Cellular adhesion gene SELP is associated with rheumatoid arthritis and displays differential allelic expression

Association of the rs3917647 polymorphism of the SELP gene with malnutrition in gastric cancer

BACKGROUND

Malnutrition and cachexia are common syndromes in patients with gastric cancer (GC) and are associated with poor quality of life and poor disease prognosis. However, there is still a lack of molecular factors that can predict malnutrition or cachexia in cancer. Studies have shown that among the potential contributors to the development of cancer cachexia, the level of the inflammatory response to P-selectin is regulated by single nucleotide polymorphisms (SNPs) located in the promoter region of the SELP gene. The aim of this study was to evaluate the association between the single nucleotide polymorphism (SNP)-2028 A/G of the SELP gene and malnutrition in patients receiving chemotherapy for gastric cancer (GC).

METHODS

The study group consisted of 220 GC patients treated with chemotherapy at Jinhua Municipal Central Hospital. DNA was extracted from peripheral leukocytes of whole blood samples using an animal DNA extraction kit. DNA was amplified using a 1.1 × T3 Super PCR mix, and loci corresponding to the peaks were genotyped using SNP1 software.

RESULTS

Patients carrying the A allele had a reduced risk of developing malnutrition compared to patients with the GG genotype (P < 0.001; OR = 3.411; 95% CI = 1.785-6.516). In addition, multivariate analysis indicated that the AA genotype significantly (more than 16-fold) reduced the risk of developing malnutrition (P < 0.001; OR = 0.062; 95% CI = 0.015-0.255).

CONCLUSION

SELP -2028A/G SNP may be a useful marker for assessing the risk of malnutrition in GC patients.

The roles of P-selectin in cancer cachexia

P-selectin, a cell adhesion molecule of the selectin family, is expressed on the surface of activated endothelial cells (ECs) and platelets. Binding of P-selectin to P-selectin glycoprotein ligand-1 (PSGL-1) supports the leukocytes capture and rolling on stimulated ECs and increases the aggregation of leukocytes and activated platelets. Cancer cachexia is a systemic inflammation disorder characterized by metabolic disturbances, reduced body weight, loss of appetite, fat depletion, and progressive muscle atrophy. Cachexia status is associated with increased pro-inflammatory cytokines such as tumor necrosis factor-alpha (TNF-α), which activates ECs to release P-selectin. Single-nucleotide polymorphisms (SNPs) loci of P-selectin encoding gene SELP are associated with higher level of plasma P-selectin and increase the susceptibility to cachexia in cancer patients. Elevated P-selectin expression has been observed in the hypothalamus, liver, and gastrocnemius muscle in animal models with cancer cachexia. Increased P-selectin may cause excessive inflammatory processes, muscle atrophy, and blood hypercoagulation, thus facilitating the development of cancer cachexia. In this review, physiological functions of P-selectin and its potential roles in cancer cachexia have been summarized. We also discuss the therapeutic potential of P-selectin inhibitors for the treatment of cancer cachexia.

The impact of SELP gene Thr715Pro polymorphism on sP-selectin level and association with cardiovascular disease in Saudi diabetic patients: A cross-sectional case-control study

Background

Cardiovascular diseases (CVD) are leading cause of mortality in patients with type 2 diabetes mellitus (T2DM). Increased soluble sP-selectin and 715Thr > Pro polymorphism were studied in CVD and T2DM, but association between them hasn't been explored in Saudi Arabia. We aimed to assess sP-selectin levels in T2DM and T2DM-associated CVD patients in comparison to healthy control cohort. Also, we sought to investigate relationship between Thr715Pro polymorphism and sP-selectin levels and disease state.

Methods

This is a cross-sectional case-control study. sP-selectin level (measured by Enzyme-linked immunosorbent assay) and prevalence of Thr715Pro polymorphism (assessed by Sanger sequencing) were investigated in 136 Saudi participants. The study comprised 3 groups: group1 included 41 T2DM patients; group 2 (48 T2DM patients with CVD), and group 3 (47 healthy controls).

Results

sP-selectin levels were significantly higher in diabetics and diabetics + CVD groups as compared to the corresponding control. In addition, results showed that the prevalence of 715Thr > Pro polymorphism is 11.75 % in the study population amongst the three study groups (9.55 % Thr/Pro, and 2.2 % Pro/Pro). No statistical difference was found between sP-selectin levels in subject carrying the wildtype genotype of this polymorphism and these who carry the mutant gene. There could be an association between this polymorphism and T2DM, whilst the polymorphism may protect diabetic patients from having CVD. However, odds ratio is not statistically significant in both cases.

