Identification of molecular sub-networks associated with cell survival in a chronically SIVmac-infected human CD4+ T cell line

Inferring upstream regulatory genes of FOXP3 in human regulatory T cells from time-series transcriptomic data

The discovery of upstream regulatory genes of a gene of interest still remains challenging. Here we applied a scalable computational method to unbiasedly predict candidate regulatory genes of critical transcription factors by searching the whole genome. We illustrated our approach with a case study on the master regulator FOXP3 of human primary regulatory T cells (Tregs). While target genes of FOXP3 have been identified, its upstream regulatory machinery still remains elusive. Our methodology selected five top-ranked candidates that were tested via proof-of-concept experiments. Following knockdown, three out of five candidates showed significant effects on the mRNA expression of FOXP3 across multiple donors. This provides insights into the regulatory mechanisms modulating FOXP3 transcriptional expression in Tregs. Overall, at the genome level this represents a high level of accuracy in predicting upstream regulatory genes of key genes of interest.

Arsenic trioxide-induced apoptosis contributes to suppression of viral reservoir in SIV-infected rhesus macaques

Latent viral reservoir is recognized as the major obstacle to achieving a functional cure for HIV infection. We previously reported that arsenic trioxide (As2O3) combined with antiretroviral therapy (ART) can reactivate the viral reservoir and delay viral rebound after ART interruption in chronically simian immunodeficiency virus (SIV)-infected macaques. In this study, we further investigated the effect of As2O3 independent of ART in chronically SIV-infected macaques. We found that As2O3-only treatment significantly increased the CD4/CD8 ratio, improved SIV-specific T cell responses, and reactivated viral latency in chronically SIVmac239-infected macaques. RNA-sequencing analysis revealed that As2O3 treatment downregulated the expression levels of genes related to HIV entry and infection, while the expression levels of genes related to transcription initiation, cell apoptosis, and host restriction factors were significantly upregulated. Importantly, we found that As2O3 treatment specifically induced apoptosis of SIV-infected CD4+ T cells. These findings revealed that As2O3 might not only impact viral latency, but also induce the apoptosis of HIV-infected cells and thus block the secondary infection of bystanders. Moreover, we investigated the therapeutic potential of this regimen in acutely SIVmac239-infected macaques and found that As2O3 + ART treatment effectively restored the CD4+ T cell count, delayed disease progression, and improved survival in acutely SIV-infected macaques. In sum, this work provides new insights to develop As2O3 as a component of the "shock-and-kill" strategy toward HIV functional cure. IMPORTANCE Although antiretroviral therapy (ART) can effectively suppress the viral load of AIDS patients, it cannot functionally cure HIV infection due to the existence of HIV reservoir. Strategies toward HIV functional cure are still highly anticipated to ultimately end the pandemic of AIDS. Herein, we investigated the direct role of As2O3 independent of ART in chronically SIV-infected macaques and explored the underlying mechanisms of the potential of As2O3 in the treatment of HIV/SIV infection. Meanwhile, we investigated the therapeutic effects of ART+As2O3 in acutely SIVmac239-infected macaques. This study showed that As2O3 has the potential to be launched into the "shock-and-kill" strategy to suppress HIV/SIV reservoir due to its latency-reversing and apoptosis-inducing properties.

Exacerbated AIDS progression by PD-1 blockade during therapeutic vaccination in chronically SIV-infected rhesus macaques after ART treatment interruption

The persistence of latent HIV-1-infected cells, named the latent reservoir, is the major barrier to HIV-1 eradication, and the formation and maintenance of latent reservoir might be exacerbated by activation of the immunoinhibitory pathway and dysfunction of CD8⁺ T cells during HIV-1 infection. Our previous findings demonstrated that prophylactic vaccination combined with PD-1 blockade generated distinct immune response profiles and conferred effective control of highly pathogenic SIVmac239 infection in rhesus macaques. However, to our surprise, herein we found that a therapeutic vaccination in combination with PD-1 blockade resulted in activation of the viral reservoir, faster viral rebound after treatment interruption, accelerated acquired immune deficiency syndrome (AIDS) progression and ultimately death in chronically SIV-infected macaques after ART treatment interruption. Our study further demonstrated that the SIV provirus was preferentially enriched in PD-1⁺CD4⁺ T cells due to their susceptibility to viral entry, potent proliferation ability and inability to perform viral transcription. In addition, the viral latency was effectively reactivated upon PD-1 blockade. Together, these results suggest that PD-1 blockade may be a double-edged sword for HIV-1 immunotherapy, and they provide important insight for the rational design of immunotherapy strategies toward an HIV-1 cure. Importance As one of the most challenging public health problems, there is no clinically effective cure strategies against HIV-1 infection yet. We have demonstrated that prophylactic vaccination combined with PD-1 blockade generated distinct immune response profiles and conferred better control of highly pathogenic SIVmac239 infection in rhesus macaques. In the present study, to our surprise, PD-1 blockade during therapeutic vaccination accelerated the reactivation of latent reservoir and then AIDS progression in chronically SIV-infected macaques after ART treatment interruption. Our further study demonstrated that the latent SIV provirus was preferentially enriched in PD-1⁺CD4⁺ T cells because of its susceptibility of viral entry, inhibition of SIV transcription and potent ability of proliferation, and the viral latency was effectively reactivated by PD-1 blockade. Therefore, PD-1 blockade might be a double-edged sword for AIDS therapy. These findings provoke extensive interests to further exploit novel therapeutic treatment against HIV-1 infection and other emerging infectious diseases.

