• damage-associated protein
• endothelial cell
• glycocalyx
• permeability
• regulated cell death
• sepsis

• Blood transcriptome analysis
• Septicemia
• Super-elderly infected population
• Susceptibility
• The underlying mechanism
• card16 protein

• Humans
• Sepsis/genetics
• Sepsis/blood
• Sepsis/immunology
• Aged
• Gene Expression Profiling
• Male
• Female
• Transcriptome
• Disease Susceptibility
• CARD Signaling Adaptor Proteins/genetics
• Signal Transduction/genetics
• Aged, 80 and over
• Gene Expression Regulation
• Computational Biology/methods
• Gene Regulatory Networks
• NF-kappa B/metabolism
• NF-kappa B/genetics
• Case-Control Studies

• structural variation
• evolutionary biology

• DFG-SFB1211 B6 Deutsche Forschungsgemeinschaft (German Research Foundation)

• Animals
• Humans
• Mice
• alpha-Defensins/genetics
• DNA
• Gene Dosage
• Immunity, Innate/genetics
• Kidney/metabolism
• Peptides, Cyclic/genetics
• Urinary Tract Infections/genetics
• Urinary Tract Infections/metabolism

• R01 DK106286 NIDDK NIH HHS
• R01 DK117934 NIDDK NIH HHS
• R01 DK132366 NIDDK NIH HHS
• HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)

• CXCL7
• HNP-1
• SAA1
• bikunin/AMBP
• endothelial damage
• hemadsorption
• oxidized DNA
• septic shock

• Humans
• Shock, Septic/metabolism
• Shock, Septic/therapy
• Shock, Septic/blood
• Endoplasmic Reticulum Stress
• Biomarkers
• Alpha-Globulins/metabolism
• Reactive Oxygen Species/metabolism
• Human Umbilical Vein Endothelial Cells/metabolism
• Cell Survival
• Endothelial Cells/metabolism
• Male

• NLRP3
• caspase1
• cell signaling
• drug treatment
• endothelial dysfuction
• organ injury
• protein protein interaction
• pyroptosis

Sepsis is a severe systemic inflammatory response to infections that is accompanied by organ dysfunction. Although the ancestral genetic background is a relevant factor for sepsis susceptibility, there is a lack of studies using the genetic singularities of a recently admixed population to identify loci involved in sepsis susceptibility. Here we aimed to discover new sepsis loci by completing the first admixture mapping study of sepsis in Canary Islanders, leveraging their distinctive genetic makeup as a mixture of Europeans and African ancestries. We used a case-control approach and inferred local ancestry blocks from genome-wide data from 113,414 polymorphisms genotyped in 343 patients with sepsis and 410 unrelated controls, all ascertained for grandparental origin in the Canary Islands (Spain). Deviations in local ancestries between cases and controls were tested using logistic regressions, followed by fine-mapping analyses based on imputed genotypes, in silico functional assessments, and gene expression analysis centered on the region of interest. The admixture mapping analysis detected that local European ancestry in a locus spanning 1.2 megabases of chromosome 8p23.1 was associated with sepsis (lowest p = 1.37 × 10⁻⁴; Odds Ratio [OR] = 0.51; 95%CI = 0.40–0.66). Fine-mapping studies prioritized the variant rs13249564 within intron 1 of MFHAS1 gene associated with sepsis (p = 9.94 × 10⁻⁴; OR = 0.65; 95%CI = 0.50–0.84). Functional and gene expression analyses focused on 8p23.1 allowed us to identify alternative genes with possible biological plausibility such as defensins, which are well-known effector molecules of innate immunity. By completing the first admixture mapping study of sepsis, our results revealed a new genetic locus (8p23.1) harboring a number of genes with plausible implications in sepsis susceptibility.

