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Understanding complex interactions in biomedical networks is crucial for advancements in biomedicine, but traditional link prediction (LP) methods are limited in capturing this complexity. Representation-based learning techniques improve prediction accuracy by mapping nodes to low-dimensional embeddings, yet they often struggle with interpretability and scalability. We present BioPathNet, a novel graph neural network framework based on the Neural Bellman-Ford Network (NBFNet), addressing these limitations through path-based reasoning for LP in biomedical knowledge graphs. Unlike node-embedding frameworks, BioPathNet learns representations between node pairs by considering all relations along paths, enhancing prediction accuracy and interpretability. This allows visualization of influential paths and facilitates biological validation. BioPathNet leverages a background regulatory graph (BRG) for enhanced message passing and uses stringent negative sampling to improve precision. In evaluations across various LP tasks, such as gene function annotation, drug-disease indication, synthetic lethality, and lncRNA-mRNA interaction prediction, BioPathNet consistently outperformed shallow node embedding methods, relational graph neural networks and task-specific state-of-the-art methods, demonstrating robust performance and versatility. Our study predicts novel drug indications for diseases like acute lymphoblastic leukemia (ALL) and Alzheimer's, validated by medical experts and clinical trials. We also identified new synthetic lethality gene pairs and regulatory interactions involving lncRNAs and target genes, confirmed through literature reviews. BioPathNet's interpretability will enable researchers to trace prediction paths and gain molecular insights, making it a valuable tool for drug discovery, personalized medicine and biology in general.
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This study aims to develop a method to detect bovine multi-cytokines based on flow cytometry. Previously we have prepared and screened monoclonal antibodies against bovine cytokines IFN-γ, IL-2, TNF-α, IP-10 and MCP-1. These bovine cytokine monoclonal antibodies were fluorescently labeled, and the combination of antibody and cell surface molecules were used to develop the method for detecting bovine multi-cytokines. Subsequently, the developed method was used to determine the cytokine expression profile of Mycobacterium bovis BCG infected bovine peripheral blood mononuclear cells in vitro, and evaluate the cytokine expression level of peripheral blood CD4+ T cells of tuberculosis-positive cattle. The bovine multi-cytokine flow cytometry detection method can effectively determine the cytokine expression of BCG-infected bovine peripheral blood T lymphocytes. Among them, the expression levels of IFN-γ, IL-2, and TNF-α continue to increase after 40 hours of infection, while the expression levels of IP-10 and MCP-1 decreased. The combined detection of IFN-γ, IL-2, and TNF-α on CD4+ T lymphocytes in peripheral blood of cattle can effectively distinguish tuberculosis-positive and tuberculosis-negative samples. This method may facilitate evaluating the level of cellular immune response after bovine pathogen infection and vaccine injection.
Assuntos
Citocinas , Tuberculose , Bovinos , Animais , Vacina BCG/metabolismo , Fator de Necrose Tumoral alfa/metabolismo , Interleucina-2 , Citometria de Fluxo/métodos , Quimiocina CXCL10/metabolismo , Leucócitos Mononucleares , Linfócitos T CD4-Positivos/metabolismo , Anticorpos Monoclonais/metabolismoRESUMO
The involvement of long noncoding RNA (lncRNA) SNHG16 has been reported in several human cancers. Notwithstanding, the role of lncRNA SNHG16 is yet largely unknown in human lung cancer. Consequently, this study was undertaken to investigate the role and therapeutic potential of SNHG16 in human lung cancer. The results showed a significant (P < 0.05) transcriptional upregulation of SNHG16 in lung cancer tissues and cell lines. However, downregulation of SNHG16 resulted in significant (P < 0.05) inhibition of lung cancer A549 and SK-LU-1 cell proliferation. DAPI and annexin V/PI assays revealed apoptosis to be responsible for inhibition of cell proliferation and colony formation observed upon SNHG16 knockdown. This was accompanied by enhancement of Bax and suppression of Bcl-2 expression in A549 and SK-LU-1 cells. Transwell assays revealed that silencing of SNHG16 also significantly (P < 0.05) inhibited migration and invasion of A549 and SK-LU-1 cells. Bioinformatic analysis revealed that SNHG16 interacted with ALDH2 to exert its effects in human lung cancer cells. The expression of ALDH2 was found to be significantly (P < 0.05) suppressed in human lung cancer tissues and cell lines. Overexpression of ALDH2 inhibited the proliferation and colony formation of the A549 and SK-LU-1 cells. However, silencing of ALDH2 could avoid the tumor-suppressive effects of SNHG16 knockdown. Finally, SNHG16 silencing was also found to inhibit in vivo tumor growth. Collectively, the study unveils the molecular role of SNHG16 in regulating the development of lung cancer by interacting with ALDH2.
