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1.
Proc Natl Acad Sci U S A ; 121(16): e2319119121, 2024 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-38588435

RESUMO

The advancement of atomically precise dinuclear heterogeneous catalysts holds great potential in achieving efficient catalytic ozonation performance and contributes to the understanding of synergy mechanisms during reaction conditions. Herein, we demonstrate a "ship-in-a-bottle and pyrolysis" strategy that utilizes Fe2(CO)9 dinuclear-cluster to precisely construct Fe2 site, consisting of two Fe1-N3 units connected by Fe-Fe bonds and firmly bonded to N-doped carbon. Systematic characterizations and theoretical modeling reveal that the Fe-Fe coordination motif markedly reduced the devotion of the antibonding state in the Fe-O bond because of the strong orbital coupling interaction of dual Fe d-d orbitals. This facilitates O-O covalent bond cleavage of O3 and enhances binding strength with reaction intermediates (atomic oxygen species; *O and *OO), thus boosting catalytic ozonation performance. As a result, Fe dinuclear site catalyst exhibits 100% ozonation efficiency for CH3SH elimination, outperforming commercial MnO2 catalysts by 1,200-fold. This research provides insights into the atomic-level structure-activity relationship of ozonation catalysts and extends the use of dinuclear catalysts in catalytic ozonation and beyond.

2.
Pharmacol Rev ; 75(3): 532-553, 2023 05.
Artigo em Inglês | MEDLINE | ID: mdl-36627210

RESUMO

The development of cutting-edge techniques to study specific brain regions and neural circuits that regulate sleep-wake brain states and general anesthesia (GA), has increased our understanding of these states that exhibit similar neurophysiologic traits. This review summarizes current knowledge focusing on cell subtypes and neural circuits that control wakefulness, rapid eye movement (REM) sleep, non-REM sleep, and GA. We also review novel insights into their interactions and raise unresolved questions and challenges in this field. Comparisons of the overlapping neural substrates of sleep-wake and GA regulation will help us to understand sleep-wake transitions and how anesthetics cause reversible loss of consciousness. SIGNIFICANCE STATEMENT: General anesthesia (GA), sharing numerous neurophysiologic traits with the process of natural sleep, is administered to millions of surgical patients annually. In the past decade, studies exploring the neural mechanisms underlying sleep-wake and GA have advanced our understanding of their interactions and how anesthetics cause reversible loss of consciousness. Pharmacotherapies targeting the neural substrates associated with sleep-wake and GA regulations have significance for clinical practice in GA and sleep medicine.


Assuntos
Sono REM , Sono , Humanos , Sono REM/fisiologia , Anestesia Geral/efeitos adversos , Encéfalo/fisiologia , Inconsciência
3.
Nano Lett ; 24(25): 7593-7600, 2024 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-38869928

RESUMO

In traditional optical wireless communication (OWC) systems, the simultaneous use of multiple sets of light-emitting diodes (LEDs) and photodetectors (PDs) increases the system complexity and instability. Here we report bifunctional light-emitting photodetectors (LEPDs) fabricated with quasi-2D perovskite (F-PEA)2Cs4Pb5I11Br5 as light-emitting/detecting layers for efficient, miniaturized, and intelligent bidirectional OWC. By simply changing the solvent composition of the precursor solution and using antisolvent engineering, we manipulated the crystal orientation and phase distribution of (F-PEA)2Cs4Pb5I11Br5, realizing high irradiance (4.36 µW cm-2) and a -3 dB refresh rate (0.21 MHz) of electroluminescence in LED mode as well as low noise (below 1 pA Hz-1/2) and high responsivity (0.1 A W-1) in PD mode. The rapid and accurate OWC process was demonstrated through interaction of LEPDs. We also demonstrated the high-fidelity compression and digitization of high-resolution (256 × 256 pixels) color images using the four-step phase shift method to realize intelligent encrypted image OWC.

4.
Nano Lett ; 24(38): 11921-11928, 2024 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-39268850

RESUMO

Advanced photodetectors are crucial for high-fidelity optical communication. However, the tradeoff between high external quantum efficiency (EQE) and high light fidelity (Li-Fi) frequency often limits data transmission accuracy and timeliness. Here, we report a photodetector consisting of lead sulfide (PbS) colloidal quantum dots (CQDs) with near-infrared responsiveness and perovskite frameworks responsible for the charge transport to overcome the EQE × Li-Fi constraint. Optimizing the PbS CQDs distribution and trap depth in the perovskite layer enhances charge injection, achieving a device gain of 11892% for 1200 nm photons and a response frequency of 24 kHz at -2 V. The device exhibits a record EQE × Li-Fi frequency product of 106 Hz. We have applied the detector to near-infrared optical communications at a data transfer rate of 2000 bits per second (2 kbps) to demonstrate the advances in high fidelity, the device retains over 98% of the original waveform information in its output.