Evaluation of Reinfection in COVID-19 Patients in the World: A Narrative Review

Background: The evaluation of reinfection and the genetic structure of all human and virus genomes could help to develop programs and protocols for providing services and ultimately to prevent the disease by producing more effective vaccines. Therefore, the aim of this study was to investigate the presence and occurrence of COVID-19 reinfection through a narrative review study. Methods: We searched the Medline (PubMed), Embase, Scopus, Web of Science, Cochrane library, Ovid, and CINHAL databases. Inclusion criteria included all studies whose main purpose was to provide information about the occurrence or presence of reinfection in patients with COVID-19. An independent samples t test was used to compare the continuous outcomes between the 2 groups. Results: The mean duration of the first episode in the group with mild or moderate COVID-19 was 24.42±1.67 days, and it was 21.80±3.79 days in the group with severe COVID-19. The mean duration of the second episode (reinfection) in patients with mild or moderate form was 15.38 ± 5.57 days, and it was 19.20±2.98 days in patients with severe form. In both episodes, the duration of the disease did not significantly differ between the 2 groups (p=0.484 in the first episode; p=0.675 in the second episode), but the interval to the occurrence of reinfection in patients with the mild or moderate form was significantly longer than those with the severe form (p<0.001). In this instance, the time interval in patients with the mild or moderate form was 36.63±5.71 days while in those with the severe form of the disease it was 29.70±5.65 days. Besides, the genomes of the viruses isolated from the first and second episode were different. Conclusion: According to the results, all patients should be very careful about the severity of the second episode because of the more need for medical interventions for saving the patients. The interval between the first end and the second episode as well as the duration of each episode is highly important for better management of the disease.

A roadmap towards personalized immunology

Big data generation and computational processing will enable medicine to evolve from a "one-size-fits-all" approach to precise patient stratification and treatment. Significant achievements using "Omics" data have been made especially in personalized oncology. However, immune cells relative to tumor cells show a much higher degree of complexity in heterogeneity, dynamics, memory-capability, plasticity and "social" interactions. There is still a long way ahead on translating our capability to identify potentially targetable personalized biomarkers into effective personalized therapy in immune-centralized diseases. Here, we discuss the recent advances and successful applications in "Omics" data utilization and network analysis on patients' samples of clinical trials and studies, as well as the major challenges and strategies towards personalized stratification and treatment for infectious or non-communicable inflammatory diseases such as autoimmune diseases or allergies. We provide a roadmap and highlight experimental, clinical, computational analysis, data management, ethical and regulatory issues to accelerate the implementation of personalized immunology.

Network-Guided Key Gene Discovery for a Given Cellular Process

Identification of key genes for a given physiological or pathological process is an essential but still very challenging task for the entire biomedical research community. Statistics-based approaches, such as genome-wide association study (GWAS)- or quantitative trait locus (QTL)-related analysis have already made enormous contributions to identifying key genes associated with a given disease or phenotype, the success of which is however very much dependent on a huge number of samples. Recent advances in network biology, especially network inference directly from genome-scale data and the following-up network analysis, opens up new avenues to predict key genes driving a given biological process or cellular function. Here we review and compare the current approaches in predicting key genes, which have no chances to stand out by classic differential expression analysis, from gene-regulatory, protein-protein interaction, or gene expression correlation networks. We elaborate these network-based approaches mainly in the context of immunology and infection, and urge more usage of correlation network-based predictions. Such network-based key gene discovery approaches driven by information-enriched 'omics' data should be very useful for systematic key gene discoveries for any given biochemical process or cellular function, and also valuable for novel drug target discovery and novel diagnostic, prognostic and therapeutic-efficiency marker prediction for a specific disease or disorder.