Sepsis is a common cause of death in the ICUs characterized by an abnormal host response [37]. Patients with sepsis have a highly modulated blood transcriptome, leading to enhanced inflammatory response and early and profound changes in innate and adaptive immunity [38, 39]. As sepsis manifests in the activation of the innate immune system along with the suppression of both innate and adaptive immune systems,several biomarkers have been identified that are indicative of sepsis's immune dysfunction thus contributing to the prognosis of the condition [39]. However, no biomarker has sufficient specificity or sensitivity to provide a benchmark for its usage in clinical practice. Few tests are available that can distinguish sepsis from other inflammatory conditions, or provide the likely outcome. Therefore, identifying early IRGs in blood samples is of paramount importance. This is to elucidate the molecular mechanisms by which sepsis progresses and to provide potential targets for early diagnosis and subsequent therapeutic development. In critically ill patients, the easy availability of whole blood offers a major advantage for monitoring immunological dysfunction.
Recently, methodological advances in the field of sequencing technologies, especially RNA-seq have been instrumental in providing a more detailed and quantitative view of gene expression. More and more studies begin to focus on using machine learning to better predict the clinical outcome of sepsis. It remains to be determined which genes are expressed to assess immune function in sepsis and can predict two extremes of clinical recovery (survivors vs. non-survivors). To the best of our knowledge, this is the first sepsis prediction model built to explain each prediction and to jointly analyze DEGs in blood transcript with immune-related genes during the early course of sepsis (Fig. 8). Thus, we identified 25 and 36 IRGs in different up- and down-regulated expressions. Screening criteria for the 25 and 36 IRGs included their differential expression in any two blood samples.
Our findings support the idea that the pro-and anti-inflammatory response can occur simultaneously at the onset of sepsis and contributes to death [19]. GO and KEGG analysis showed that different up-regulated expressed IRGs are all pro-inflammatory in biological processes, including immune response, innate immune defense against Gram-positive bacteria, and innate immunity in the mucosa to activating cytokine-cytokine receptor interaction and TNF signaling pathway. The down-regulated IRGs are mainly related to promoting the immunosuppressive cellular program, including T cell receptors, costimulation of T cells, immune response, T cell activation, and positive regulation of T cell proliferation through downregulation of T-cell receptor signaling pathway, Graft-versus-host disease, allograft rejection, Type I diabetes mellitus, and autoimmune thyroid disease pathway. Similarly, PPI networking shows uniform findings suggesting that immune-related gene expression signatures can define different immune response states in sepsis [39]. Our findings also validated the methods utilized by prior research studies for defining a gene expression signature that could envisage individual survival, which performed poorly in our sepsis cohort [40]. Based on these, we suggest a multitude of factors responsible for sepsis mortality, and in contrast with prior research, an early gene expression signature can define an individual immune response and is consistently associated with a worse prognosis.
Also, the IRGs score on the expression of the six survival-associated IRGs assisted in the grouping of septic patients as survivors or non-survivors. The nomogram model of IRGs score in combination with SOFA or APACHE II performed well in predicting mortality (28-day) of sepsis, indicated by a high C-index value of 0.81, an acceptable calibration. Our study showed that six survival-associated IRGs were differentially expressed within the first 24 h after sepsis and undergoing 5 days post-infection, which are central to the prognostic of sepsis and can define individual sepsis immune state signatures, referring to individualized therapy to guide sepsis survival; these data largely accord with previous reports. For example, Siegler et al.[41] found that decreased transcription of HLA-DPA1 can modulate monocyte activation during sepsis. Several clinical trials of immunostimulatory therapy strategies targeting the reversibility of down-regulation of HLA-DPA1 could restore the immune function in septic patients [42, 43]. In another trial in acute myeloid leukemia (AML) patients, these epigenetic changes, including HLA-DPA1 expression may be reversible with appropriate therapy which makes resensitizing AML cells to the graft-versus-leukemia effect may be feasible. Other studies reported the significance of MMP9 in the pathogenesis of sepsis and septic shock [44], considering it a promising novel biomarker to predict the severity and outcome of sepsis [45, 46]. Currently, numerous clinical studies have shown that inhibitors targeting MMP9, including andecaliximab (ADX) [47], tissue plasminogen activator (tPA) [48], and doxycycline [49] are benefits in many diseases. MMP9 is associated with the efficacy of immunotherapy. Similarly, IL18RAP is a subunit of the heterodimeric receptor for interleukin 18 and is reported to drive NK cell activation to impair Treg activity [50]. IL-18 plays an inflammatory role in rheumatoid arthritis. The expression of IL18RAP has been suggested as a potential predictor of treatment response in rheumatoid arthritis that is not specific to a particular drug type [51]. Lee and colleagues conducted a meta-analysis and found that higher levels of PTX-3 are observed in septic patients in non-survivors compared to survivors. They concluded that high PTX-3 is also a significant predictor of mortality. Another study found that glatiramer acetate targets the reduction of PTX-3 levels and can ameliorate the neurodegenerative impact on Multiple Sclerosis (MS) patients [52]. As a marker of sepsis severity and predictor of mortality outcomes [53, 54], human RNase3, is a member of the RNase superfamily involved in host immunity. RNase3 exhibits immune effects through independent modes in a macrophage-cell line infection model [55] and has been used as inflammation parameters in patients with cypress allergy treated with immunotherapy [56]. In addition, S100 proteins are of interest as mediators of calcium-associated signal transduction that change subcellular distribution in response to extracellular stimuli. They also function as chemotactic agents and may play a role in the pathogenesis of the epidermal disease, including inflammation [57]. A number of pharmacological approaches have been used to modulate S100 signaling in cancer and auto-inflammatory diseases [58–60]. Therefore, our cohort study developed a prognostic modeling tool for sepsis survival based on IRG expression profiles, which might serve to guide individualized therapy for sepsis survival.