5.
Emerg Infect Dis ; 30(4): 826-828, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38526372

RESUMO

In 2022, we assessed avian influenza A virus subtype H5N6 seroprevalence among the general population in Guangdong Province, China, amid rising numbers of human infections. Among the tested samples, we found 1 to be seropositive, suggesting that the virus poses a low but present risk to the general population.


Assuntos
Influenza Aviária , Influenza Humana , Animais , Humanos , Influenza Aviária/epidemiologia , Estudos Soroepidemiológicos , Influenza Humana/epidemiologia , China/epidemiologia , Aves
6.
Am J Transplant ; 24(10): 1837-1856, 2024 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-38642712

RESUMO

Immune checkpoint inhibitors (ICIs) as a downstaging or bridging therapy for liver transplantation (LT) in hepatocellular carcinoma patients are rapidly increasing. However, the evidence about the feasibility and safety of pre-LT ICI therapy is limited and controversial. To this end, a multicenter, retrospective cohort study was conducted in 11 Chinese centers. The results showed that 83 recipients received pre-LT ICI therapy during the study period. The median post-LT follow-up was 8.1 (interquartile range 3.3-14.6) months. During the short follow-up, 23 (27.7%) recipients developed allograft rejection, and 7 of them (30.4%) were diagnosed by liver biopsy. Multivariate logistics regression analysis showed that the time interval between the last administration of ICI therapy and LT (TLAT) ≥ 30 days was an independent protective factor for allograft rejection (odds ratio = 0.096, 95% confidence interval 0.026-0.357; P < .001). Multivariate Cox analysis showed that allograft rejection was an independent risk factor for overall survival (hazard ratio = 9.960, 95% confidence interval 1.006-98.610; P = .043). We conclude that patients who receive a pre-LT ICI therapy with a TLAT shorter than 30 days have a much higher risk of allograft rejection than those with a TLAT longer than 30 days. The presence of rejection episodes might be associated with higher post-LT mortality.


Assuntos
Carcinoma Hepatocelular , Rejeição de Enxerto , Inibidores de Checkpoint Imunológico , Neoplasias Hepáticas , Transplante de Fígado , Humanos , Carcinoma Hepatocelular/tratamento farmacológico , Carcinoma Hepatocelular/patologia , Carcinoma Hepatocelular/mortalidade , Carcinoma Hepatocelular/cirurgia , Estudos Retrospectivos , Masculino , Feminino , Neoplasias Hepáticas/tratamento farmacológico , Neoplasias Hepáticas/mortalidade , Neoplasias Hepáticas/cirurgia , Inibidores de Checkpoint Imunológico/uso terapêutico , Pessoa de Meia-Idade , Rejeição de Enxerto/etiologia , Seguimentos , Prognóstico , Sobrevivência de Enxerto/efeitos dos fármacos , Taxa de Sobrevida , Fatores de Risco
7.
Small ; : e2404696, 2024 Aug 18.
Artigo em Inglês | MEDLINE | ID: mdl-39155427

RESUMO

Graphitic carbon nitride (g-C3N4) is a prominent photocatalyst that has attracted substantial interest in the field of photocatalytic environmental remediation due to the low cost of fabrication, robust chemical structure, adaptable and tunable energy bandgaps, superior photoelectrochemical properties, cost-effective feedstocks, and distinctive framework. Nonetheless, the practical application of bulk g-C3N4 in the photocatalysis field is limited by the fast recombination of photogenerated e--h+ pairs, insufficient surface-active sites, and restricted redox capacity. Consequently, a great deal of research has been devoted to solving these scientific challenges for large-scale applications. This review concisely presents the latest advancements in g-C3N4-based photocatalyst modification strategies, and offers a comprehensive analysis of the benefits and preparation techniques for each strategy. It aims to articulate the complex relationship between theory, microstructure, and activities of g-C3N4-based photocatalysts for atmospheric protection. Finally, both the challenges and opportunities for the development of g-C3N4-based photocatalysts are highlighted. It is highly believed that this special review will provide new insight into the synthesis, modification, and broadening of g-C3N4-based photocatalysts for atmospheric protection.