• European
• local ancestry
• polymorphism
• sepsis
• susceptibility

• CHDPs (cationic host defense peptides)
• kinocidins
• platelet microbicidal proteins (PMP)
• platelets

• Adolescent
• Adult
• Aged
• Aged, 80 and over
• Child
• Colitis, Ulcerative/blood
• Colitis, Ulcerative/diagnosis
• Colitis, Ulcerative/genetics
• DNA Copy Number Variations
• Female
• Gene Dosage
• Humans
• Immunity, Innate
• Male
• Middle Aged
• Peptides, Cyclic/blood
• Peptides, Cyclic/genetics
• Severity of Illness Index
• Young Adult
• alpha-Defensins/blood
• alpha-Defensins/genetics

• Asian
• periprosthetic joint infection
• synovasure
• α-defensin

• cancer genomics
• data mining

• Computational Biology/methods
• Epstein-Barr Virus Infections/complications
• Epstein-Barr Virus Infections/virology
• Gene Expression Regulation, Viral
• Herpesvirus 4, Human/genetics
• Humans
• Kaplan-Meier Estimate
• Leukemia, Myeloid, Acute/complications
• Leukemia, Myeloid, Acute/etiology
• Leukemia, Myeloid, Acute/mortality
• Leukemia, Myeloid, Acute/pathology
• MicroRNAs
• Prognosis
• Proportional Hazards Models
• RNA, Viral
• ROC Curve

• R01 CA134051 NCI NIH HHS
• R01 CA189806 NCI NIH HHS
• UL1 TR000161 NCATS NIH HHS
• U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)
• The Thrasher Research Fund 02833-7 UMCCTS Pilot Project Program U1 LTR000161-04

• copy number polymorphism
• defensins
• endothelium
• pyroptosis
• sepsis

• Discrepancy proteome
• Gangrenous cholecystitis
• Proteomics

Early onset of lung injury is considerable common after cardiac surgery and is associated with increasing in morbidity and mortality, but current clinical predictors for the occurrence of this complication always have limited positive warning value. This study aimed to evaluate whether elevated plasma levels of human neutrophil peptides (HNPs) 1–3 herald impaired lung function in infants and young children after cardiac surgery necessitating cardiopulmonary bypass (CPB).

Consecutive children younger than 3 years old who underwent cardiac surgery were prospectively enrolled. Plasma concentrations of HNPs 1–3 and inflammatory cytokines were measured before, and immediately after CPB, as well as at 1 h, 12 h, and 24 h after CPB.

Thirty patients were enrolled, 18 (60%) of whom were infants. Plasma levels of HNPs 1–3 and the pro-inflammatory cytokine interleukin-6 (IL-6) significantly increased immediately after CPB (P < 0.001), while IL-8 increased 1 h after the CPB operation (P = 0.002). The anti-inflammatory cytokine IL-10 levels were also significantly elevated immediately after CPB compared with the baseline (P < 0.001). The stepwise multiple linear regression analysis showed that the plasma HNPs 1–3 levels immediately after CPB was independent correlated with the declined lung function, as reflected by the PaO₂/FiO₂ ratio on the first 2 days after operation (for the first day: OR, −1.067, 95% CI, −0.548 to −1.574; P < 0.001; for the second day: OR, −0.667, 95% CI, −0.183 to −1.148; P = 0.009) and prolonged mechanical ventilation time (OR, 0.039, 95% CI, 0.005 to 0.056; P = 0.011). Plasma levels of HNPs 1–3 and IL-10 returned to the baseline values, while IL-6 and IL-8 levels remained significantly higher than baseline 24 h after CPB (P ≤ 0.01).

Elevated HNPs 1–3 levels immediately after CPB correlate with impaired lung function, and HNPs 1–3 could serve as a quantifiable early alarmin biomarker for onset of lung injury in infants and young children undergoing cardiac surgery with CPB.

The online version of this article (10.1186/s12890-017-0558-4) contains supplementary material, which is available to authorized users.

