Towards Lightweight Graph Neural Network Search with Curriculum Graph Sparsification

Graph Neural Architecture Search (GNAS) has achieved superior performance on various graph-structured tasks. However, existing GNAS studies overlook the applications of GNAS in resource-constraint scenarios. This paper proposes to design a joint graph data and architecture mechanism, which identifies important sub-architectures via the valuable graph data. To search for optimal lightweight Graph Neural Networks (GNNs), we propose a Lightweight Graph Neural Architecture Search with Graph SparsIfication and Network Pruning (GASSIP) method. In particular, GASSIP comprises an operation-pruned architecture search module to enable efficient lightweight GNN search. Meanwhile, we design a novel curriculum graph data sparsification module with an architecture-aware edge-removing difficulty measurement to help select optimal sub-architectures. With the aid of two differentiable masks, we iteratively optimize these two modules to efficiently search for the optimal lightweight architecture. Extensive experiments on five benchmarks demonstrate the effectiveness of GASSIP. Particularly, our method achieves on-par or even higher node classification performance with half or fewer model parameters of searched GNNs and a sparser graph.Comment: Accepted by KDD 2024. The two first authors made equal contribution

A novel triazolonaphthalimide induces apoptosis and inhibits tumor growth by targeting DNA and DNA-associated processes

DNA and DNA-associated processes have been classes of the most important targets of chemotherapeutic drugs. As classic DNA intercalators and topoisomerase inhibitors, naphthalimides have been extensively investigated as potential anti-cancer drugs. We recently synthesized a novel series of triazolonaphthalimides with excellent anti-cancer activities. In the present study, one of the most potent triazolonaphthalimides, LSS-11, was investigated. LSS-11 bound to DNA in vitro and in cell mainly by minor groove binding and significantly increased the stability of DNA, which could be fundamental for the biological activities of LSS-11. In addition to inhibiting DNA topoisomerase II-catalyzed decatenation of knotted circulated DNA, LSS-11 dramatically inhibited DNA replication mediated by polymerase chain reaction and isothermal helicase-dependent amplification, as well as the expression of luciferase driven by a minimal TA promoter in cell. Furthermore, LSS-11 exhibited strong cytotoxicity in selected human colon cancer cell lines by inducing cell cycle arrest and apoptosis, which was accompanied by DNA damage response. Finally, LSS-11 potently inhibited the growth of S180 murine sarcoma and SW480 human colorectal cancer xenografts in vivo without significant major toxicities. These results suggest that LSS-11 deserves further research and development as a novel anti-cancer agent, and provided new understandings of mechanisms by which LSS-11 inhibited multiple DNA-associated processes and tumor growth.Natural Science Foundation of China [81472657, 81273370, 81272468]; PKUCare Pharmaceutical RD CenterSCI(E)ARTICLE2337394-37408

Recurrent mucinous carcinoma with sarcomatoid and sarcomatous mural nodules: a case report and literature review

Ovarian mucinous tumors with sarcomatous mural nodules are rare. Sarcomatous nodules have a bad prognosis. Its diagnosis and treatment are controversial.It is still controversial whether malignant mural nodules represent a dedifferentiated form of mucinous tumors or collisional tumors. This is a case report of a 32-year-old female diagnosed with ovarian mucinous tumor recurred as a mucinous carcinoma combined with sarcomatoid and undifferentiated sarcoma mural nodules after surgery and chemotherapy. The primary lesion did not have a sarcomatous component after comprehensive sampling and repeated review, while the recurrent lesion had a predominantly sarcomatous component. The patient received a second operation and postoperative chemotherapy plus Anlotinib with no progression at 16 months of follow-up. Primary mucinous carcinoma and sarcomatous mural nodules revealed the same K-RAS mutation(c.35G>T, pG12V), TP53 mutation (c.817C>T, p.R273C), MLL2 mutation(c.13450C>T, p.R4484) and NF1 mutation(c.7876A>G, p.S2626G). We present a comprehensive analysis on morphologic characteristics, molecular detection results, clinical management, and prognosis of ovarian mucinous tumors with mural nodules of sarcomatoid and undifferentiated sarcoma. Mutation sharing between primary mucinous carcinoma and recurrent sarcomatous nodules supports monoclonal origin of primary and recurrent tumors, suggesting a tendency for sarcomatous differentiation during the progression of epithelial tumors. Malignant mural nodules represent dedifferentiation in mucinous ovarian tumors rather than collision of two different tumor types. Therefore, it is imperative to conduct comprehensive sampling, rigorous clinical examination, and postoperative follow-up in order to thoroughly evaluate all mural nodules of ovarian mucinous tumors due to their potential for malignancy and sarcomatous differentiation