Conclusion

Our study supports the previous researches' results that Thr715Pro is neither influencing the sP-selectin level nor the risk of CVD in T2DM patients.

Identification of Potential Serum Protein Biomarkers in Thymoma with Myasthenia Gravis After Docetaxel Treatment

INTRODUCTION

Myasthenia gravis (MG) is a devastating acquired autoimmune disease that can seriously affect the patient's quality of life. It is also a common complication of thymoma. Previous studies have shown that docetaxel alleviates myasthenic symptoms in thymoma with MG (TMG). However, little is known about the protein expression profiles and biomarkers for efficacy after docetaxel treatment.

METHODS

We recruited 9 healthy controls and 30 patients with TMG for the serum proteomics study with data-independent acquisition (DIA) technology. We further recruited additional 30 patients for the key protein validation by enzyme-linked immunosorbent assay (ELISA).

RESULTS

We identified 43 proteins by trend analysis and analyzed the interaction between these proteins and MG pathogenic proteins from the DisGNET database and the correlation analysis with clinical data of patients with TMG. Among these, KRAS and SELP were screened out and validated. KRAS and SELP increased in patients with TMG and decreased significantly after docetaxel treatment.

CONCLUSIONS

Our study revealed that the serum proteins were differentially expressed after docetaxel treatment, suggesting their important role in patients with TMG, as well as the critical role of KRAS and SELP as biomarkers in evaluating the efficacy of docetaxel treatment.

The SELP, CD93, IL2RG, and VAV1 Genes Associated with Atherosclerosis May Be Potential Diagnostic Biomarkers for Psoriasis

Purpose

Psoriasis and atherosclerosis are immunometabolic diseases. This study aimed to integrate bioinformatics and updated public resources to find potential biological markers associated with atherosclerosis that can cause psoriasis.

Patients and Methods

Microarray datasets were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were screened, and functional enrichment analysis was performed. We identified psoriasis and atherosclerosis common immune-related genes (PA-IRGs) by overlapping immune-related genes (IRGs) with genes in the module most associated with psoriasis and atherosclerosis obtained by weighted gene co-expression network analysis (WGCNAs). Receiver operating characteristic (ROC) was conducted to evaluate the predictive ability. The skin expression levels of diagnostic biomarkers were further verified by immunohistochemical staining. CIBERSORT, single-sample gene set enrichment analysis (ssGSEA), and Pearson's correlation analysis were applied to evaluate immune and lipid metabolism relationships in psoriatic tissues. In addition, a lincRNA-miRNA-mRNA network was constructed to find the pathogenesis in which diagnostic markers may be involved.

Results

Four PA-IRGs (SELP, CD93, IL2RG, and VAV1) demonstrated the optimal diagnostic value, with an AUC above 0.8. The immune cell infiltration analysis showed that dendritic resting cells, NK cell activation, neutrophils, macrophages M2, macrophages M0, and B-cell memory were highly abundant in psoriasis. Immune response analysis showed that TNF family members, chemokine receptors, interferons, natural killer cells, and TGF-β family members might be involved in psoriasis. Diagnostic biomarkers are strongly associated with various infiltrating immune cells, immune responses, and lipid metabolism. A lincRNA-miRNA-mRNA regulatory network consisting of 31 lincRNAs and 23 miRNAs was constructed. LINC00662 is involved in modulating four diagnostic biomarkers.

Conclusion

This study identified atherosclerosis-related genes SELP, CD93, VAV1, and IL2RG as potential psoriasis diagnostic markers. Provide novel insights into the possible regulatory mechanisms involved in psoriasis.

Proteomic profiling of extracellular vesicles in synovial fluid and plasma from Oligoarticular Juvenile Idiopathic Arthritis patients reveals novel immunopathogenic biomarkers

Introduction

New early low-invasive biomarkers are demanded for the management of Oligoarticular Juvenile Idiopathic Arthritis (OJIA), the most common chronic pediatric rheumatic disease in Western countries and a leading cause of disability. A deeper understanding of the molecular basis of OJIA pathophysiology is essential for identifying new biomarkers for earlier disease diagnosis and patient stratification and to guide targeted therapeutic intervention. Proteomic profiling of extracellular vesicles (EVs) released in biological fluids has recently emerged as a minimally invasive approach to elucidate adult arthritis pathogenic mechanisms and identify new biomarkers. However, EV-prot expression and potential as biomarkers in OJIA have not been explored. This study represents the first detailed longitudinal characterization of the EV-proteome in OJIA patients.