Sepsis immunotherapy relies on understanding the interactions between the host response and immune cells. However, owing to sepsis heterogeneity, it can be challenging to recognize associations between immune cell infiltration and various clinicopathological factors. In the current study, we utilized the CIBERSORT database to study the relationship between immunocyte infiltration and IRGs score. Neutrophils and eosinophils infiltration were more abundant in the high IRGs score group and negatively associated with IRGs scores. Neutrophils are critical for the early control of invading pathogens [61]. Various reports show the aberrant function of neutrophils preceding the advancement of nosocomial infections [62]. Individuals with severely reduced neutrophil functions are at risk of nosocomial infections [62]. The reduced neutrophil function also further leads to Pseudomonas aeruginosa secondary infection susceptibility according to the murine model manifesting in polymicrobial sepsis [63]. Moreover, extracorporeal cell therapy with donor granulocytes was found to decrease various biomarkers of sepsis and improve sepsis severity in ten patients with septic shock [64]. While over numbers will result in increased disease severity and even death [65]. Like neutrophils, eosinophils perform a major role in sepsis prognosis, and their abnormal activity results in poor prognosis. However, it is unclear whether eosinophils are simply a marker of disease severity or a reflection of impaired type 2 immune responses. This is because it is unclear if they are necessary for cellular repair. So, gaining an insight into the mechanism through which eosinophils are reduced in sepsis is necessary. In our study, we identified that monocytes/macrophages and dendritic cells were infiltration in the high IRGs group, and are positively associated with our IRGs score. As we know that monocytes and macrophages in circulation have important roles against bacterial invasion that may reinstate the peripheral immune response to protect the host from infection morbidity [66]. Similarly, dendritic cells are activated to induce adaptive immune responses for controlling infection that gives rise to sepsis survival [67, 68]. Besides, B-lymphocytes, T-lymphocytes, and NK cells were significantly infiltration in the high IRGs group, and were positive with IRGs score, which is in accord with the reduced or dysfunction of these cells may promote immunoparalysis, which is one hallmark for sepsis survival [69]. In addition, to delineate the potential molecular mechanism of survivor-associated IRGs' role, GSEA-KEGG analysis suggested that the possibility of survivor-associated IRGs regulating cell adhesion molecules (CAMs), chemokine signaling, and antigen processing and presentation pathways, all having a crucial role in mediating immune cells activation, thus acting as a vital factor in guarding host response, association with sepsis survival [68, 70, 71]. Clinical studies have shown numerous critically ill COVID-19 patients developed organ dysfunction due to dysregulated response to infection and met the criteria for sepsis [69]. Therefore, we also analyzed patients with COVID-19 who had been diagnosed with sepsis. A differential expression of IRGs associated with survival was also validated in the sepsis cohort from the GEO database, indicating that IRGs can also be used to predict COVID-19 in treated patients with sepsis. However, the numbers of included cases were too small. More detailed and well-designed clinical studies are required to explore these issues in-depth [72, 73]. Finally, according to genetic links targets, Pulmicort Nebuamp BOSS and methacholine BOSS immunomodulators therapies were identified as promising anti-sepsis and anti-COVID-19 therapeutics.
Limitations
There are some limitations to this study. Firstly, transcriptome analyses are not reflective of the overall immune state. Secondly, other vital contributing factors such as various causes and co-morbidities were not taken into account in our study owing to the database's limited clinical information, so we couldn't d exclude related interfering factors on the IRGs score. Furthermore, though we verify the prognosis role of the IRGs in blood samples at the onset of sepsis, however, the host immune status itself was different at different time points in sepsis, we didn't verify the prognosis role of the IRGs at the late stage of sepsis, which may weaken the stability of the results. Finally, our study sample size was not large due to the need for complete clinical data. Hence, further larger clinical studies of our findings are warranted in the future.