Machine learning-based predictive models and drug prediction for schizophrenia in multiple programmed cell death patterns

Abstract

BackgroundSchizophrenia (SC) is one of the most common mental illnesses. However, the underlying genes that cause it and its effective treatments are unknown. Programmed cell death (PCD) is associated with many immune diseases and plays an important role in schizophrenia, which may be a diagnostic indicator of the disease.MethodsTwo groups as training and validation groups were chosen for schizophrenia datasets from the Gene Expression Omnibus Database (GEO). Furthermore, the PCD-related genes of the 12 patterns were extracted from databases such as KEGG. Limma analysis was performed for differentially expressed genes (DEG) identification and functional enrichment analysis. Machine learning was employed to identify minimum absolute contractions and select operator (LASSO) regression to determine candidate immune-related center genes, construct protein–protein interaction networks (PPI), establish artificial neural networks (ANN), and validate with consensus clustering (CC) analysis, then Receiver operating characteristic curve (ROC curve) was drawn for diagnosis of schizophrenia. Immune cell infiltration was developed to investigate immune cell dysregulation in schizophrenia, and finally, related drugs with candidate genes were collected via the Network analyst online platform.ResultsIn schizophrenia, 263 genes were crossed between DEG and PCD-related genes, and machine learning was used to select 42 candidate genes. Ten genes with the most significant differences were selected to establish a diagnostic prediction model by differential expression profiling. It was validated using artificial neural networks (ANN) and consensus clustering (CC), while ROC curves were plotted to assess diagnostic value. According to the findings, the predictive model had a high diagnostic value. Immune infiltration analysis revealed significant differences in Cytotoxic and NK cells in schizophrenia patients. Six candidate gene-related drugs were collected from the Network analyst online platform.ConclusionOur study systematically discovered 10 candidate hub genes (DPF2, ATG7, GSK3A, TFDP2, ACVR1, CX3CR1, AP4M1, DEPDC5, NR4A2, and IKBKB). A good diagnostic prediction model was obtained through comprehensive analysis in the training (AUC 0.91, CI 0.95–0.86) and validation group (AUC 0.94, CI 1.00–0.85). Furthermore, drugs that may be useful in the treatment of schizophrenia have been obtained (Valproic Acid, Epigallocatechin gallate).

Bioinformatics analysis and prediction of Alzheimer’s disease and alcohol dependence based on Ferroptosis-related genes

“…Multiple studies have demonstrated that neuronal cell death often transpires due to ferroptosis ( Ren et al, 2023 ; Wang D. et al, 2023 ). In our previous research, we have identified connections between psycho-neuro-degeneration and various factors, including programmed cell death (PCD), mitochondrial function, vesicular transport, and cuproptosis ( Feng and Shen, 2023 ; Feng et al, 2023 ; Shen et al, 2023 ).…”

Exploring the Intersection of Schizophrenia, Machine Learning, and Genomics: A Scoping Review (Preprint)

“…Using a RF approach, they found 103 additional gene interactions were expanded to schizophrenia-associated networks, which were shared amongst both the dorsolateral prefrontal cortex and amygdala regions [51]. Another study by Feng and Shen used neural networks using programmed cell-death-related genes as features and found 10 candidate hub genes (DPF2, ATG7, GSK3A, TFDP2, ACVR1, CX3CR1, AP4M1, DEPDC5, NR4A2, and IKBKB) [52]. Finally, a study on fresh frozen post-mortem brain tissue aimed to identify DNA methylation patterns specific to schizophrenia patients.…”