• Alarmin
• Cardiac surgery
• Cardiopulmonary bypass
• Congenital heart disease
• Human neutrophil peptides (HNPs) 1–3
• Infant
• Lung injury
• Young children

• genetics and development
• pyelonephritis
• vesico-ureteral reflux

• Adolescent
• Child
• Child, Preschool
• Female
• Humans
• Infant
• Male
• Peptides, Cyclic/genetics
• Polymorphism, Genetic
• Risk Factors
• Urinary Tract Infections/etiology
• Urinary Tract Infections/genetics
• Vesico-Ureteral Reflux/complications
• Vesico-Ureteral Reflux/genetics
• alpha-Defensins/genetics
• alpha-Defensins/physiology

• U01 DK074062 NIDDK NIH HHS
• UL1 TR000005 NCATS NIH HHS
• UL1 RR024153 NCRR NIH HHS
• U01 DK074082 NIDDK NIH HHS
• UL1 TR001878 NCATS NIH HHS
• RC4 DK090937 NIDDK NIH HHS
• U01 DK074063 NIDDK NIH HHS
• K08 DK094970 NIDDK NIH HHS
• U01 DK074059 NIDDK NIH HHS
• U01 DK074053 NIDDK NIH HHS
• UL1 TR000003 NCATS NIH HHS
• U01 DK074064 NIDDK NIH HHS
• K08 DK102594 NIDDK NIH HHS

• IL8
• Polymorphism
• Sepsis

• Case-Control Studies
• Gene Dosage/genetics
• Genetic Predisposition to Disease/genetics
• Genetic Variation/genetics
• Genome-Wide Association Study
• Genotype
• Glomerulonephritis, IGA/blood
• Humans
• Kidney Diseases/genetics
• Odds Ratio
• Peptides, Cyclic/genetics
• Phenotype
• alpha-Defensins/genetics

• G1002528 Medical Research Council

• ankylosing spondylitis
• cell killing
• iTRAQ
• proteomic

• Allele
• Chinese Han population
• Genotype
• IRAK-4
• Prognosis
• Severe sepsis
• Single nucleotide polymorphism
• Susceptibility

Sepsis is a leading cause of mortality and morbidity in the critical illness. Multiple immune inflammatory processes take part in the pathogenesis of sepsis. Defensins are endogenous antimicrobial peptides with three disulphide bonds created by six cysteine residues. Besides the intrinsic microbicidal properties, defensins are active players which modulate both innate and adaptive immunity against various infections. Defensins can recruit neutrophils, enhance phagocytosis, chemoattract T cells and dendritic cells, promote complement activation, and induce IL-1β production and pyrotosis. Previous publications have documented that defensins play important roles in a series of immune inflammatory diseases including sepsis. This review aims to briefly summarize in vitro, in vivo, and genetic studies on defensins' effects as well as corresponding mechanisms within sepsis and highlights their promising findings which may be potential targets in future therapies of sepsis.

AIM: To investigate the genetic background of human defensin expression in type 1 and 2 diabetes.

METHODS: Associations between DEFA1/DEFA3 gene copy number polymorphism and diabetes as well as between the promoter polymorphisms of DEFB1 and diabetes were studied. The copy number variation of the DEFA1/DEFA3 genes was determined in 257 diabetic patients (117 patients with type 1 and 140 with type 2 diabetes). The control group consisted of 221 age- and gender-matched healthy blood donors. The cumulative copy numbers of the DEFA1/DEFA3 genes were detected by using quantitative PCR analysis. To evaluate the HNP 1-3 (human neutrophil peptide 1-3 or α-defensin) levels in the circulation, plasma HNP 1-3 concentrations were measured by ELISA. The expression of DEFA1/A3 in peripheral leukocytes of the diabetic patients was measured by quantitative RT PCR analysis. Three SNPs of the human DEFB1 (human defensin β-1) gene: DEFB1 G-20A (rs11362), DEFB1 C-44G (rs1800972) and DEFB1 G-52A (rs1799946) were genotyped by Custom TaqMan^® Real Time PCR assay.

