Gene correlation network analysis to identify regulatory factors in sepsis.

BACKGROUND AND OBJECTIVES: Sepsis is a leading cause of mortality and morbidity in the intensive care unit. Regulatory mechanisms underlying the disease progression and prognosis are largely unknown. The study aimed to identify master regulators of mortality-related modules, providing potential therapeutic target for further translational experiments. METHODS: The dataset GSE65682 from the Gene Expression Omnibus (GEO) database was utilized for bioinformatic analysis. Consensus weighted gene co-expression netwoek analysis (WGCNA) was performed to identify modules of sepsis. The module most significantly associated with mortality were further analyzed for the identification of master regulators of transcription factors and miRNA. RESULTS: A total number of 682 subjects with various causes of sepsis were included for consensus WGCNA analysis, which identified 27 modules. The network was well preserved among different causes of sepsis. Two modules designated as black and light yellow module were found to be associated with mortality outcome. Key regulators of the black and light yellow modules were the transcription factor CEBPB (normalized enrichment score = 5.53) and ETV6 (NES = 6), respectively. The top 5 miRNA regulated the most number of genes were hsa-miR-335-5p (n = 59), hsa-miR-26b-5p (n = 57), hsa-miR-16-5p (n = 44), hsa-miR-17-5p (n = 42), and hsa-miR-124-3p (n = 38). Clustering analysis in 2-dimension space derived from manifold learning identified two subclasses of sepsis, which showed significant association with survival in Cox proportional hazard model (p = 0.018). CONCLUSIONS: The present study showed that the black and light-yellow modules were significantly associated with mortality outcome. Master regulators of the module included transcription factor CEBPB and ETV6. miRNA-target interactions identified significantly enriched miRNA.

The landscape of isoform switches in sepsis: a multicenter cohort study.

Sepsis is caused by an uncontrolled inflammatory response, whose underlying mechanisms are not fully understood. It is well known that the majority of human genes can be expressed as alternative isoforms. While isoform switching is implicated in many diseases and is particularly prominent in cancer, it has never been reported in the context of sepsis. Patients presented to the emergency department of three tertiary care hospitals from January 2020 to December 2020 were enrolled. Clinical variables and genome-wide transcriptome of peripheral blood mononuclear cells (PBMC) were obtained. Isoform switching analysis were performed to identify significant isoform switches and relevant biological consequences. A total of 48 subjects with sepsis, involving 42 survivors and 6 non-survivors, admitted to the emergency department of three tertiary care hospitals were enrolled in this study. PBMCs were extracted for RNA sequencing (RNA-seq). Patients (n = 4) with mild stroke or acute coronary syndrome without infection were enrolled in this study as controls. The most frequent functional changes resulting from isoform switching were changes affecting the open reading frame, protein domains and intron retention. Many genes without differences in gene expression showed significant isoform switching. Many genes with significant isoform switches ([Formula: see text]> 0.1) were associated with higher mortality risk, including PIGS, CASP3, LITAF, HBB and RUVBL2. The study for the first time described the landscape of isoform switching in sepsis, including differentially expressed isoform fractions between patients with and without sepsis and survivors and nonsurvivors. The biological consequences of isoform switching, including protein domain loss, signal peptide gain, and intron retention, were identified.

Single-cell transcriptome profiling reveals heterogeneous neutrophils with prognostic values in sepsis.

Neutrophils constitute the largest proportion of nucleated peripheral blood cells, and neutrophils have substantial heterogeneity. We profiled nearly 300,000 human peripheral blood cells in this study using single-cell RNA sequencing. A large proportion (>50%) of these cells were annotated as neutrophils. Neutrophils were further clustered into four subtypes, including Neu1, Neu2, Neu3, and Neu4. Neu1 is characterized by high expression of MMP9, HP, and RGL4. Neu1 was associated with septic shock and significantly correlated with the sequential organ failure assessment (SOFA) score. A gene expression module in Neu1 named Neu1_C (characterized by expression of NFKBIA, CXCL8, G0S2, and FTH1) was highly predictive of septic shock with an area under the curve of 0.81. The results were extensively validated in external bulk datasets by using single-cell deconvolution methods. In summary, our study establishes a general framework for studying neutrophil-related mechanisms, prognostic biomarkers, and potential therapeutic targets for septic shock.

Integrated Single Cell and Bulk RNA-Seq Analysis Revealed Immunomodulatory Effects of Ulinastatin in Sepsis: A Multicenter Cohort Study.

