TA can be detected via this effect with a linear response in the of 0.1-10 µM concentration range and a lower detection limit of 30 nM within 1 min. The use of such QDs as a quenchable fluorescent probe warrants good selectivity even in the presence of relatively high concentration of potentially interferents and makes the method suitable for real sample analysis. Graphical abstract Tannic acid can be rapidly and selectively detected in food using a MoO3-x quantum dots based fluorometric assay.

Fluorometric determination of dopamine by using molybdenum disulfide quantum dots.

A method is described for the rapid fluorometric determination of dopamine (DA) by using molybdenum disulfide quantum dots (MoS2 QDs) that were fabricated via an ammonium hydroxide etching method. The probe has a fluorescence (with excitation/emission peaks at 267/380 nm) that is quenched by DA with high selectivity over various interferences. This is attributed to a reaction that occurs between DA and the molybdate ions in pH 9 solutions of MoS2 QDs. The formation of organic molybdate complexes and of dopamine-quinone results in strong quenching of the fluorescence of the QDs which is due to both electron transfer and an inner filter effect. Under the optimum conditions, the assay works in the 0.1-100 µM DA concentration range, with two linear ranges and a 10 nM detection limit. The method was applied to the determination of DA in spiked artificial urine samples, where it gave recoveries ranging from 97.6 to 102.2%, demonstrating that the method a promising tool for rapid and selective detection of DA. Graphical abstract MoS2 QDs are facilely synthesized via the etching effect of ammonium hydroxide for highly selective fluorometric detection of dopamine.

Loss of corepressor PER2 under hypoxia up-regulates OCT1-mediated EMT gene expression and enhances tumor malignancy.

The circadian clock gene Period2 (PER2) has been suggested to be a tumor suppressor. However, detailed mechanistic evidence has not been provided to support this hypothesis. We found that loss of PER2 enhanced invasion and activated expression of epithelial-mesenchymal transition (EMT) genes including TWIST1, SLUG, and SNAIL. This finding was corroborated by clinical observation that PER2 down-regulation was associated with poor prognosis in breast cancer patients. We further demonstrated that PER2 served as a transcriptional corepressor, which recruited polycomb proteins EZH2 and SUZ12 as well as HDAC2 to octamer transcription factor 1 (OCT1) (POU2F1) binding sites of the TWIST1 and SLUG promoters to repress expression of these EMT genes. Hypoxia, a condition commonly observed in tumors, caused PER2 degradation and disrupted the PER2 repressor complex, leading to activation of EMT gene expression. This result was further supported by clinical data showing a significant negative correlation between hypoxia and PER2. Thus, our findings clearly demonstrate the tumor suppression function of PER2 and elucidate a pathway by which hypoxia promotes EMT via degradation of PER2.

AllergenAI: a deep learning model predicting allergenicity based on protein sequence.

Innovations in protein engineering can help redesign allergenic proteins to reduce adverse reactions in sensitive individuals. To accomplish this aim, a better knowledge of the molecular properties of allergenic proteins and the molecular features that make a protein allergenic is needed. We present a novel AI-based tool, AllergenAI, to quantify the allergenic potential of a given protein. Our approach is solely based on protein sequences, differentiating it from previous tools that use some knowledge of the allergens' physicochemical and other properties in addition to sequence homology. We used the collected data on protein sequences of allergenic proteins as archived in the three well-established databases, SDAP 2.0, COMPARE, and AlgPred 2, to train a convolutional neural network and assessed its prediction performance by cross-validation. We then used Allergen AI to find novel potential proteins of the cupin family in date palm, spinach, maize, and red clover plants with a high allergenicity score that might have an adverse allergenic effect on sensitive individuals. By analyzing the feature importance scores (FIS) of vicilins, we identified a proline-alanine-rich (P-A) motif in the top 50% of FIS regions that overlapped with known IgE epitope regions of vicilin allergens. Furthermore, using∼ 1600 allergen structures in our SDAP database, we showed the potential to incorporate 3D information in a CNN model. Future, incorporating 3D information in training data should enhance the accuracy. AllergenAI is a novel foundation for identifying the critical features that distinguish allergenic proteins.

Repurposing anti-osteoporosis drugs for autoimmune diseases: A two-sample Mendelian randomization study.

Background: Despite the increasing availability of therapeutic drugs for autoimmune diseases, many patients still struggle to achieve their treatment goals. Our aim was to identify whether drugs originally used to treat bone density could be applied to the treatment of autoimmune diseases through Mendelian randomization (MR). Methods: Using summary statistics from genome-wide association studies, we used a two-sample MR design to estimate the correlation between autoimmune diseases and BMD-related drug targets. Data from the DrugBank and ChEMBL databases were used to identify the drug targets of anti-osteoporosis medications. The Wald ratio test or inverse-variance weighting method was used to assess the impact of genetic variation in drug target(s) on autoimmune disease therapy. Results: Through our analysis, we discovered a negative correlation between genetic variability in a specific gene (ESR1) in raloxifene/colecalciferol and various autoimmune disorders such as ankylosing spondylitis, endometriosis, IgA nephropathy, rheumatoid arthritis, sarcoidosis, systemic lupus erythematosus, and type 1 diabetes. Conclusion: These results indicate a possible link between genetic differences in the drug targeting ESR1 and susceptibility to autoimmune disorders. Hence, our study offers significant support for the possible use of drugs targeting ESR1 for the management of autoimmune disorders. MR and drug repurposing are utilized to investigate the relationship between autoimmune diseases and bone mineral density, with a focus on ESR1.