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Mycobacterium bovis, the causative agent of bovine tuberculosis (bTB), poses a risk of infection for livestock, humans, and wildlife. An interferon (IFN)-γ release assay has been used with tuberculin skin tests to detect bTB; however, infected animals may still be missed. Previous studies have suggested that bovine interleukin-2 (BoIL-2) may act as a potential biological marker for the diagnosis of bovine infectious diseases. However, a detailed evaluation of IL-2 as a diagnostic target for bTB is lacking. Therefore, we established hybridoma cell lines that produced monoclonal antibodies (mAbs) recognizing the native BoIL-2 and developed a flow cytometry assay, based on the BoIL-2 mAbs, for detecting M. bovis-specific IL-2. Subsequently, the method was utilized for a preliminary investigation of bTB in cattle; significantly (P < 0.0001) more CD4+IL-2+ T cells were detected in infected cattle than in healthy animals when a specific mycobacterial antigen CFP-10-ESAT-6 fusion protein was used. Moreover, our method demonstrated high coincidence rates with the BOVIGAM® test and an IFN-γ flow cytometry assay for the diagnosis of bTB. These findings show that the present method may be useful for detecting bTB.
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Citometria de Fluxo/veterinária , Interleucina-2/análise , Mycobacterium bovis/isolamento & purificação , Tuberculose Bovina/diagnóstico , Animais , Anticorpos Monoclonais , Bovinos , Citometria de Fluxo/métodos , Hibridomas , Camundongos Endogâmicos BALB C , Mycobacterium bovis/imunologia , Teste Tuberculínico/métodos , Teste Tuberculínico/veterinária , Tuberculose Bovina/imunologiaRESUMO
Objective To prepare monoclonal antibodies (mAbs) against bovine tumor necrosis factor-alpha (BoTNF-α). Methods Recombinant BoTNF-α with His tag (rHis-BoTNF-α) was expressed in a prokaryotic system as immunogen, and recombinant BoTNF-α with GST tag (rGST-BoTNF-α) was expressed as detection antigen. The mAbs were developed by hybridoma cell technology. The reactivity of mAbs with rHis-BoTNF-α and rGST-BoTNF-α was detected by Western blot analysis. Indirect ELISA was used to detect the titer and specificity of mAbs, and the reactivity to commercialized recombinant BoTNF-α (rBoTNF-α) was also evaluated. The reactivity of mAbs against natural antigens was identified by flow cytometry. Results Seven hybridomas stably secreting anti-rBoTNF-α mAbs were successfully obtained. The results showed that all seven mAbs had good reactivity and specificity. Flow cytometry analysis also showed that mAb 4G4 had good reactivity with natural BoTNF-α antigens. Conclusion The anti-rBoTNF-α mAbs are successfully achieved.