Sepsis is a leading cause of morbidity and mortality in the intensive care unit, which is caused by unregulated inflammatory response leading to organ injuries. Ulinastatin (UTI), an immunomodulatory agent, is widely used in clinical practice and is associated with improved outcomes in sepsis. But its underlying mechanisms are largely unknown. Our study integrated bulk and single cell RNA-seq data to systematically explore the potential mechanisms of the effects of UTI in sepsis. After adjusting for potential confounders in the negative binomial regression model, there were more genes being downregulated than being upregulated in the UTI group. These down-regulated genes were enriched in the neutrophil involved immunity such as neutrophil activation and degranulation, indicating the immunomodulatory effects of UTI is mediated via regulation of neutrophil activity. By deconvoluting the bulk RNA-seq samples to obtain fractions of cell types, the Myeloid-derived suppressor cells (MDSC) were significantly expanded in the UTI treated samples. Further cell-cell communication analysis revealed some signaling pathways such as ANEEXIN, GRN and RESISTIN that might be involved in the immunomodulatory effects of UTI. The study provides a comprehensive reference map of transcriptional states of sepsis treated with UTI, as well as a general framework for studying UTI-related mechanisms.

Latent transition analysis of cardiac arrest patients treated in the intensive care unit.

BACKGROUND AND OBJECTIVE: Post-cardiac arrest (CA) syndrome is heterogenous in their clinical presentations and outcomes. This study aimed to explore the transition and stability of subphenotypes (profiles) of CA treated in the intensive care unit (ICU). PATIENTS AND METHODS: Clinical features of CA patients on day 1 and 3 after ICU admission were modeled by latent transition analysis (LTA) to explore the transition between subphenotypes over time. The association between different transition patterns and mortality outcome was explored using multivariable logistic regression. RESULTS: We identified 848 eligible patients from the database. The LPA identified three distinct subphenotypes: Profile 1 accounted for the largest proportion (73%) and was considered as the baseline subphenotype. Profile 2 (13%) was characterized by brain injury and profile 3 (14%) was characterized by multiple organ dysfunctions. The same three subphenotypes were identified on day 3. The LTA showed consistent subphenotypes. A majority of patients in profile 2 (72%) and 3 (82%) on day 1 switched to profile 1 on day 3. In the logistic regression model, patients in profile 1 on day 1 transitioned to profile 3 had worse survival outcome than those continue to remain in profile 1 (OR: 20.64; 95% CI: 6.01 to 70.94; p < 0.001) and transitioned to profile 2 (OR: 8.42; 95% CI: 2.22 to 31.97; p = 0.002) on day 3. CONCLUSION: The study identified three subphenotypes of CA, which was consistent on day 1 and 3 after ICU admission. Patients who transitioned to profile 3 on day 3 had significantly worse survival outcome than those remained in profile 1 or 2.

Individualized Mechanical power-based ventilation strategy for acute respiratory failure formalized by finite mixture modeling and dynamic treatment regimen.

BACKGROUND: Mechanical ventilation (MV) is the key to the successful treatment of acute respiratory failure (ARF) in the intensive care unit (ICU). The study aims to formalize the concept of individualized MV strategy with finite mixture modeling (FMM) and dynamic treatment regime (DTR). METHODS: ARF patients requiring MV for over 48 h from 2008 to 2019 were included. FMM was conducted to identify classes of ARF. Static and dynamic mechanical power (MP_static and MP_dynamic) and relevant clinical variables were calculated/collected from hours 0 to 48 at an interval of 8 h. Δ M P was calculated as the difference between actual and optimal MP. FINDINGS: A total of 8768 patients were included for analysis with a mortality rate of 27%. FFM identified three classes of ARF, namely, the class 1 (baseline), class 2 (critical) and class 3 (refractory respiratory failure). The effect size of MP_static on mortality is the smallest in class 1 (HR for every 5 Joules/min increase: 1.29; 95% CI: 1.15 to 1.45; p < 0.001) and the largest in class 3 (HR for every 5 Joules/min increase: 1.83; 95% CI: 1.52 to 2.20; p < 0.001). INTERPRETATION: MP has differing therapeutic effects for subtypes of ARF. Optimal MP estimated by DTR model may help to improve survival outcome. FUNDING: The study was funded by Health Science and Technology Plan of Zhejiang Province (2021KY745), Key Research & Development project of Zhejiang Province (2021C03071) and Yilu "Gexin" - Fluid Therapy Research Fund Project (YLGX-ZZ-2,020,005).

Interleukin­Iß promotes cartilage degeneration by regulating forkhead box protein O4 and type â ¡ collagen.