Methods

Fourty-five OJIA patients were recruited at disease onset and followed up for 24 months, and protein expression profiling was carried out by liquid chromatography-tandem mass spectrometry in EVs isolated from plasma (PL) and synovial fluid (SF) samples.

Results

We first compared the EV-proteome of SF vs paired PL and identified a panel of EV-prots whose expression was significantly deregulated in SF. Interaction network and GO enrichment analyses performed on deregulated EV-prots through STRING database and ShinyGO webserver revealed enrichment in processes related to cartilage/bone metabolism and inflammation, suggesting their role in OJIA pathogenesis and potential value as early molecular indicators of OJIA development. Comparative analysis of the EV-proteome in PL and SF from OJIA patients vs PL from age/gender-matched control children was then carried out. We detected altered expression of a panel of EV-prots able to differentiate new-onset OJIA patients from control children, potentially representing a disease-associated signature measurable at both the systemic and local levels with diagnostic potential. Deregulated EV-prots were significantly associated with biological processes related to innate immunity, antigen processing and presentation, and cytoskeleton organization. Finally, we ran WGCNA on the SF- and PL-derived EV-prot datasets and identified a few EV-prot modules associated with different clinical parameters stratifying OJIA patients in distinct subgroups.

Discussion

These data provide novel mechanistic insights into OJIA pathophysiology and an important contribution in the search of new candidate molecular biomarkers for the disease.

Proteome Analysis of Temporomandibular Joint with Disc Displacement

Disc displacement without reduction is a common disorder of the temporomandibular joint, causing clinical symptoms and sometimes condylar degeneration. In some cases, bone regeneration is detected following disc-repositioning procedures. Until now, however, systems-wide knowledge of the protein levels for condylar outcome with disc position is still lacking. Here, we performed comprehensive expression profiling of synovial fluid from 109 patients with disc displacement without reduction using high-resolution data-independent acquisition mass spectrometry and characterized differences in 1,714 proteins. Based on magnetic resonance imaging, samples were divided into groups with versus without condylar absorption and subgroups with versus without new bone. For the proteomic analysis, 32 proteins in groups presented with statistical significance (>2-fold, P < 0.05). Pathways such as response to inorganic substances, blood coagulation, and estrogen signaling were significantly expressed in the group with bone absorption as compared with pathways such as regulation of body fluid levels, vesicle-mediated transport, and focal adhesion, which were enriched in the group without bone absorption. In subgroup analysis, 45 proteins of significant importance (>2-fold, P < 0.05) were associated with pathways including would healing, glycolysis and gluconeogenesis, and amino acid metabolism. Combined with clinical examination, molecules such as acetyl-CoA carboxylase beta (ACACB) and transforming growth factor beta 1 (TGFB1) were related to features such as visual analog scale and maximum interincisal opening (P < 0.05). In addition, 7 proteins were examined by Western blotting, including progesterone immunomodulatory binding factor 1 (PIBF1), histidine-rich glycoprotein (HRG), and protein kinase C and casein kinase substrate in neurons 2 (PACSIN2). In conclusion, this study provides the first proteome analysis of condylar absorption at disc displacement without reduction and postoperative new bone formation after disc reposition. Integrated with clinical data, this analysis provides an important insight into the proteomics of condylar modification at disc position.

Early Prediction of Clinical Response to Anti-TNF Treatment using Multi-omics and Machine Learning in Rheumatoid Arthritis

Objectives

Advances in immunotherapy by blocking TNF have remarkably improved treatment outcomes for Rheumatoid arthritis (RA) patients. Although treatment specifically targets TNF, the downstream mechanisms of immune suppression are not completely understood. The aim of this study was to detect biomarkers and expression signatures of treatment response to TNF inhibition.

Methods

Peripheral blood mononuclear cells (PBMCs) from 39 female patients were collected before anti-TNF treatment initiation (day 0) and after 3 months. The study cohort included patients previously treated with MTX who failed to respond adequately. Response to treatment was defined based on the EULAR criteria and classified 23 patients as responders and 16 as non-responders. We investigated differences in gene expression in PBMCs, the proportion of cell types and cell phenotypes in peripheral blood using flow cytometry and the level of proteins in plasma. Finally, we used machine learning models to predict non-response to anti-TNF treatment.