8.
Small ; 20(31): e2311879, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38461527

RESUMO

Carbon-defect engineering in single-atom metal-nitrogen-carbon (M─N─C) catalysts by straightforward and robust strategy, enhancing their catalytic activity for volatile organic compounds, and uncovering the carbon vacancy-catalytic activity relationship are meaningful but challenging. In this study, an iron-nitrogen-carbon (Fe─N─C) catalyst is intentionally designed through a carbon-thermal-diffusion strategy, exposing extensively the carbon-defective Fe─N4 sites within a micro-mesoporous carbon matrix. The optimization of Fe─N4 sites results in exceptional catalytic ozonation efficiency, surpassing that of intact Fe─N4 sites and commercial MnO2 by 10 and 312 times, respectively. Theoretical calculations and experimental data demonstrated that carbon-defect engineering induces selective cleavage of C─N bond neighboring the Fe─N4 motif. This induces an increase in non-uniform charges and Fermi density, leading to elevated energy levels at the center of Fe d-band. Compared to the intact atomic configuration, carbon-defective Fe─N4 site is more activated to strengthen the interaction with O3 and weaken the O─O bond, thereby reducing the barriers for highly active surface atomic oxygen (*O/*OO), ultimately achieving efficient oxidation of CH3SH and its intermediates. This research not only offers a viable approach to enhance the catalytic ozonation activity of M─N─C but also advances the fundamental comprehension of how periphery carbon environment influences the characteristics and efficacy of M─N4 sites.

9.
Bioinformatics ; 39(9)2023 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-37669154

RESUMO

MOTIVATION: Computationally predicting major histocompatibility complex class I (MHC-I) peptide binding affinity is an important problem in immunological bioinformatics, which is also crucial for the identification of neoantigens for personalized therapeutic cancer vaccines. Recent cutting-edge deep learning-based methods for this problem cannot achieve satisfactory performance, especially for non-9-mer peptides. This is because such methods generate the input by simply concatenating the two given sequences: a peptide and (the pseudo sequence of) an MHC class I molecule, which cannot precisely capture the anchor positions of the MHC binding motif for the peptides with variable lengths. We thus developed an anchor position-aware and high-performance deep model, DeepMHCI, with a position-wise gated layer and a residual binding interaction convolution layer. This allows the model to control the information flow in peptides to be aware of anchor positions and model the interactions between peptides and the MHC pseudo (binding) sequence directly with multiple convolutional kernels. RESULTS: The performance of DeepMHCI has been thoroughly validated by extensive experiments on four benchmark datasets under various settings, such as 5-fold cross-validation, validation with the independent testing set, external HPV vaccine identification, and external CD8+ epitope identification. Experimental results with visualization of binding motifs demonstrate that DeepMHCI outperformed all competing methods, especially on non-9-mer peptides binding prediction. AVAILABILITY AND IMPLEMENTATION: DeepMHCI is publicly available at https://github.com/ZhuLab-Fudan/DeepMHCI.


Assuntos
Algoritmos , Benchmarking , Biologia Computacional , Epitopos , Peptídeos
10.
Anesthesiology ; 140(1): 102-115, 2024 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-37812765

RESUMO

BACKGROUND: Multiple neural structures involved in maintaining wakefulness have been found to promote arousal from general anesthesia. The medial septum is a critical region that modulates arousal behavior. This study hypothesized that glutamatergic neurons in the medial septum play a crucial role in regulating states of consciousness during sevoflurane general anesthesia. METHODS: Adult male mice were used in this study. The effects of sevoflurane anesthesia on neuronal activity were determined by fiber photometry. Lesions and chemogenetic manipulations were used to study the effects of the altered activity of medial septal glutamatergic neurons on anesthesia induction, emergence, and sensitivity to sevoflurane. Optogenetic stimulation was used to observe the role of acute activation of medial septal glutamatergic neurons on cortical activity and behavioral changes during sevoflurane-induced continuous steady state of general anesthesia and burst suppression state. RESULTS: The authors found that medial septal glutamatergic neuronal activity decreased during sevoflurane anesthesia induction and recovered in the early period of emergence. Chemogenetic activation of medial septal glutamatergic neurons prolonged the induction time (mean ± SD, hM3Dq-clozapine N-oxide vs. hM3Dq-saline, 297.5 ± 60.1 s vs. 229.4 ± 29.9 s, P < 0.001, n = 11) and decreased the emergence time (53.2 ± 11.8 s vs. 77.5 ± 33.5 s, P = 0.025, n = 11). Lesions or chemogenetic inhibition of these neurons produced the opposite effects. During steady state of general anesthesia and deep anesthesia-induced burst suppression state, acute optogenetic activation of medial septal glutamatergic neurons induced cortical activation and behavioral emergence. CONCLUSIONS: The study findings reveal that activation of medial septal glutamatergic neurons has arousal-promoting effects during sevoflurane anesthesia in male mice. The activation of these neurons prolongs the induction and accelerates the emergence of anesthesia.