Osteoarthritis (OA) is one of the most prevalent pain­inducing and disabling diseases globally. Aging is a primary contributing factor to the progression of OA. Forkhead box protein O4 (FOXO4) is known to be involved in the cell cycle and apoptosis regulation. The aim of the present study was to investigate the association between FOXO4 expression and chondrocyte degeneration in rats. Chondrocytes were assigned to the control (4­week­old rats), natural degeneration (16­week­old rats) or induced degeneration (IL­1ß­treated chondrocytes from 4­week­old rats) groups. Immunocytochemical analysis with ß­galactosidase staining revealed a greater number of stained cells present in the natural and induced degeneration groups than in the control group. PCR analysis indicated lower mRNA expression levels of collagen type II α1 chain (Col2α) and higher levels of FOXO4, and western blotting revealed reduced Col2α protein expression levels and significantly elevated FOXO4 levels in the natural and induced degeneration groups, compared with those in the control group. The results of the present study revealed that FOXO4 expression was altered in the natural and induced degeneration groups, and further research and exploration are needed to clarify the underlying mechanism.

Deep learning-based clustering robustly identified two classes of sepsis with both prognostic and predictive values.

BACKGROUND: Sepsis is a heterogenous syndrome and individualized management strategy is the key to successful treatment. Genome wide expression profiling has been utilized for identifying subclasses of sepsis, but the clinical utility of these subclasses was limited because of the classification instability, and the lack of a robust class prediction model with extensive external validation. The study aimed to develop a parsimonious class model for the prediction of class membership and validate the model for its prognostic and predictive capability in external datasets. METHODS: The Gene Expression Omnibus (GEO) and ArrayExpress databases were searched from inception to April 2020. Datasets containing whole blood gene expression profiling in adult sepsis patients were included. Autoencoder was used to extract representative features for k-means clustering. Genetic algorithms (GA) were employed to derive a parsimonious 5-gene class prediction model. The class model was then applied to external datasets (n = 780) to evaluate its prognostic and predictive performance. FINDINGS: A total of 12 datasets involving 1613 patients were included. Two classes were identified in the discovery cohort (n = 685). Class 1 was characterized by immunosuppression with higher mortality than class 2 (21.8% [70/321] vs. 12.1% [44/364]; p < 0.01 for Chi-square test). A 5-gene class model (C14orf159, AKNA, PILRA, STOM and USP4) was developed with GA. In external validation cohorts, the 5-gene class model (AUC: 0.707; 95% CI: 0.664 - 0.750) performed better in predicting mortality than sepsis response signature (SRS) endotypes (AUC: 0.610; 95% CI: 0.521 - 0.700), and performed equivalently to the APACHE II score (AUC: 0.681; 95% CI: 0.595 - 0.767). In the dataset E-MTAB-7581, the use of hydrocortisone was associated with increased risk of mortality (OR: 3.15 [1.13, 8.82]; p = 0.029) in class 2. The effect was not statistically significant in class 1 (OR: 1.88 [0.70, 5.09]; p = 0.211). INTERPRETATION: Our study identified two classes of sepsis that showed different mortality rates and responses to hydrocortisone therapy. Class 1 was characterized by immunosuppression with higher mortality rate than class 2. We further developed a 5-gene class model to predict class membership. FUNDING: The study was funded by the National Natural Science Foundation of China (Grant No. 81,901,929).

Incorporation of point-of-care ultrasound into morning round is associated with improvement in clinical outcomes in critically ill patients with sepsis.

OBJECTIVES: Point-of-care ultrasound (POCUS) has been widely used in the intensive care unit (ICU). However, it is largely unknown whether the use of POCUS is associated with improved patient-important outcomes. The study aimed to investigate whether incorporation of POCUS during morning round on a routine basis was able to improve clinical outcomes in critically ill patients with sepsis. DESIGN: It was a prospective observational study. SETTING: A tertiary care emergency intensive care unit. PATIENTS: All patients admitted to the emergency ICU from January 2016 to December 2017 were screened for potential eligibility. Sepsis was defined as infection plus signs of organ dysfunction. INTERVENTION: The intervention group incorporated POCUS during morning round on a routine basis, and a checklist was developed to improve the compliance. The control group did not have the mandates to perform POCUS during morning round, but could use POCUS when necessary. MEASUREMENTS: Clinical outcomes of mortality, length of stay in ICU, durations of vasopressors and mechanical ventilation were compared between the intervention and control groups. Multivariable regression model was employed to adjust for confounding factors. MAIN RESULTS: A total of 129 subjects, including 88 in the control group and 41 in the intervention group, were included for analysis. Univariate analysis showed that the intervention group had shorter durations of mechanical ventilation (MV) (4.5 ±â€¯1.2 vs. 5.7 ±â€¯1.0 days; p = 0.034) and more negative fluid balance (-143 vs. 48 ml/24 h; p = 0.003) on day 3. In multivariable model, routine incorporation of POCUS was associated with lower risk of prolonged (>7 days) ICU stay (OR: 0.39, 95% CI: 0.29-0.88; p = 0.029). CONCLUSIONS: The study showed that incorporation of POCUS during morning round on a routine basis was associated with shortened duration of MV and length of stay in ICU. The possible mechanism underlying the relationship may be via reduced fluid administration. Future randomized controlled trials are needed to validate current findings.