Results

The gene expression analysis in baseline samples revealed notably higher expression of the gene EPPK1 in future responders. We detected the suppression of genes and proteins following treatment, including suppressed expression of the T cell inhibitor gene CHI3L1 and its protein YKL-40. The gene expression results were replicated in an independent cohort. Finally, machine learning models mainly based on transcriptomic data showed high predictive utility in classifying non-response to anti-TNF treatment in RA.

Conclusions

Our integrative multi-omics analyses identified new biomarkers for the prediction of response, found pathways influenced by treatment and suggested new predictive models of anti-TNF treatment in RA patients.

The Ser290Asn and Thr715Pro Polymorphisms of the SELP Gene Are Associated with A Lower Risk of Developing Acute Coronary Syndrome and Low Soluble P-Selectin Levels in A Mexican Population ‡

Recent studies have shown that P-selectin promotes the early formation of atherosclerotic plaque. The aim of the present study was to evaluate whether the SELP gene single nucleotide polymorphisms (SNPs) are associated with presence of acute coronary syndrome (ACS) and with plasma P-selectin levels in a case-control association study. The sample size was estimated for a statistical power of 80%. We genotyped three SELP (SELP Ser290Asn, SELP Leu599Val, and SELP Thr715Pro) SNPs using 5’ exonuclease TaqMan assays in 625 patients with ACS and 700 healthy controls. The associations were evaluated with logistic regressions under the co-dominant, dominant, recessive, over-dominant and additive inheritance models. The genotype contribution to the plasma P-selectin levels was evaluated by a Student’s t-test. Under different models, the SELP Ser290Asn (OR = 0.59, pC_Co-Dominant = 0.047; OR = 0.59, pC_Dominant = 0.014; OR = 0.58, pC_{Over-Dominant} = 0.061, and OR = 0.62, pC_Additive = 0.015) and SELP Thr715Pro (OR = 0.61, pC_Dominant = 0.028; OR = 0.63, pC_{Over-Dominant} = 0.044, and OR = 0.62, pC_Additive = 0.023) SNPs were associated with a lower risk of ACS. In addition, these SNPs were associated with low plasma P-selectin levels. In summary, this study established that the SELP Ser290Asn and SELP Thr715Pro SNPs are associated with a lower risk of developing ACS and with decreased P-selectin levels in plasma in a Mexican population.

Reduced miR-26b Expression in Megakaryocytes and Platelets Contributes to Elevated Level of Platelet Activation Status in Sepsis

In sepsis, platelets may become activated via toll-like receptors (TLRs), causing microvascular thrombosis. Megakaryocytes (MKs) also express these receptors; thus, severe infection may modulate thrombopoiesis. To explore the relevance of altered miRNAs in platelet activation upon sepsis, we first investigated sepsis-induced miRNA expression in platelets of septic patients. The effect of abnormal Dicer level on miRNA expression was also evaluated. miRNAs were profiled in septic vs. normal platelets using TaqMan Open Array. We validated platelet miR-26b with its target SELP (P-selectin) mRNA levels and correlated them with clinical outcomes. The impact of sepsis on MK transcriptome was analyzed in MEG-01 cells after lipopolysaccharide (LPS) treatment by RNA-seq. Sepsis-reduced miR-26b was further studied using Dicer1 siRNA and calpain inhibition in MEG-01 cells. Out of 390 platelet miRNAs detected, there were 121 significantly decreased, and 61 upregulated in sepsis vs. controls. Septic platelets showed attenuated miR-26b, which were associated with disease severity and mortality. SELP mRNA level was elevated in sepsis, especially in platelets with increased mean platelet volume, causing higher P-selectin expression. Downregulation of Dicer1 generated lower miR-26b with higher SELP mRNA, while calpeptin restored miR-26b in MEG-01 cells. In conclusion, decreased miR-26b in MKs and platelets contributes to an increased level of platelet activation status in sepsis.