Generation of host-directed and virus-specific antivirals using targeted protein degradation promoted by small molecules and viral RNA mimics.

Targeted protein degradation (TPD), as exemplified by proteolysis-targeting chimera (PROTAC), is an emerging drug discovery platform. PROTAC molecules, which typically contain a target protein ligand linked to an E3 ligase ligand, recruit a target protein to the E3 ligase to induce its ubiquitination and degradation. Here, we applied PROTAC approaches to develop broad-spectrum antivirals targeting key host factors for many viruses and virus-specific antivirals targeting unique viral proteins. For host-directed antivirals, we identified a small-molecule degrader, FM-74-103, that elicits selective degradation of human GSPT1, a translation termination factor. FM-74-103-mediated GSPT1 degradation inhibits both RNA and DNA viruses. Among virus-specific antivirals, we developed viral RNA oligonucleotide-based bifunctional molecules (Destroyers). As a proof of principle, RNA mimics of viral promoter sequences were used as heterobifunctional molecules to recruit and target influenza viral polymerase for degradation. This work highlights the broad utility of TPD to rationally design and develop next-generation antivirals

Bifidobacterium animalis subsp. lactis BB-12 attenuates diabetic retinopathy through gut microbiota modulation: evidence for the gut–retinal axis

PurposePrevious studies have shown that Bifidobacterium animalis subsp. lactis BB-12 plays a role in maintaining the intestinal barrier and regulating inflammation; however, its potential connection to ocular diseases has not been thoroughly explored. Diabetic retinopathy (DR) is a common ocular complication of diabetes and is closely associated with metabolic dysregulation. This study investigated whether BB-12 supplementation could affect systemic diabetic symptoms, the progression of DR, and the stability of gut microbiota.Materials and methodsDiabetic db/db mice were utilized to monitor metabolic parameters, assess hepatic and lipid profiles, evaluate retinal function via ERG, and examine retinal morphology through OCT and HE staining. Treg/Th17 balance was analyzed by flow cytometry, and gut microbiota composition was profiled using 16S rRNA sequencing.ResultsThe results showed that BB-12 reduced obesity, decreased hepatic steatosis, improved retinal blood vessel health and vision, and influenced both the Treg/Th17 balance and gut dysbiosis in diabetic mice.ConclusionsThese findings lay the groundwork for regulatory role of intestinal microbiota on systemic and ocular complications of diabetes, and further examination of the gut-retina axis

Systems pharmacology identifies ajugol-mediated NF-κB/caspase-3 inhibition and isoacteoside-driven p62/mTOR-mediated autophagy as key mechanisms of Rehmanniae Radix and its processed form in Alzheimer’s treatment

BackgroundAlzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by the deposition of senile plaques, neurofibrillary tangles, and neuronal dysfunction, resulting in severe cognitive and memory decline. The root of the Scrophulariaceae plant Rehmannia glutinosa (Gaertn.) DC. (Rehmanniae radix; RR) and its product Rehmanniae radix praeparata (RRP) possess high nutritional and medicinal value. Both show therapeutic potential for AD in traditional medical settings. However, the differences in their bioactive components and the mechanisms of action underlying their anti-AD effects remain unclear.MethodsIn this study, APP/PS1 mice were used as the animal model of AD. Ultra-high-performance liquid chromatography coupled with Q-Exactive tandem mass spectrometry (MS/MS) (UPLC–QE-MS/MS), network pharmacology, proteomics, molecular docking, and 16S rRNA sequencing were used to investigate the differences in the medicinal components of RR and RRP and their mechanisms of action in the treatment of AD. The mechanisms of action of two identified critical components, ajugol and isoacteoside, were further verified in the D-galactose/AlCl3-induced Institute of Cancer Research (ICR) mouse model of AD—with cognitive function evaluated using the Morris water maze and open-field tests—and the amyloid-beta (Aβ)-induced BV2 cell model of inflammation.ResultsAjugol and isoacteoside were identified as the key anti-AD bioactive compounds in RR and RRP, respectively, through UPLC–QE-MS/MS. Integrated network pharmacology, proteomics, and 16S rRNA sequencing implicated neuroinflammation, apoptosis, and autophagy as critical pathways for their anti-AD effects. Subsequently, in vivo and in vitro experiments demonstrated that ajugol exerted its effects mainly by modulating the TLR/NF-κB/NLRP3 and BCL-2/BAX/cytochrome C/caspase-3 pathways, while isoacteoside primarily acted via the LC3-Ⅱ/P62/p-mTOR/mTOR pathway. Ajugol and isoacteoside mitigated cognitive impairment in AD models, decreased Aβ plaque accumulation in hippocampal tissues, and attenuated inflammatory injury-induced cytotoxicity in BV2 microglia, thereby suppressing AD progression.ConclusionIn this work, we systematically elucidated the differential mechanisms underlying the anti-AD effects of ajugol and isoacteoside. We found that ajugol primarily acts via the TLR/NF-κB/NLRP3 and BCL-2/BAX/cytochrome C/caspase-3 pathways, while isoacteoside acts via the LC3-II/P62/p-mTOR/mTOR pathway. These findings establish a foundation for developing RRP-based complementary medicines and functional foods

Pulsed electromagnetic stimulation promotes neuronal maturation by up-regulating cholesterol biosynthesis

Background: Stem cell therapies have emerged as transformative therapeutic strategies for neurological disorders. However, neurons derived from transplanted stem cells often exhibit low survival rates and remain in an immature state. While pulsed electromagnetic fields (PEMF) may enhance neuronal differentiation, the extent of this effect and its molecular mechanisms remain poorly characterized. Method: Human induced pluripotent stem cells (iPSCs) induced cortical neurons received daily PEMF stimulation (1 mT, 15 Hz, 3.75 ms pulse duration) for 7 days during differentiation. Neuronal differentiation and synaptic maturation were assessed using immunocytochemistry, qPCR, western blotting, and live-cell imaging to evaluate neurite outgrowth. Functional maturation was analyzed through calcium imaging and patch-clamp electrophysiology. Transcriptomic profiling identified key pathways involved in PEMF-modulated neuronal maturation, with the role of FDFT1-mediated cholesterol biosynthesis mechanistically validated through pharmacological inhibition and genetic knockdown. Result: PEMF accelerated early-stage neuronal differentiation without altering neurite outgrowth and enhanced synaptic maturation after sustained stimulation. PEMF-treated neurons displayed heightened spontaneous calcium signaling and improved functional maturation, including enhanced excitability, action potential kinetics, and voltage-gated ion channel activity. Transcriptomics revealed significant upregulation of cholesterol biosynthesis pathways, with FDFT1 (squalene synthase) as a central regulator. Pharmacological inhibition or genetic knockdown of FDFT1 abolished PEMF-induced neuronal differentiation and synaptic maturation. Conclusion: PEMF accelerates early-stage differentiation of human cortical neurons and enhances synaptic maturation following sustained stimulation. These effects are mechanistically linked to the activation of FDFT1-mediated cholesterol biosynthesis. This non-invasive PEMF stimulation approach represents a promising strategy to optimize stem cell-based therapies for neurological disorders

