Unraveling transcriptomic signatures and dysregulated pathways in systemic lupus erythematosus across disease states.

OBJECTIVES: This study aims to elucidate the transcriptomic signatures and dysregulated pathways in patients with Systemic Lupus Erythematosus (SLE), with a particular focus on those persisting during disease remission. METHODS: We conducted bulk RNA-sequencing of peripheral blood mononuclear cells (PBMCs) from a well-defined cohort comprising 26 remission patients meeting the Low Lupus Disease Activity State (LLDAS) criteria, 76 patients experiencing disease flares, and 15 healthy controls. To elucidate immune signature changes associated with varying disease states, we performed extensive analyses, including the identification of differentially expressed genes and pathways, as well as the construction of protein-protein interaction networks. RESULTS: Several transcriptomic features recovered during remission compared to the active disease state, including down-regulation of plasma and cell cycle signatures, as well as up-regulation of lymphocytes. However, specific innate immune response signatures, such as the interferon (IFN) signature, and gene modules involved in chromatin structure modification, persisted across different disease states. Drug repurposing analysis revealed certain drug classes that can target these persistent signatures, potentially preventing disease relapse. CONCLUSION: Our comprehensive transcriptomic study revealed gene expression signatures for SLE in both active and remission states. The discovery of gene expression modules persisting in the remission stage may shed light on the underlying mechanisms of vulnerability to relapse in these patients, providing valuable insights for their treatment.

Corrigendum: Out of the Qinghai-Tibetan plateau: origin, evolution and historical biogeography of Morchella (both Elata and Esculenta clades).

[This corrects the article DOI: 10.3389/fmicb.2022.1078663.].

Identification of module genes and functional pathway analysis in septic shock subtypes by integrated bioinformatics analysis.

BACKGROUND: The present study aimed to identify the module genes and key gene functions and biological pathways of septic shock (SS) through integrated bioinformatics analysis. METHODS: In the study, we performed batch correction and principal component analysis on 282 SS samples and 79 normal control samples in three datasets, GSE26440, GSE95233 and GSE57065, to obtain a combined corrected gene expression matrix containing 21,654 transcripts. Patients with SS were then divided into three molecular subtypes according to sample subtyping analysis. RESULTS: By analyzing the demographic characteristics of the different subtypes, we found no statistically significant differences in gender ratio and age composition among the three groups. Then, three subtypes of differentially expressed genes (DEGs) and specific upregulated DEGs (SDEGs) were identified by differential gene expression analysis. We found 7361 DEGs in the type I group, 5594 DEGs in the type II group, and 7159 DEGs in the type III group. There were 1698 SDEGs in the type I group, 2443 in the type II group, and 1831 in the type III group. In addition, we analyzed the correlation between the expression data of 5972 SDEGs in the three subtypes and the gender and age of 227 patients, constructed a weighted gene co-expression network, and identified 11 gene modules, among which the module with the highest correlation with gender ratio was MEgrey. The modules with the highest correlation with age composition were MEgrey60 and MElightyellow. Then, by analyzing the differences in module genes among different subgroups of SS, we obtained the differential expression of 11 module genes in four groups: type I, type II, type III and the control group. Finally, we analyzed the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment of all module DEGs, and the GO function and KEGG pathway enrichment of different module genes were different. CONCLUSIONS: Our findings aim to identify the specific genes and intrinsic molecular functional pathways of SS subtypes, as well as further explore the genetic and molecular pathophysiological mechanisms of SS.

Out of the Qinghai-Tibetan plateau: Origin, evolution and historical biogeography of Morchella (both Elata and Esculenta clades).

Introduction: Morchella has become a research hotspot because of its wide distribution, delicious taste, and phenotypic plasticity. The Qinghai-Tibet Plateau subkingdoms (QTPs) are known as the cradle of Ice age biodiversity. However, the diversity of Morchella in the QTPs has been poorly investigated, especially in phylogenetic diversity, origin, and biogeography. Methods: The genealogical concordance phylogenetic species recognition (GCPSR, based on Bayesian evolutionary analysis using sequences from the internal transcribed spacer (ITS), nuclear large subunit rDNA (nrLSU), translation elongation factor 1-α (EF1-α), and the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2)), differentiation time estimation, and ancestral region reconstruction were used to infer Morchella's phylogenetic relationships and historical biogeography in the QTPs. Results: Firstly, a total of 18 Morchella phylogenetic species are recognized in the QTPs, including 10 Elata clades and 8 Esculenta clades of 216 individuals Secondly, the divergences of the 18 phylogenetic species were 50.24-4.20 Mya (Eocene-Pliocene), which was closely related to the geological activities in the QTPs. Furthermore, the ancestor of Morchella probably originated in the Northern regions (Qilian Shan, Elata cade) and southwestern regions (Shangri-La, Esculenta clade) of QTPs and might have migrated from North America (Rufobrunnea clade) via Beringian Land Bridge (BLB) and Long-Distance Dispersal (LDD) expansions during the Late Cretaceous. Moreover, as the cradle of species origin and diversity, the fungi species in the QTPs have spread out and diffused to Eurasia and South Africa starting in the Paleogene Period. Conclusion: This is the first report that Esculenta and Elata clade of Morchella originated from the QTPs because of orogenic, and rapid differentiation of fungi is strongly linked to geological uplift movement and refuge in marginal areas of the QTPs. Our findings contribute to increasing the diversity of Morchella and offer more evidence for the origin theory of the QTPs.

Genome-wide association study on Northern Chinese identifies KLF2, DOT1L and STAB2 associated with systemic lupus erythematosus.