Assuntos
Estado de Consciência , Neurônios , Camundongos , Animais , Masculino , Sevoflurano/farmacologia , Vigília/fisiologia , Anestesia Geral
11.
Acta Pharmacol Sin ; 45(9): 1777-1792, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-38671193

RESUMO

Despite the widespread prevalence and important medical impact of insomnia, effective agents with few side effects are lacking in clinics. This is most likely due to relatively poor understanding of the etiology and pathophysiology of insomnia, and the lack of appropriate animal models for screening new compounds. As the main homeostatic, circadian, and neurochemical modulations of sleep remain essentially similar between humans and rodents, rodent models are often used to elucidate the mechanisms of insomnia and to develop novel therapeutic targets. In this article, we focus on several rodent models of insomnia induced by stress, diseases, drugs, disruption of the circadian clock, and other means such as genetic manipulation of specific neuronal activity, respectively, which could be used to screen for novel hypnotics. Moreover, important advantages and constraints of some animal models are discussed. Finally, this review highlights that the rodent models of insomnia may play a crucial role in novel drug development to optimize the management of insomnia.


Assuntos
Modelos Animais de Doenças , Descoberta de Drogas , Distúrbios do Início e da Manutenção do Sono , Animais , Distúrbios do Início e da Manutenção do Sono/tratamento farmacológico , Humanos , Hipnóticos e Sedativos/uso terapêutico , Hipnóticos e Sedativos/farmacologia , Roedores
12.
Artigo em Inglês | MEDLINE | ID: mdl-39420836

RESUMO

Berberine (BBR) is used to treat diarrhea clinically. However, its reproductive toxicity is unclear. This study aims to investigate the impact of BBR on the male reproductive system. Intragastric BBR administration for 14 consecutive days results in a significant decrease in the serum testosterone concentration, epididymal sperm concentration, mating rate and fecundity of male mice. Testicular treatment with testosterone propionate (TP) partially reverses the damage caused by BBR to the male reproductive system. Mechanistically, the decrease in Muribaculaceae abundance in the gut microbiota of mice is the principal cause of the BBR-induced decrease in the sperm concentration. Both fecal microbiota transplantation (FMT) and polyethylene glycol (PEG) treatment demonstrate that Muribaculaceae is necessary for spermatogenesis. The intragastric administration of Muribaculaceae intestinale to BBR-treated mice restores the sperm concentration and testosterone levels. Metabolomic analysis reveals that BBR affects arginine and proline metabolism, of which ornithine level is downregulated. Combined analysis via 16S rRNA metagenomics sequencing and metabolomics shows that Muribaculaceae regulates ornithine level. The transcriptomic results of the testes indicate that the expressions of genes related to the low-density lipoprotein receptor (LDLR)-mediated testosterone synthesis pathway decrease after BBR administration. The transcriptional activity of the Ldlr gene in TM3 cells is increased with increased ornithine supplementation in the culture media, leading to increased testosterone synthesis. Overall, this study reveals an association between a BBR-induced decrease in Muribaculaceae abundance and defective spermatogenesis, providing a prospective therapeutic approach for addressing infertility-related decreases in serum testosterone triggered by changes in the gut microbiota composition.