Polygenic risk score for type 2 diabetes shows context-dependent effects across populations

Polygenic risk scores hold prognostic value for identifying individuals at higher risk of type 2 diabetes. However, further characterization is needed to understand the generalizability of type 2 diabetes polygenic risk scores in diverse populations across various contexts. We systematically characterize a multi-ancestry type 2 diabetes polygenic risk score among 244,637 cases and 637,891 controls across diverse populations from the Population Architecture Genomics and Epidemiology Study and 13 additional biobanks and cohorts. Polygenic risk score performance is context dependent, with better performance in those who are younger, male, without hypertension, and not obese or overweight. Additionally, the polygenic risk score is associated with various diabetes-related cardiometabolic traits and type 2 diabetes complications, suggesting its utility for stratifying risk of complications and identifying shared genetic architecture between type 2 diabetes and other diseases. These findings highlight the need to account for context when evaluating polygenic risk score as a tool for type 2 diabetes risk prognostication and the potentially generalizable associations of type 2 diabetes polygenic risk score with diabetes-related traits, despite differential performance in type 2 diabetes prediction across diverse populations. Our study provides a comprehensive resource to characterize a type 2 diabetes polygenic risk score.</p

Genetic Discovery and Risk Characterization in Type 2 Diabetes across Diverse Populations

Genomic discovery and characterization of risk loci for type 2 diabetes (T2D) have been conducted primarily in individuals of European ancestry. We conducted a multiethnic genome-wide association study of T2D among 53,102 cases and 193,679 control subjects from African, Hispanic, Asian, Native Hawaiian, and European population groups in the Population Architecture Genomics and Epidemiology (PAGE) and Diabetes Genetics Replication and Meta-analysis (DIAGRAM) Consortia. In individuals of African ancestry, we discovered a risk variant in th

Genome-Wide Association Study of White Blood Cell Count in 16,388 African Americans: the Continental Origins and Genetic Epidemiology Network (COGENT)

Total white blood cell (WBC) and neutrophil counts are lower among individuals of African descent due to the common African-derived “null” variant of the Duffy Antigen Receptor for Chemokines (DARC) gene. Additional common genetic polymorphisms were recently associated with total WBC and WBC sub-type levels in European and Japanese populations. No additional loci that account for WBC variability have been identified in African Americans. In order to address this, we performed a large genome-wide association study (GWAS) of total WBC and cell subtype counts in 16,388 African-American participants from 7 population-based cohorts available in the Continental Origins and Genetic Epidemiology Network. In addition to the DARC locus on chromosome 1q23, we identified two other regions (chromosomes 4q13 and 16q22) associated with WBC in African Americans (P<2.5×10−8). The lead SNP (rs9131) on chromosome 4q13 is located in the CXCL2 gene, which encodes a chemotactic cytokine for polymorphonuclear leukocytes. Independent evidence of the novel CXCL2 association with WBC was present in 3,551 Hispanic Americans, 14,767 Japanese, and 19,509 European Americans. The index SNP (rs12149261) on chromosome 16q22 associated with WBC count is located in a large inter-chromosomal segmental duplication encompassing part of the hydrocephalus inducing homolog (HYDIN) gene. We demonstrate that the chromosome 16q22 association finding is most likely due to a genotyping artifact as a consequence of sequence similarity between duplicated regions on chromosomes 16q22 and 1q21. Among the WBC loci recently identified in European or Japanese populations, replication was observed in our African-American meta-analysis for rs445 of CDK6 on chromosome 7q21 and rs4065321 of PSMD3-CSF3 region on chromosome 17q21. In summary, the CXCL2, CDK6, and PSMD3-CSF3 regions are associated with WBC count in African American and other populations. We also demonstrate that large inter-chromosomal duplications can result in false positive associations in GWAS