RESULTS: Significant differences were observed in HNP1-3 levels between the healthy subjects and both groups of diabetic patients. The mean ± SE was 28.78 ± 4.2 ng/mL in type 1 diabetes, and 29.82 ± 5.36 ng/mL in type 2 diabetes, vs 11.94 ± 2.96 ng/mL in controls; P < 0.01 respectively. There was no significant difference between patients with type 1 and type 2 diabetes in the high plasma concentrations of HNP1-3. The highest concentrations of α-defensin were found in diabetic patients with nephropathy (49.4 ± 4.8 ng/mL), neuropathy (38.7 ± 4.8 ng/mL) or cardiovascular complications (45.6 ± 1.45 ng/L). There was no significant difference in the cumulative copy numbers of DEFA1/DEFA3 genes between controls and patients, or between patients with the two types of diabetes. Comparisons of HNP 1-3 plasma level and DEFA1/A3 copy number of the same patient did not reveal significant relationship between defensin-α levels and the gene copy numbers (r² = 0.01). Similarly, no positive correlation was observed between the copy numbers and the mRNA expression levels of DEFA1/A3. Regarding the C-44G polymorphism of DEFB1, the GG “protective” genotype was much less frequent (1%-2%) among both groups of patients than among controls (9%).

CONCLUSION: Elevated HNP1-3 levels in diabetes are independent of DEFA1/DEFA3 copy numbers, but GG genotype of C-44G SNP in DEFB1 gene may result in decreased defensin β-1 production.

• α-defensins
• HNP1-3
• β-defensin 1
• Diabetes
• Copy number polymorphism
• Single nucleotide polymorphism

• Adult
• Diabetes Mellitus, Type 1/blood
• Diabetes Mellitus, Type 1/diagnosis
• Diabetes Mellitus, Type 1/genetics
• Diabetes Mellitus, Type 2/blood
• Diabetes Mellitus, Type 2/diagnosis
• Diabetes Mellitus, Type 2/genetics
• Female
• Gene Dosage
• Gene Expression Regulation
• Genetic Predisposition to Disease
• Humans
• Male
• Phenotype
• Polymorphism, Single Nucleotide
• Promoter Regions, Genetic
• RNA, Messenger/analysis
• Retrospective Studies
• Risk Assessment
• Risk Factors
• alpha-Defensins/blood
• alpha-Defensins/genetics
• beta-Defensins/blood
• beta-Defensins/genetics

Specific granule deficiency (SGD) is a rare congenital disorder characterized by recurrent infections. The disease is caused by inactivating mutations of the CCAAT/enhancer binding protein-ε (C/EBP-ε) gene. As a consequence, specific and gelatinase granules lack most matrix proteins. Furthermore, azurophil granules contain diminished amounts of their most abundant proteins, α-defensins, also known as human neutrophil peptides (HNPs). In accordance with this, in vitro models have demonstrated induction of HNPs by C/EBP-ε. Since mice do not express myeloid defensins, they cannot per se be used to characterize the role of C/EBP-ε in controlling HNP expression in vivo. We therefore crossed a transgenic HNP-1-expressing mouse with the Cebpe^-/- mouse to study the in vivo significance of C/EBP-ε for HNP-1 transcription and expression. Surprisingly, neither expression nor processing of HNP-1 was affected by lack of C/EBP-ε in these mice. Transduction of C/EBP-ε into primary bone marrow cells from HNP-1 mice induced some HNP-1 expression, but not to levels comparable to expression human cells. Taken together, our data infer that the HNP-1 of the transgenic mouse does not show an expression pattern equivalent to endogenous secondary granule proteins. This limits the use of these transgenic mice as a model for human conditions.

Copy number variation (CNV) in the range from 2 to 12 per diploid genome is an outstanding feature of the beta-defensin gene (DEFB) cluster on human chromosome 8p23.1 numerously demonstrated by different methods. So far, CNV was proven for a 115 kb region between DEFB4 and 21 kb proximal of DEFB107 but the borders for the entire CNV repeat unit are still unknown. Our study aimed to narrow down the distal border of the DEFB cluster.