13.
Sensors (Basel) ; 24(14)2024 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-39065874

RESUMO

Synthetic Aperture Radar (SAR) is renowned for its all-weather and all-time imaging capabilities, making it invaluable for ship target recognition. Despite the advancements in deep learning models, the efficiency of Convolutional Neural Networks (CNNs) in the frequency domain is often constrained by memory limitations and the stringent real-time requirements of embedded systems. To surmount these obstacles, we introduce the Split_ Composite method, an innovative convolution acceleration technique grounded in Fast Fourier Transform (FFT). This method employs input block decomposition and a composite zero-padding approach to streamline memory bandwidth and computational complexity via optimized frequency-domain convolution and image reconstruction. By capitalizing on FFT's inherent periodicity to augment frequency resolution, Split_ Composite facilitates weight sharing, curtailing both memory access and computational demands. Our experiments, conducted using the OpenSARShip-4 dataset, confirm that the Split_ Composite method upholds high recognition precision while markedly enhancing inference velocity, especially in the realm of large-scale data processing, thereby exhibiting exceptional scalability and efficiency. When juxtaposed with state-of-the-art convolution optimization technologies such as Winograd and TensorRT, Split_ Composite has demonstrated a significant lead in inference speed without compromising the precision of recognition.

14.
Molecules ; 29(12)2024 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-38930930

RESUMO

Considering that heavy-metal contamination of seawater is getting worse, building a quick, accurate and portable device for detecting trace zinc in seawater in real time would be very beneficial. In this work, a microfluidic system was developed that includes a planar disc electrode, a micro-cavity for detection, an electrochemical workstation, a computer, a container for waste liquid reprocessing, an external pipeline and other components as well as a graphene/cerium oxide/nano-cerium oxide/Nafion composite membrane was used to modify the planar disc electrode (GR/CeO2/Nafion/Au) to investigate the electrochemical behaviour of Zn(II) using cyclic voltammetry, square-wave voltammetry and orthogonal test methods. Under optimal experimental conditions, the peak reaction current of Zn(II) showed a good linear relationship with the concentration of Zn(II) in the range of 1-900 µg/L with a correlation coefficient of 0.998, and the detection limit of the method was 0.87 µg/L. In addition, the microfluidic system had good stability, reproducibility and anti-interference. The system was used for determining zinc ions in real seawater samples, and the results were very similar to those of inductively coupled plasma-emission spectrometry, demonstrating the practicality of the system for the detection of trace zinc.

15.
Angew Chem Int Ed Engl ; 63(27): e202403463, 2024 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-38661020

RESUMO

Metal sulfide (MS) is regarded as a promising candidate of the anode materials for sodium-ion battery (SIB) with ideal capacity and low cost, yet still suffers from the inferior cycling stability and voltage degradation. Herein, the coordination relationship between the discharge product Na2S with the Na+ (NaPF6) in the electrolyte, is revealed as the root cause for the cycling failure of MS. Na+-coordination effect assistants the dissolution of Na2S, further delocalizing Na2S from the reaction interface under the function of electric field, which leads to the solo oxidation of the discharge product element metal without the participation of Na2S. Besides, the higher highest occupied molecular orbital of Na2S suggest the facilitated Na2S solo oxidation to produce sodium polysulfides (NaPSs). Based on these, lowering the Na+ concentration of the electrolyte is proposed as a potential improvement strategy to change the coordination environment of Na2S, suppressing the side reactions of the solo-oxidation of element metal and Na2S. Consequently, the enhanced conversion reaction reversibility and prolonged cycle life are achieved. This work renders in-depth perception of failure mechanism and inspiration for realizing advanced conversion-type anode.

16.
J Neurochem ; 166(2): 233-247, 2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-37353897

RESUMO

The cholinergic neurons in the nucleus basalis of Meynert (NBM) are a key structure in cognition, the dysfunction of which is associated with various neurological disorders, especially dementias. However, the whole-brain neural connectivity to cholinergic neurons in the NBM remains to be further and comprehensively researched. Using virus-based, specific, retrograde, and anterograde tracing, we illustrated the monosynaptic inputs and axon projections of NBM cholinergic neurons in choline acetyltransferase (ChAT)-Cre transgenic mice. Our results showed that NBM cholinergic neurons received mainly inputs from the caudate putamen and the posterior limb of the anterior commissure in the subcortex. Moreover, the majority of cholinergic terminals from the NBM were observed in the cortex mantle, including the motor cortex, sensory cortex, and visual cortex. Interestingly, although NBM cholinergic neurons received input projections from the caudate putamen, interstitial nucleus of the posterior limb of the anterior commissure, and central amygdaloid nucleus, NBM cholinergic neurons sparsely sent axon projection to innervate these areas. Furthermore, primary motor cortex, secondary motor cortex, and primary somatosensory cortex received abundant inputs from the NBM but sent few outputs to the NBM. Taken together, our results reveal the detailed and specific connectivity of cholinergic neurons of the NBM and provide a neuroanatomic foundation for further studies to explore the important physiological functions of NBM cholinergic neurons.