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Anticorpos Monoclonais/imunologia , Animais , Especificidade de Anticorpos , Bovinos , Ensaio de Imunoadsorção Enzimática , Hibridomas , Camundongos , Camundongos Endogâmicos BALB C , Fator de Necrose Tumoral alfaRESUMO
BACKGROUND: Control of Mycobacterium tuberculosis (Mtb) infection requires CD4+ T-cell responses and major histocompatibility complex class II (MHC II) presentation of Mtb antigens (Ags). Dendritic cells (DCs) are the most potent of the Ag-presenting cells and are central to the initiation of T-cell immune responses. Much research has indicated that DCs play an important role in anti-mycobacterial immune responses at early infection time points, but the kinetics of Ag presentation by these cells during these events are incompletely understood. RESULTS: In the present study, we evaluated in vivo dynamics of early Ag presentation by murine lymph-node (LN) DCs in response to Mycobacterium bovis bacillus Calmette-Guérin (BCG) Ag85A protein. Results showed that the early Ag-presenting activity of murine DCs induced by M. bovis BCG Ag85A protein in vivo was transient, appearing at 4 h and being barely detectable at 72 h. The transcription levels of CIITA, MHC II and the expression of MHC II molecule on the cell surface increased following BCG infection. Moreover, BCG was found to survive within the inguinal LN DC pool, representing a continuing source of mycobacterial Ag85A protein, with which LN DCs formed Ag85A peptide-MHCII complexes in vivo. CONCLUSIONS: Our results demonstrate that a decrease in Ag85A peptide production as a result of the inhibition of Ag processing to is largely responsible for the short duration of Ag presentation by LN DCs during BCG infection in vivo.
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Aciltransferases/imunologia , Apresentação de Antígeno/imunologia , Antígenos de Bactérias/imunologia , Células Dendríticas/imunologia , Linfonodos/imunologia , Mycobacterium bovis/imunologia , Tuberculose/imunologia , Aciltransferases/metabolismo , Adjuvantes Imunológicos/administração & dosagem , Animais , Antígenos de Bactérias/metabolismo , Vacina BCG/administração & dosagem , Vacina BCG/imunologia , Sobrevivência Celular/imunologia , Células Dendríticas/metabolismo , Células Dendríticas/microbiologia , Antígenos de Histocompatibilidade Classe II/imunologia , Antígenos de Histocompatibilidade Classe II/metabolismo , Interferon gama/imunologia , Interferon gama/metabolismo , Linfonodos/metabolismo , Linfonodos/microbiologia , Camundongos Endogâmicos C57BL , Mycobacterium bovis/fisiologia , Fatores de Tempo , Tuberculose/prevenção & controle , Tuberculose/veterináriaRESUMO
OBJECTIVE: To evaluate the effectiveness of the Functional Assessment of Cancer Therapy-Hepatobiliary (FACT-Hep) questionnaire in measuring the quality of life in patients with primary hepatic carcinoma (PHC) in China. METHODS: FACT-Hep questionnaire was translated into Chinese and revised properly. From September 2005 to April 2006, one hundred and eighty patients with primary liver carcinoma were admitted and measured by using the Chinese version of FACT-Hep questionnaire, and the reliabilities, validities and responsibilities of the questionnaire were assessed. RESULTS: Correlation coefficient was higher between items and dimension of their corresponding domain (0.5933+/-0.1652) than that between the items and other domains (0.2749+/-0.1922). Six principal constituents were extracted by factor analysis and represented all domains of the questionnaire. The combinations of components were consistent with what was expected. The correlation coefficient of criterion-related validity was 0.828. The test-retest reliability correlation coefficients of physical, social/family, emotion, function, symptom and total questionnaire were 0.731, 0.334, 0.953, 0.786, 0.785 and 0.801 respectively, and the values of Cronbach's alpha were 0.7397, 0.4193, 0.7914, 0.8250, 0.8399 and 0.9161, respectively. There were statistical differences in scores of FACT-Hep questionnaire in different PHC stages or in different Child-Pugh classes (P<0.05). CONCLUSION: The FACT-Hep questionnaire can measure the quality of life in patients with PHC with good reliability, validity and responsiveness; it can be used in assessing the disease-specific health-related quality of life of patients with hepatobiliary cancers.