We established tests for length polymorphisms based on amplification and capillary electrophoresis with laser-induced fluorescence (CE-LIF) analysis of seven insertion/deletion (indel) containing regions spread over the entire cluster. The tests were carried out with 25 genomic DNAs with different previously determined cluster copy numbers. CNV was demonstrated for six indels between ~1 kb distal of DEFB108P and 10 kb proximal of DEFB107. In contrast, the most distal indel is not affected by CNV.

Our analysis fixes the minimal length of proven CNV to 157 kb including DEFB108P but excluding DEFB109P. The distal border between CNV and non-CNV part of the DEF cluster is located in the 59 kb interval chr8:7,171,082-7,230,128.

Multi-allelic copy number variants include examples of extensive variation between individuals in the copy number of important genes, most notably genes involved in immune function. The definition of this variation, and analysis of its impact on function, has been hampered by the technical difficulty of large-scale but accurate typing of genomic copy number. The copy-variable alpha-defensin locus DEFA1A3 on human chromosome 8 commonly varies between 4 and 10 copies per diploid genome, and presents considerable challenges for accurate high-throughput typing.

In this study, we developed two paralogue ratio tests and three allelic ratio measurements that, in combination, provide an accurate and scalable method for measurement of DEFA1A3 gene number. We combined information from different measurements in a maximum-likelihood framework which suggests that most samples can be assigned to an integer copy number with high confidence, and applied it to typing 589 unrelated European DNA samples. Typing the members of three-generation pedigrees provided further reassurance that correct integer copy numbers had been assigned. Our results have allowed us to discover that the SNP rs4300027 is strongly associated with DEFA1A3 gene copy number in European samples.

We have developed an accurate and robust method for measurement of DEFA1A3 copy number. Interrogation of rs4300027 and associated SNPs in Genome-Wide Association Study SNP data provides no evidence that alpha-defensin copy number is a strong risk factor for phenotypes such as Crohn’s disease, type I diabetes, HIV progression and multiple sclerosis.

The online version of this article (doi:10.1186/1471-2164-14-719) contains supplementary material, which is available to authorized users.

• Alpha-defensins
• antimicrobial peptides
• myelopoiesis
• neutrophils

• Defensin
• cytokine
• immunomodulation
• pyroptosis
• signal transduction

Human ß-defensins are a family of antimicrobial peptides located at the mucosal surface. Both sequence multi-site variations (MSV) and copy-number variants (CNV) of the defensin-encoding genes are associated with increased risk for various diseases, including cancer and inflammatory conditions such as psoriasis and acute pancreatitis. In a case–control study, we investigated the association between MSV in DEFB104 as well as defensin gene (DEF) cluster copy number (CN), and pancreatic ductal adenocarcinoma (PDAC) and chronic pancreatitis (CP).

Two groups of PDAC (N=70) and CP (N=60) patients were compared to matched healthy control groups CARLA1 (N=232) and CARLA2 (N=160), respectively. Four DEFB104 MSV were haplotyped by PCR, cloning and sequencing. DEF cluster CN was determined by multiplex ligation-dependent probe amplification.

Neither the PDAC nor the CP cohorts show significant differences in the DEFB104 haplotype distribution compared to the respective control groups CARLA1 and CARLA2, respectively.

The diploid DEF cluster CN exhibit a significantly different distribution between PDAC and CARLA1 (Fisher’s exact test P=0.027), but not between CP and CARLA2 (P=0.867).

Different DEF cluster b CN distribution between PDAC patients and healthy controls indicate a potential protective effect of higher CNs against the disease.

The complex balance between environmental and host factors is an important determinant of susceptibility to infection. Disturbances of this equilibrium may result in multifactorial diseases as illustrated by the summer mortality syndrome, a worldwide and complex phenomenon that affects the oysters, Crassostrea gigas. The summer mortality syndrome reveals a physiological intolerance making this oyster species susceptible to diseases. Exploration of genetic basis governing the oyster resistance or susceptibility to infections is thus a major goal for understanding field mortality events. In this context, we used high-throughput genomic approaches to identify genetic traits that may characterize inherent survival capacities in C. gigas.