Assuntos
Núcleo Basal de Meynert , Substância Branca , Camundongos , Animais , Neurônios Colinérgicos , Córtex Cerebral , Axônios , Camundongos Transgênicos
17.
Eur J Neurosci ; 58(3): 2807-2823, 2023 08.
Artigo em Inglês | MEDLINE | ID: mdl-37452644

RESUMO

The bed nucleus of the stria terminalis (BNST) is a neuropeptide-enriched brain region that modulates a wide variety of emotional behaviours and states, including stress, anxiety, reward and social interaction. The BNST consists of diverse subregions and neuronal ensembles; however, because of the high molecular heterogeneity within BNST neurons, the mechanisms through which the BNST regulates distinct emotional behaviours remain largely unclear. Prior studies have identified BNST calretinin (CR)-expressing neurons, which lack neuropeptides. Here, employing virus-based cell-type-specific retrograde and anterograde tracing systems, we mapped the whole-brain monosynaptic inputs and axonal projections of BNST CR-expressing neurons in male mice. We found that BNST CR-expressing neurons received inputs mainly from the amygdalopiriform transition area, central amygdala and hippocampus and moderately from the medial preoptic area, basolateral amygdala, paraventricular thalamus and lateral hypothalamus. Within the BNST, plenty of input neurons were primarily located in the oval and interfascicular subregions. Furthermore, numerous BNST CR-expressing neuronal boutons were observed within the BNST but not in other brain regions, thus suggesting that these neurons are a type of interneuron. These results will help further elucidate the neuronal circuits underlying the elaborate and distinct functions of the BNST.


Assuntos
Neuropeptídeos , Núcleos Septais , Camundongos , Masculino , Animais , Núcleos Septais/metabolismo , Calbindina 2 , Encéfalo/metabolismo , Neuropeptídeos/metabolismo , Interneurônios/metabolismo
18.
Gastroenterology ; 162(4): 1272-1287.e16, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-34953915

RESUMO

BACKGROUND & AIMS: Chromatin architecture governs cell lineages by regulating the specific gene expression; however, its role in the diversity of cancer development remains unknown. Among pancreatic cancers, pancreatic ductal adenocarcinoma (PDAC) and intraductal papillary mucinous neoplasms (IPMN) with an associated invasive carcinoma (IPMNinv) arise from 2 distinct precursors, and their fundamental differences remain obscure. Here, we aimed to assess the difference of chromatin architecture regulating the transcriptional signatures or biological features in pancreatic cancers. METHODS: We established 28 human organoids from distinct subtypes of pancreatic tumors, including IPMN, IPMNinv, and PDAC. We performed exome sequencing (seq), RNA-seq, assay for transposase-accessible chromatin-seq, chromatin immunoprecipitation-seq, high-throughput chromosome conformation capture, and phenotypic analyses with short hairpin RNA or clustered regularly interspaced short palindromic repeats interference. RESULTS: Established organoids successfully reproduced the histology of primary tumors. IPMN and IPMNinv organoids harbored GNAS, RNF43, or KLF4 mutations and showed the distinct expression profiles compared with PDAC. Chromatin accessibility profiles revealed the gain of stomach-specific open regions in IPMN and the pattern of diverse gastrointestinal tissues in IPMNinv. In contrast, PDAC presented an impressive loss of accessible regions compared with normal pancreatic ducts. Transcription factor footprint analysis and functional assays identified that MNX1 and HNF1B were biologically indispensable for IPMN lineages. The upregulation of MNX1 was specifically marked in the human IPMN lineage tissues. The MNX1-HNF1B axis governed a set of genes, including MYC, SOX9, and OLFM4, which are known to be essential for gastrointestinal stem cells. High-throughput chromosome conformation capture analysis suggested the HNF1B target genes to be 3-dimensionally connected in the genome of IPMNinv. CONCLUSIONS: Our organoid analyses identified the MNX1-HNF1B axis to be biologically significant in IPMN lineages.