[Effect of collagen peptides from walleye pollock skin on bone microstructure of ovariectomized rats].

Objective: To investigate the effect of collagen peptides from walleye pollock skin on the microstructure of osteoporosis model in ovariectomized rats, and to explore the feasibility of preventing and treating oste- oporosis. Methods: Sixty adult Wistar female rats, weighing (250±10) g, were randomly divided into 5 groups (12 rats each group): normal group (group A), osteoporosis model group (group B), osteoporosis model+collagen peptides from walleye pollock skin prevention group (group C), osteoporosis model+low concentration of collagen peptides from walleye pollock skin treatment group (group D), and osteoporosis model+high concentration of collagen peptides from walleye pollock skin treatment group (group E). The rats in groups B, C, D, and E were removed bilateral ovarian to establish osteoporosis model. The rats in group C were treated with stomach perfusion of the collagen peptides from walleye pollock skin (1.0 g/kg) from 4 weeks after operation for 6 weeks; and the rats in groups D and E were treated with stomach perfusion of the collagen peptides from walleye pollock skin (0.5, 1.0 g/kg respectively) at 6 weeks after operation for 6 weeks. The rats in groups A and B were given equal volume of normal saline at the same time after operation. At 24 hours after the last administration, the femoral gray value of rats in groups A and B were measured by X-ray film; HE staining was performed on the proximal tibial bone of the left side in 4 groups; the histopathological changes of the bone were observed and the trabecular number (TN), mean trabecular plate thickness (MTPT), mean trabecular plate spacing (MTPS), trabecular bone volume (TBV), mean bone cortical thickness (MBCT) were measured; immunohistochemical staining was performed to observe the expression levels of caltitonin receptor (CTR) and interleukin 1 (IL-1). Results: The femoral gray value of group B was significantly lower than that of group A ( t=45.130, P=0.000), which indicated that the ovariectomized rat model was successfully prepared. Histological observation showed that TN, MTPS, TBV, and MBCT in groups A, C, and E were significantly different from those in group B ( P<0.05). The histological parameters of bone tissue in group C were significantly different from those in groups D and E ( P<0.05). TN, MTPS, TBV, and MBCT in group D were significantly different from those in group A ( P<0.05); only MTPS in group E was significantly different from that in group A ( P<0.05). MTPS, TBV, and MBCT in group E were significantly different from those in group D ( P<0.05). The immunohistochemical staining showed that the levels of CTR and IL-1 in groups A, C, D, and E were lower than those in group B, in groups C and E were lower than in group D, showing significant differences ( P<0.05). Conclusion: Collagen peptides from walleye pollock skin can improve the bone microstructure of osteoporotic rats, and its mechanism may be related to the inhibition of CTR and IL-1 expression in bone tissue, but it has not been found to prevent osteoporosis.

[Quantitative genetic analysis and multiple trait selection of pharmaceutical composition on Ginkgo biloba L. leaves].

The China possesses more than 70% Ginkgo resources in the world. The purposes of this research are to collect fine seedling and grafting clones in China, to probe genetic law on flavone glycosides and terpenes on Ginkgo leaves, and select leaf-used cultivars of high-pharmaceutical composition. In this research, we have collected 87 clones from 13 provenances and have carried out randomized block experiment at Tancheng, Laizhou and Yaoxiang in Shandong Province. Flavone glycosides and terpenes were determined through HPLC method from an improved Van Beek (1991) techniques and Shimadzu Lc-10 AD (Japan). Data and breeding analyses were carried out through IBMPC and SPQG30 software. The results of variance analyses show that there are significant differences to flavone glycosides, terpenes in clones, and the law of genetic parameters on heritability (h2) and genetic variability coefficient (Gcv), is clone > sex > provenance to flavone glycosides in ginkgo leaves. The sigma g2, h2, Gcv and delta G' in male tree clone leaves are higher than female clone leaves on flavone glycosides. We have found that there is a maximum flavone content clone among males and a maximum terpene clone among females. The results of Q-cluster analyses are consistent with R-factor analyses of twenty higher terpenes clones. The results of index selection show that the ri.Y2, E(I) and CGS' of multiple traits selection including (gamma) trait are higher than single trait and multiple traits selection excluding gamma. The direct or index selection is more suited to leaf-used cultivars of Ginkgo. The genetic stability of each clone was appraised by Wricke's ecovalence method and Nassar & Huhu noparameter method. Flavone glycosides and terpenes are more than 2.09%-2.57% and 0.33%-0.41%, respectively, and we have selected four clones.