Using digital gene expression (DGE), we analyzed the transcriptomes of hemocytes (immunocompetent cells) of oysters able or not able to survive infections by Vibrio species shown to be involved in summer mortalities. Hemocytes were nonlethally collected from oysters before Vibrio experimental infection, and two DGE libraries were generated from individuals that survived or did not survive. Exploration of DGE data and microfluidic qPCR analyses at individual level showed an extraordinary polymorphism in gene expressions, but also a set of hemocyte-expressed genes whose basal mRNA levels discriminate oyster capacity to survive infections by the pathogenic V. splendidus LGP32. Finally, we identified a signature of 14 genes that predicted oyster survival capacity. Their expressions are likely driven by distinct transcriptional regulation processes associated or not associated to gene copy number variation (CNV).

We provide here for the first time in oyster a gene expression survival signature that represents a useful tool for understanding mortality events and for assessing genetic traits of interest for disease resistance selection programs.

• defensin
• antimicrobial peptide
• epididymis
• cytotoxicity
• lipopolysaccharide
• inflammation

• Amino Acid Sequence
• Animals
• Defensins/chemistry
• Defensins/genetics
• Defensins/metabolism
• Defensins/pharmacology
• Disease
• Genomics
• Humans
• Immunity
• Molecular Sequence Data
• Protein Isoforms/chemistry
• Protein Isoforms/genetics
• Protein Isoforms/metabolism
• Protein Isoforms/pharmacology

Effective innate responses against potential pathogens are essential in the living world and possibly contributed to the evolutionary success of invertebrates. Taken together, antimicrobial peptide (AMP) precursors of defensin, mytilin, myticin and mytimycin can represent about 40% of the hemocyte transcriptome in mussels injected with viral-like and bacterial preparations, and unique profiles of myticin C variants are expressed in single mussels. Based on amplicon pyrosequencing, we have ascertained and compared the natural and Vibrio-induced diversity of AMP transcripts in mussel hemocytes from three European regions.

Hemolymph was collected from mussels farmed in the coastal regions of Palavas (France), Vigo (Spain) and Venice (Italy). To represent the AMP families known in M. galloprovincialis, nine transcript sequences have been selected, amplified from hemocyte RNA and subjected to pyrosequencing. Hemolymph from farmed (offshore) and wild (lagoon) Venice mussels, both injected with 10⁷Vibrio cells, were similarly processed. Amplicon pyrosequencing emphasized the AMP transcript diversity, with Single Nucleotide Changes (SNC) minimal for mytilin B/C and maximal for arthropod-like defensin and myticin C. Ratio of non-synonymous vs. synonymous changes also greatly differed between AMP isotypes. Overall, each amplicon revealed similar levels of nucleotidic variation across geographical regions, with two main sequence patterns confirmed for mytimycin and no substantial changes after immunostimulation.

Barcoding and bidirectional pyrosequencing allowed us to map and compare the transcript diversity of known mussel AMPs. Though most of the genuine cds variation was common to the analyzed samples we could estimate from 9 to 106 peptide variants in hemolymph pools representing 100 mussels, depending on the AMP isoform and sampling site. In this study, no prevailing SNC patterns related to geographical origin or Vibrio injection emerged. Whether or not the contact with potential pathogens can increase the amount of AMP transcript variants in mussels requires additional study.

• Alternative Splicing
• Animals
• Antimicrobial Cationic Peptides/genetics
• Europe
• Genetic Variation
• Hemocytes
• Hemolymph
• Mytilus/genetics
• Nucleic Acid Amplification Techniques
• Polymorphism, Single Nucleotide
• RNA, Messenger/genetics
• Sequence Analysis, DNA/methods
• Transcriptome