Assuntos
Adenocarcinoma Mucinoso , Carcinoma Ductal Pancreático , Fator 1-beta Nuclear de Hepatócito , Proteínas de Homeodomínio , Neoplasias Intraductais Pancreáticas , Fatores de Transcrição , Adenocarcinoma Mucinoso/genética , Carcinoma Ductal Pancreático/patologia , Cromatina , Fator 1-beta Nuclear de Hepatócito/genética , Proteínas de Homeodomínio/genética , Humanos , Neoplasias Intraductais Pancreáticas/genética , Fatores de Transcrição/genética , Neoplasias Pancreáticas
19.
Bioinformatics ; 38(Suppl 1): i220-i228, 2022 06 24.
Artigo em Inglês | MEDLINE | ID: mdl-35758790

RESUMO

MOTIVATION: Computationally predicting major histocompatibility complex (MHC)-peptide binding affinity is an important problem in immunological bioinformatics. Recent cutting-edge deep learning-based methods for this problem are unable to achieve satisfactory performance for MHC class II molecules. This is because such methods generate the input by simply concatenating the two given sequences: (the estimated binding core of) a peptide and (the pseudo sequence of) an MHC class II molecule, ignoring biological knowledge behind the interactions of the two molecules. We thus propose a binding core-aware deep learning-based model, DeepMHCII, with a binding interaction convolution layer, which allows to integrate all potential binding cores (in a given peptide) with the MHC pseudo (binding) sequence, through modeling the interaction with multiple convolutional kernels. RESULTS: Extensive empirical experiments with four large-scale datasets demonstrate that DeepMHCII significantly outperformed four state-of-the-art methods under numerous settings, such as 5-fold cross-validation, leave one molecule out, validation with independent testing sets and binding core prediction. All these results and visualization of the predicted binding cores indicate the effectiveness of our model, DeepMHCII, and the importance of properly modeling biological facts in deep learning for high predictive performance and efficient knowledge discovery. AVAILABILITY AND IMPLEMENTATION: DeepMHCII is publicly available at https://github.com/yourh/DeepMHCII. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Antígenos de Histocompatibilidade Classe II , Peptídeos , Algoritmos , Antígenos de Histocompatibilidade Classe II/metabolismo , Peptídeos/química , Ligação Proteica , Transporte Proteico
20.
J Transl Med ; 21(1): 734, 2023 10 18.
Artigo em Inglês | MEDLINE | ID: mdl-37853415

RESUMO

BACKGROUND AND AIMS: The recurrence and metastasis of hepatocellular carcinoma (HCC) are mainly caused by microvascular invasion (MVI). Our study aimed to uncover the cellular atlas of MVI+ HCC and investigate the underlying immune infiltration patterns with radiomics features. METHODS: Three MVI positive HCC and three MVI negative HCC samples were collected for single-cell RNA-seq analysis. 26 MVI positive HCC and 30 MVI negative HCC tissues were underwent bulk RNA-seq analysis. For radiomics analysis, radiomics features score (Radscore) were built using preoperative contrast MRI for MVI prediction and overall survival prediction. We deciphered the metabolism profiles of MVI+ HCC using scMetabolism and scFEA. The correlation of Radscore with the level of APOE+ macrophages and iCAFs was identified. Whole Exome Sequencing (WES) was applied to distinguish intrahepatic metastasis (IM) and multicentric occurrence (MO). Transcriptome profiles were compared between IM and MO. RESULTS: Elevated levels of APOE+ macrophages and iCAFs were detected in MVI+ HCC. There was a strong correlation between the infiltration of APOE+ macrophages and iCAFs, as confirmed by immunofluorescent staining. MVI positive tumors exhibited increased lipid metabolism, which was attributed to the increased presence of APOE+ macrophages. APOE+ macrophages and iCAFs were also found in high levels in IM, as opposed to MO. The difference of infiltration level and Radscore between two nodules in IM was relatively small. Furthermore, we developed Radscore for predicting MVI and HCC prognostication that were also able to predict the level of infiltration of APOE+ macrophages and iCAFs. CONCLUSION: This study demonstrated the interactions of cell subpopulations and distinct metabolism profiles in MVI+ HCC. Besides, MVI prediction Radscore and MVI prognostic Radscore were highly correlated with the infiltration of APOE+ macrophages and iCAFs, which helped to understand the biological significance of radiomics and optimize treatment strategy for MVI+ HCC.


Assuntos
Carcinoma Hepatocelular , Neoplasias Hepáticas , Humanos , Carcinoma Hepatocelular/patologia , Neoplasias Hepáticas/patologia , Estudos Retrospectivos , Invasividade Neoplásica , Apolipoproteínas E/genética
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