From Reactive to Proactive - The Future Life Design to Promote Health and Extend the Human Lifespan.

Disease treatment and prevention have improved the human lifespan. Current studies on aging, such as the biological clock and senolytic drugs have focused on the medical treatments of various disorders and health maintenance. However, to efficiently extend the human lifespan to its theoretical maximum, medicine can take a further proactive approach and identify the inapparent disorders that affect the gestation, body growth, and reproductive stages of the so-called "healthy" population. The goal is to upgrade the standard health status to a new level by targeting the inapparent disorders. Thus, future research can shift from reaction, response, and prevention to proactive, quality promotion and vigor prolonging; from single disease-oriented to multiple dimension protocol for a healthy body; from treatment of symptom onset to keep away from disorders; and from the healthy aging management to a healthy promotion design beginning at the birth.

Rehabilitation with brain-computer interface and upper limb motor function in ischemic stroke: A randomized controlled trial.

BACKGROUND: Upper limb motor dysfunction is a major problem in the rehabilitation of patients with stroke. Brain-computer interface (BCI) is a kind of communication system that converts the "ideas" in the brain into instructions and has been used in stroke rehabilitation. This study aimed to investigate the efficacy and safety of BCI in rehabilitation training on upper limb motor function among patients with ischemic stroke. METHODS: This was an investigator-initiated, multicenter, randomized, open-label, blank-controlled clinical trial with blinded outcome assessment conducted at 17 centers in China. Patients were assigned in a 1:1 ratio to the BCI group or the control group based on traditional rehabilitation training. The primary efficacy outcome is the difference in improvement of the Fugl-Meyer Assessment upper extremity (FMA-UE) score between two groups at month 1 after randomization. The safety outcomes were any adverse events within 3 months. FINDINGS: A total of 296 patients with ischemic stroke were enrolled and randomly allocated to the BCI group (n = 150) and the control group (n = 146). The primary efficacy outcomes of FMA-UE score change from baseline to 1 month were 13.17 (95% confidence interval [CI], 11.56-14.79) in the BCI group and 9.83 (95% CI, 8.19-11.47) in the control group (mean difference between groups was 3.35; 95% CI, 1.05-5.65; p = 0.0045). Adverse events occurred in 33 patients (22.00%) in the BCI group and in 31 patients (21.23%) in the control group. CONCLUSIONS: BCI rehabilitation training can further improve upper limb motor function based on traditional rehabilitation training in patients with ischemic stroke. This study was registered at ClinicalTrials.gov: NCT04387474. FUNDING: This work was supported by the National Key R&D Program of China (2018YFC1312903), the National Key Research and Development Program of China (2022YFC3600600), the Training Fund for Open Projects at Clinical Institutes and Departments of Capital Medical University (CCMU2022ZKYXZ009), the Beijing Natural Science Foundation Haidian original innovation joint fund (L222123), the Fund for Young Talents of Beijing Medical Management Center (QML20230505), and the high-level public health talents (xuekegugan-02-47).

Optimizing oral immune tolerance to Type II collagen in patients with rheumatoid arthritis: The importance of dose, interfering medication and genetics.

OBJECTIVES: Oral immune tolerance (OT) is a complex process with unknown genetic regulation. Our aim is to explore possible genetic control of OT in patients with rheumatoid arthritis (RA). METHODS: RA patients with increased interferon γ production invitro when their isolated peripheral blood mononuclear cells (PBMC) were cultured with type II bovine collagen α1 chain [α1 (II)] were enrolled in this study and were randomly assigned to the "Low dose" type II collagen (CII) group (30 µg/day for 10 weeks, followed by 50 µg/day for 10 weeks, followed by 70 µg/day for 10 weeks) or "High dose" CII group (90 µg/day for 10 weeks, followed by 110 µg/day for 10 weeks, followed by 130 µg/day for 10 weeks). Heparinized blood was obtained at baseline and after each of the 10 weeks treatment for analysis of the invitro production of IFNγ by their PBMC stimulated by α1(II) . Single nucleotide polymorphism (SNP) analysis of the responders and non-responders to oral CII was conducted using GeneChip Mapping 10 K 2.0 Array. RESULTS: The SNP A-15,737 was found to associate with the ability of CII to suppress IFNγ production by α1(CII)-stimulated RA PBMC. The potential for SNP A-15,737 to associate with the OT response for patients with another autoimmune disease [OT induced by oral type I bovine collagen (CI) in patients with diffuse cutaneous systemic sclersodid (dsSSc)] was also explored. CONCLUSIONS: The ROT1 region plays a role in the control of IFNγ production after oral dosing of auto-antigens, thereby determining if oral tolerance to that antigen will develop.

Defect Engineering and Emission Tuning of Wide-Bandgap MAPbCl3 Perovskite.

Lead-chloride perovskites are promising candidates for optoelectronic applications, such as visible-blind UV photodetection. It remains unclear how the deep defects in this wide-bandgap material impact the carrier recombination dynamics. In this work, we study the defect properties of MAPbCl3 (MA = CH3NH3) based on photoluminescence (PL) measurements. Our investigations show that apart from the intrinsic emission, four sub-bandgap emissions emerge, which are very likely to originate from the radiative recombination of excitons bound to several intrinsic vacancy and interstitial defects. The intensity of various emission features can be tuned by adjusting the type and ratio of precursors used during synthesis. Our study not only provides important insights into the defect property and carrier recombination mechanism in this class of material but also demonstrates efficient strategies for defect passivation and engineering, paving the way for further development of lead-chloride perovskite-based optoelectronic devices.