Combining single-cell RNA-sequencing and bulk data to reveal immunity-related genes expression pattern in the systemic lupus erythematosus and target organ kidney

Background:Systemic lupus erythematosus(SLE)is a complex chronic autoimmune disease with no known cure.However,the regulatory mechanism of immunity-related genes is not fully understood in SLE.In order to explore new therapeutic targets,we used bioinformatical methods to analyze a series of data.Methods:After downloading and processing the data from Gene Expression Omnibus database,the differentially expressed genes of SLE were analyzed.CIBERSORT algorithm was used to analyze the immune infiltration of SLE.Based on single-cell RNA-sequencing data,the role of immune-related genes in SLE and its target organ(kidney)were analyzed.Key transcription factors affecting immune-related genes were identified.Cell-cell communication networks in SLE were analyzed.Results:In total,15 hub genes and 4 transcription factors were found in the bulk data.Monocytes and macrophages in GSE81622(SLE)showed more infiltration.There were four cell types were annotated in scRNA sequencing dataset(GSE135779),as follows T cells,monocyte,NK cells and B cells.Immunity-related genes were overexpressed in monocytes.Conclusion:The present study shows that immune-related genes affect SLE through monocytes and play an important role in target organ renal injury.

Construction of cDNA Library from Intestine, Mesentery and Coelomocyte of Apostichopus japonicus Selenka Infected with Vibrio sp. and a Preliminary Analysis of Immunity-Related Genes

The aquaculture of sea cucumber Apostichopus japonicus (Echinodermata, Holothuroidea) has grown rapidly during recent years and has become an important sector of the marine industry in Northern China. However, with the rapid growth of the industry and the use of non-standard culture techniques, epidemic diseases of A. japonicus now pose increasing problems to the industry. To screen the genes with stress response to bacterial infection in sea cucumber at a genome wide level, we constructed a cDNA library from A. japonicus Selenka (Aspidochirotida: Stichopodidae) after infecting them with Vibrio sp. for 48 h. Total RNA was extracted from the intestine, mesentery and coelomocyte of infected sea cucumber using Trizol and mRNA was isolated by Oligotex mRNA Kits. The ligated cDNAs were transformed into DH5α, and a library of 3.24×105 clones (3.24×105 cfu mL-1) was obtained with the sizes of inserted fragments ranging from 0.8 to 2.5 kb. Sequencing the cDNA clones resulted in a total of 1106 ESTs that passed the quality control. BlastX and BlastN searches have identified 168 (31.5%) ESTs sharing significant homology with known sequences in NCBI protein or nucleotide databases. Among a panel of 25 putative immunity-related genes, serum lectin isoform, complement component 3, complement component 3-like genes were further studied by real-time PCR and they all increased more than 5 fold in response to Vibrio sp. challenge. Our library provides a valuable molecular tool for future study of invertebrate immunity against bacterial infection and our gene expression data indicates the importance of the immune system in the evolution and development of sea cucumber.

Immune Response of the Ridgetail White Prawn Exopalaemon carinicauda After Exposure to the Dinoflagellate Prorocentrum minimum

The dinoflagellate Prorocentrum minimum is known to affect the normal physiological function of Exopalaemon carinicauda by inducing oxidative stress,apoptosis,and cellular injury.To study the effects of P.minimum on the immune defense system of shrimp,E.carinicauda were exposed to 5×10^(3)cells mL^(-1)and 5×10^(4)cells mL^(-1)of P.minimum for 336 h in treatment groups,while E.carinicauda cultured in filtered seawater was employed as control.The total hemocyte counts(THC),hemocyanin concentration(HEM),and the activity of alkaline phosphatase(AKP)in hemolymph serum,as well as expressions of six immunity-related genes in hemocytes,hepatopancreases and gills were determined.The exposure of P.minimum significantly reduced the THC,HEM concentration and AKP activity in hemolymph serum.Immunity-related genes expressed differently in hemocytes,hepatopancreases and gills.Compared with the control group,the expressions of Crustin and pro PO in hemocytes were significantly up-regulated in the treatment groups,while the up-regulated expressions of LGBP,Lysozyme and Serpin were only found in the group exposed to 5×10^(4)cells mL^(-1)of P.minimum.In the gills of E.carinicauda exposed to P.minimum,the down-regulation of ALF,proPO and Serpin,up-regulation of LGBP and Lysozyme,as well as unaffected Crustin were observed.In hepatopancreases,the up-regulated expressions of LGBP,Crustin,Lysozyme,Serpin and proPO(only in 5×10^(3)cells mL^(-1)of P.minimum group)were found in the treatment groups.After exposure to P.minimum for 336 h,shrimps were injected with Vibrio parahaemolyticus and WSSV.The results showed that the mortality rates of shrimp in the treatment groups were significantly increased with a dose-dependent effect,which suggests that exposure to P.minimum may reduce the immunity of E.carinicauda.The research indicates that hemocytes and hepatopancreases play important roles in protecting the shrimp immune response to harmful algae,while the protection effect of hemolymph serum and gills may be suppressed.Since the exposure to P.minimum depressed the immunity of E.carinicauda,further studies are needed to confirm whether the presence of the algae will affect the susceptibility of shrimp to pathogens.

NKX2-3 and IRGM variants are associated with diseasesu sceptibility to IBD in Eastern European patients

AIM: To investigate variants of immunity-related GT-Pase family M (IRGM) and NKX2-3 genes and genotype-phenotype in Eastern European patients with inflammatory bowel disease (IBD).METHODS: We analyzed 1707 Hungarian and Czech subjects with Crohn’s disease (CD) (n = 810, age: 37.1 ± 12.6 years, duration: 10.7 ± 8.4 years) and ulcerative colitis (UC) (n = 428, age: 43.7 ± 15.0 years, duration: 12.6 ± 9.9 years), as well as 469 healthy controls. IRGM rs13361189, NKX2-3 rs10883365 and ECM1 rs13294 polymorphisms were tested by LightCy-cler allele discrimination. Detailed clinical phenotypes were determined by reviewing the medical charts. RESULTS: NKX2-3 rs10883365 variant allele was as-sociated with increased risk for CD (P = 0.009, OR = 1.24, 95% CI = 1.06-1.48) and UC (P = 0.001, OR = 1.36, 95% CI = 1.13-1.63), whereas variant IRGM allele increased risk for CD (P = 0.029, OR = 1.36, 95% CI = 1.03-1.79). In contrast, ECM1 rs13294 was not associat-ed with either CD or UC. In CD, the variant IRGM allele was associated with a colon-only location (P = 0.02, OR = 1.62, 95% CI = 1.07-2.44), whereas in UC, the ECM1 variant was associated with cutaneous manifestations (P = 0.002, OR = 3.36, 95% CI = 1.48-7.63). Variant alleles did not predict resistance to steroids or azathio-prine, efficacy of infliximab, or need for surgery. CONCLUSION: NKX2-3 and IRGM are susceptibility locifor IBD in Eastern European patients. Further studies are needed to confirm the reported phenotype-genotype associations.

ATG16L1 and NOD2 polymorphisms enhance phagocytosis in monocytes of Crohn's disease patients

AIM: To investigate if the presence of relevant genetic polymorphisms has effect on the effectual clearance of bacteria by monocytes and granulocytes in patients with Crohn’s disease (CD).