OBJECTIVES: To identify novel genetic loci associated with systemic lupus erythematosus (SLE) and to evaluate potential genetic differences between ethnic Chinese and European populations in SLE susceptibility. METHODS: A new genome-wide association study (GWAS) was conducted from Jining, North China, on 1506 individuals (512 SLE cases and 994 matched healthy controls). The association results were meta-analysed with existing data on Chinese populations from Hong Kong, Guangzhou and Central China, as well as GWAS results from four cohorts of European ancestry. A total of 26 774 individuals (9310 SLE cases and 17 464 controls) were included in this study. RESULTS: Meta-analysis on four Chinese cohorts identifies KLF2 as a novel locus associated with SLE [rs2362475; odds ratio (OR) = 0.85, P=2.00E-09]. KLF2 is likely an Asian-specific locus as no evidence of association was detected in the four European cohorts (OR = 0.98, P =0.58), with evidence of heterogeneity (P=0.0019) between the two ancestral groups. Meta-analyses of results from both Chinese and Europeans identify STAB2 (rs10082873; OR= 0.89, P=4.08E-08) and DOT1L (rs4807205; OR= 1.12, P=8.17E-09) as trans-ancestral association loci, surpassing the genome-wide significance. CONCLUSIONS: We identified three loci associated with SLE, with KLF2 a likely Chinese-specific locus, highlighting the importance of studying diverse populations in SLE genetics. We hypothesize that DOT1L and KLF2 are plausible SLE treatment targets, with inhibitors of DOT1L and inducers of KLF2 already available clinically.

[Effects of macrophage migration inhibitory factor on early acute pancreatitis].

OBJECTIVE: To investigate the value of macrophage migration inhibitor factor (MIF) in early severe acute pancreatitis (SAP). METHODS: (1) Animal experiment: according to the random number table method, 24 male Sprague-Dawley (SD) rats were divided into Sham group and SAP 3, 6 and 12 hours groups, with 6 rats in each group. SAP rat model was prepared by injecting 5% sodium taurocholate via the retrograde cholangiopancreatic duct. Liver, kidney, lung, pancreas and serum samples were harvested after 3, 6 and 12 hours. In the Sham group, tissue and serum were harvested immediately after pancreas was turned over. The histopathological changes of the pancreas were observed microscopically by hematoxylin-eosin (HE) staining. The MIF levels of serum, liver, kidney, lung and pancreas were measured by enzyme linked immunosorbent assay (ELISA). (2) Clinical study: an observational study was conducted. Seventy-two adult patients within 24 hours of the onset of abdominal pain (blood amylase was 3 times the normal level), and the clinical diagnosis met the criteria of acute pancreatitis (AP) admitted to the emergency department of the First Affiliated Hospital of Zhengzhou University from December 2018 to October 2019 were enrolled. Venous blood was extracted and serum MIF level was determined by ELISA. Acute physiology and chronic health evaluation II (APACHE II) was recorded for 24 hours. Patients were divided into SAP group (17 cases), moderate severe acute pancreatitis (MSAP) group (25 cases), and mild acute pancreatitis (MAP) group (30 cases) according to the revised Atlanta criteria for comparison between groups. RESULTS: (1) The results of animal experiments showed that the serum, liver, and pancreatic MIF levels of rats in the SAP group all reached the peak at 6 hours after modeling, and the differences were statistically significant compared with the Sham group [serum MIF (ng/L): 2 862.79±238.33 vs. 1 728.32±197.59, liver MIF (ng/L): 2 141.39±328.07 vs. 1 372.70±163.41, pancreas MIF (ng/L): 4 468.00±1 324.31 vs. 1 572.06±108.40, all P < 0.01]; although the levels of MIF in serum, liver and pancreas decreased at 12 hours after modeling, they were still significantly higher than Sham group. However, there was no statistically significant difference in MIF levels of lung and kidney in SAP rats compared with Sham group at 3, 6 and 12 hours after molding. (2) Clinical observation showed that early serum MIF levels of SAP, MSAP and MAP patients decreased in order, (14.83±2.99), (10.17±2.64), and (7.21±2.47) µg/L, respectively; APACHE II scores also decreased in order, 10.41±3.74, 7.60±3.18 and 4.00±2.41 respectively. Correlation analysis showed that serum MIF levels in patients with SAP, MSAP, and MAP had a good correlation with APACHE II scores of the respective groups, showing that MIF levels was positively correlated with disease severity (SAP: r = 0.51, P = 0.03; MSAP: r = 0.45, P = 0.02; MAP: r = 0.45, P = 0.01). CONCLUSIONS: MIF can predict the occurrence of early SAP, and it is related to the severity of early AP.

[Analysis of infection-related mortality after allogeneic hematopoietic stem cell transplantation in patients with refractory/relapse acute leukemia].

OBJECTIVE: To investigate infection-related mortality (IRM) after allogeneic hematopoietic stem cell transplantation in patients with refractory/relapse acute leukemia. METHODS: We conducted a retrospective analysis of 127 patients with refractory/relapse acute leukemia and investigated the incidence, causes and risk factors of IRM. RESULTS: Sixty-seven of the patients died after the transplantation. The 5-year overall survival and disease-free survival was (35.2∓5.3)% and (30.8∓5.6)% among these patients, respectively. IRM occurred in 28.3% (36/127) of the patients. Multivariate analysis showed that grade II-IV acute graft-versus-host diseases (aGVDH, P=0.049, OR=3.017) and post-transplant invasive fungal infection (P=0.032, OR=3.223) were independent risk factors of IRM. CONCLUSION: As a common cause of transplant-related mortality, IRM is more frequent in cases of refractory/relapse acute leukemia than in cases with a standard risk profile, and effective prophylaxis and treatment of severe GVHD remain currently the primary measures for reducing post-transplant IRM.