Network hub centrality and working memory performance in schizophrenia

Deep-HPI-pred: An R-Shiny applet for network-based classification and prediction of Host-Pathogen protein-protein interactions

Host-pathogen interactions (HPIs) are vital in numerous biological activities and are intrinsically linked to the onset and progression of infectious diseases. HPIs are pivotal in the entire lifecycle of diseases: from the onset of pathogen introduction, navigating through the mechanisms that bypass host cellular defenses, to its subsequent proliferation inside the host. At the heart of these stages lies the synergy of proteins from both the host and the pathogen. By understanding these interlinking protein dynamics, we can gain crucial insights into how diseases progress and pave the way for stronger plant defenses and the swift formulation of countermeasures. In the framework of current study, we developed a web-based R/Shiny app, Deep-HPI-pred, that uses network-driven feature learning method to predict the yet unmapped interactions between pathogen and host proteins. Leveraging citrus and CLas bacteria training datasets as case study, we spotlight the effectiveness of Deep-HPI-pred in discerning Protein-protein interaction (PPIs) between them. Deep-HPI-pred use Multilayer Perceptron (MLP) models for HPI prediction, which is based on a comprehensive evaluation of topological features and neural network architectures. When subjected to independent validation datasets, the predicted models consistently surpassed a Matthews correlation coefficient (MCC) of 0.80 in host-pathogen interactions. Remarkably, the use of Eigenvector Centrality as the leading topological feature further enhanced this performance. Further, Deep-HPI-pred also offers relevant gene ontology (GO) term information for each pathogen and host protein within the system. This protein annotation data contributes an additional layer to our understanding of the intricate dynamics within host-pathogen interactions. In the additional benchmarking studies, the Deep-HPI-pred model has proven its robustness by consistently delivering reliable results across different host-pathogen systems, including plant-pathogens (accuracy of 98.4% and 97.9%), human-virus (accuracy of 94.3%), and animal-bacteria (accuracy of 96.6%) interactomes. These results not only demonstrate the model's versatility but also pave the way for gaining comprehensive insights into the molecular underpinnings of complex host-pathogen interactions. Taken together, the Deep-HPI-pred applet offers a unified web service for both identifying and illustrating interaction networks. Deep-HPI-pred applet is freely accessible at its homepage: https://cbi.gxu.edu.cn/shiny-apps/Deep-HPI-pred/ and at github: https://github.com/tahirulqamar/Deep-HPI-pred.

Association between degree centrality and neurocognitive impairments in patients with Schizophrenia: A Longitudinal rs-fMRI Study

BACKGROUND

Evidence indicates that patients with schizophrenia (SZ) experience significant changes in their functional connectivity during antipsychotic treatment. Despite previous reports of changes in brain network degree centrality (DC) in patients with schizophrenia, the relationship between brain DC changes and neurocognitive improvement in patients with SZ after antipsychotic treatment remains elusive.

METHODS

A total of 74 patients with acute episodes of chronic SZ and 53 age- and sex-matched healthy controls were recruited. The Positive and Negative Syndrome Scale (PANSS), Symbol Digit Modalities Test, digital span test (DST), and verbal fluency test were used to evaluate the clinical symptoms and cognitive performance of the patients with SZ. Patients with SZ were treated with antipsychotics for six weeks starting at baseline and underwent MRI and clinical interviews at baseline and after six weeks, respectively. We then divided the patients with SZ into responding (RS) and non-responding (NRS) groups based on the PANSS scores (reduction rate of PANSS ≥50%). DC was calculated and analyzed to determine its correlation with clinical symptoms and cognitive performance.

RESULTS

After antipsychotic treatment, the patients with SZ showed significant improvements in clinical symptoms, semantic fluency performance. Correlation analysis revealed that the degree of DC increase in the left anterior inferior parietal lobe (aIPL) after treatment was negatively correlated with changes in the excitement score (r = -0.256, p = 0.048, adjusted p = 0.080), but this correlation failed the multiple test correction. Patients with SZ showed a significant negative correlation between DC values in the left aIPL and DST scores after treatment, which was not observed at the baseline (r = -0.359, p = 0.005, adjusted p = 0.047). In addition, we did not find a significant difference in DC between the RS and NRS groups, neither at baseline nor after treatment.

CONCLUSIONS

The results suggested that DC changes in patients with SZ after antipsychotic treatment are correlated with neurocognitive performance. Our findings provide new insights into the neuropathological mechanisms underlying antipsychotic treatment of SZ.

Aberrant Brain Dynamics in Schizophrenia During Working Memory Task: Evidence From a Replication Functional MRI Study

BACKGROUND AND HYPOTHESIS

The integration of information that typifies working memory (WM) operation requires a flexible, dynamic functional relationship among brain regions. In schizophrenia, though WM capacity is prominently impaired at higher loads, the mechanistic underpinnings are unclear. As a result, we lack convincing cognitive remediation of load-dependent deficits. We hypothesize that reduced WM capacity arises from a disruption in dynamic functional connectivity when patients face cognitive demands.

STUDY DESIGN

We calculate the dynamic voxel-wise degree centrality (dDC) across the functional connectome in 142 patients with schizophrenia and 88 healthy controls (HCs) facing different WM loads during an n-back task. We tested associations of the altered variability in dDC and clinical symptoms and identified intermediate connectivity configurations (clustered states) across time during WM operation. These analyses were repeated in another independent dataset of 169 subjects (102 with schizophrenia).

STUDY RESULTS

Compared with HCs, patients showed an increased dDC variability of supplementary motor area (SMA) for the "2back vs. 0back" contrast. This instability at the SMA seen in patients correlated with increased positive symptoms and followed a limited "U-shape" pattern at rest-condition and 2 loads. In the clustering analysis, patients showed reduced centrality in the SMA, superior temporal gyrus, and putamen. These results were replicated in a constrained search in the second independent dataset.

CONCLUSIONS

Schizophrenia is characterized by a load-dependent reduction of stable centrality in SMA; this relates to the severity of positive symptoms, especially disorganized behaviour. Restoring SMA stability in the presence of cognitive demands may have a therapeutic effect in schizophrenia.

Network biomarkers in recovered psychosis patients who discontinued antipsychotics

There are no studies investigating topological properties of resting-state fMRI (rs-fMRI) in patients who have recovered from psychosis and discontinued medication (hereafter, recovered patients [RP]). This study aimed to explore topological organization of the functional brain connectome in the RP using graph theory approach. We recruited 30 RP and 50 age and sex-matched healthy controls (HC). The RP were further divided into the subjects who were relapsed after discontinuation of antipsychotics (RP-R) and who maintained recovered state without relapse (RP-M). Using graph-based network analysis of rs-fMRI signals, global and local metrics and hub information were obtained. The robustness of the network was tested with random failure and targeted attack. As an ancillary analysis, Network-Based Statistic (NBS) was performed. Association of significant findings with psychopathology and cognitive functioning was also explored. The RP showed intact network properties in terms of global and local metrics. However, higher global functional connectivity strength and hyperconnectivity in the interconnected component were observed in the RP compared to HC. In the subgroup analysis, the RP-R were found to have lower global efficiency, longer characteristic path length and lower robustness whereas no such abnormalities were identified in the RP-M. Associations of the degree centrality of some hubs with cognitive functioning were identified in the RP-M. Even though network properties of the RP were intact, subgroup analysis revealed more altered topological organizations in the RP-R. The findings in the RP-R and RP-M may serve as network biomarkers for predicting relapse or maintained recovery after the discontinuation of antipsychotics.