[Arthroscopic treatment for post-traumatic chronic wrist pain].

OBJECTIVE: To explore the therapeutic effects of arthroscopy for post-traumatic chronic wrist pain. METHODS: From February 2007 to June 2010, 12 patients with post-traumatic chronic wrist pain treated with arthroscopy were reviewed. Among the patients, 9 patients were male and 3 patients were female, ranging in age from 19 to 47 years, with a mean of 35.6 years. After physical examinations or MR abnormal findings, all the patients underwent wrist arthroscopic examination and treatment. Eight patients with tear in the central area of the triangular fibrocartilage complex (TFCC) underwent endoscopic partial resection. Two patients with relaxation of inter-carpal ligament after injury underwent radiofrequency shrinkage. One patient with distal radioulnar joint instability was treated with Kirschner fixation through distal radius and ulna in the neutral forearm rotation after clean-up of wrist joint, and also fixed with long arm cast immobilization for 6 weeks. One patient with ulnar impaction syndrome was treated with wrist clean, border modeling of triangular cartilage plate, partial resection of distal ulna. RESULTS: All the patients were followed up with an average duration of 10 months. Modified Mayo wrist score were evaluated from preoperative mean of (51.67 +/- 15.27) ( 25 to 75 scores) to postoperative mean of (77.92 +/- 10.54) (65 to 95 scores). Eleven patients recovered to normal work. CONCLUSION: Arthroscopy is an effective method for patients with post-traumatic chronic wrist pain which can diagnosis and cure the injuries under arthroscopy.

[Observation of hemostatic effect of equilibrium pressure pneumatic tourniquet in internal fixation of bilateral tibia and fibula fracture].

OBJECTIVE: To compare the hemostatic effects and tourniquet induced side reactions of 2 different tourniquets in internal fixation of bilateral tibia and fibula fracture. METHODS: Between May 2008 and May 2010, 21 patients with bilateral tibia and fibula fracture were treated and randomly divided into 2 groups according to left and right limbs. When steel plate fixation was performed, equilibrium pressure pneumatic tourniquet (EPPT group) and common tourniquet (common group) were used to staunch the flow of blood respectively. The time of using tourniquet was 60 minutes, and the hemostatic pressure was 50 kPa. There were 12 males and 9 females with an age range of 17 to 58 years (mean, 32.5 years). Injury was caused by traffic accident in 9 patients, by heavy pound in 6 patients, and falling from height in 6 patients. According to X-ray classification, there were 15 cases of simple type, 3 cases of butterfly type, and 3 cases of comminuted type in EPPT group; there were 13 cases of simple type, 5 cases of butterfly type, and 3 cases of comminuted type in common group. The time from injury to operation was 3 to 72 hours (mean, 37.5 hours). RESULTS: The time of using tourniquet was (95.30 +/- 4.19) minutes in EPPT group and (94.11 +/- 5.16) minutes in common group, showing no significant difference (P > 0.05). All the incision of 2 groups healed by first intension. After 2 weeks of operation in common group, peroneal nerve injury occurred in 3 cases, and was cured by supporting nerve for 3 months; blister occurred in 1 case and was cured after dressing change for 3 weeks; and the injury rate was 19%. No complication occurred in EPPT group with an injury rate of 0. There was significant difference in the injury rate between 2 groups (P < 0.05). The hemostatic effects were excellent in 19 cases and good in 2 cases of EPPT group, were excellent in 10 cases, good in 3 cases, and poor in 8 cases of common group; the excellent and good rate were 100% and 61.9% respectively, showing significant difference (P < 0.05). All patients were followed up 3-24 months. Fracture healed without nonunion and deformity union in 2 groups. CONCLUSION: Comparing to common tourniquet, the EPPT can provide good bloodless field, lower hemostatic pressure, and less tourniquet complication.