Platelet/Lymphocyte, Lymphocyte/Monocyte, and Neutrophil/Lymphocyte Ratios as Biomarkers in Patients with Rheumatoid Arthritis and Rheumatoid Arthritis-Associated Interstitial Lung Disease

BACKGROUND The objective of this study was to assess the diagnostic value of platelet/lymphocyte ratio (PLR), lymphocyte/monocyte ratio (LMR), and neutrophil/lymphocyte ratio (NLR) as biomarkers in patients with rheumatoid arthritis (RA) and rheumatoid arthritis-associated interstitial lung disease (RA-ILD). MATERIAL AND METHODS Demographic and laboratory data were acquired for 198 RA and 103 RA-ILD patients and 290 healthy controls. The subjects were categorized into female and male groups and further subcategorized based on age into <60 years and ≥60 years subgroups. One-way analysis of variance (ANOVA), receiver operating characteristics (ROC), Pearson analysis, multiple linear regression analysis, and logistic regression analysis were performed to analyze the association of PLR, NLR, and LMR with RA and RA-ILD. RESULTS Mean PLR and NLR were lowest in the control group, followed by the RA and RA-ILD groups (p<0.05). Mean LMR was lowest in the RA-ILD group, followed by the RA and control groups (p<0.05). The area under the ROC (AUROC) values of the PLR to distinguish between RA and controls, RA-ILD and controls, and RA-ILD and RA were 0.676, 0.776, and 0.650, respectively (p<0.001). Multiple linear regression analysis suggested a significantly positive association between the level of PLR and the level of DAS28 (p<0.001). The odds ratio of PLR was 1.101 for RA (p=0.023) and 1.217 for RA-ILD (p<0.001) when compared to the controls. CONCLUSIONS PLR may be applied as a new biomarker for predicting and diagnosing RA and RA-ILD and for distinguishing RA-ILD patients from RA patients and healthy subjects.

1,25-Dihydroxyvitamin D3 attenuates disease severity and induces synoviocyte apoptosis in a concentration-dependent manner in rats with adjuvant-induced arthritis by inactivating the NF-κB signaling pathway

An aggressive proliferation of synoviocytes is the hallmark of rheumatoid arthritis (RA). Emerging evidence shows that inhibiting the NF-κB signaling pathway with 1,25-dihydroxyvitamin D3 [1,25(OH)2D3] may be a therapeutic approach for controlling inflammatory diseases. In this study, we demonstrated the protective effects of three different 1,25(OH)2D3 concentration on adjuvant-induced arthritis (AA) rats through the NF-κB signaling pathway and their pro-apoptotic roles in cultured adjuvant-induced arthritis synoviocytes (AIASs). AA rats were prepared by injecting complete Freund's adjuvant and independently given daily intraperitoneal injection of 1,25(OH)2D3 at concentrations of 50, 100, and 300 ng/day/kg. Subsequently, AIASs were isolated from the inflamed joints of AA rats to test the effects of 1,25(OH)2D3 on AIASs in vitro. Intraperitoneal injection of 1,25-(OH)2D3 was found to induce a concentration- and time-dependent improvement in relieving the symptoms of AA. We found an increased paw withdrawal thermal latency (PWTL) in the affected paw of AA rats as the concentration of 1,25-(OH)2D3 increased. 1,25-(OH)2D3 treatment reduced levels of inflammatory factors in synovial tissues of AA rats. In the case of cultured AIASs, 1,25-(OH)2D3 was shown to inhibit cell proliferation and induce cell apoptosis in a concentration-dependent manner. Additionally, 1,25-(OH)2D3 inhibited the activation of the NF-κB signaling pathway. In conclusion, our study provides evidence emphasizing that 1,25(OH)2D3 has the potential to attenuate disease severity in RA potentially due to its contributory role in synoviocyte proliferation and apoptosis. The protective role of 1,25(OH)2D3 against RA depends on the NF-κB signaling pathway.

Relationship Between -2028 C/T SELP Gene Polymorphism, Concentration of Plasma P-Selectin and Risk of Malnutrition in Head and Neck Cancer Patients

Until today there is a lack of molecular factors, that could predict either cancer malnutrition or cachexia. Among potential mechanisms, that contribute to development of above syndromes, the systemic inflammatory response with overproduction of cytokines and adhesion molecules is the most likely. Recent papers suggested crucial role of P-selectin adhesion molecule in the initiation of leukocytes recruitment to the site of injury during inflammation, promotion of tumor aggressiveness and contribution to cancer cachexia. The aim of the study was to investigate SELP -2028 C/T polymorphism as a risk factor of malnutrition in 66 head and neck cancer (HNC) patients subjected to radiotherapy. Genotyping was conducted by real-time PCR method by means of TaqMan SNP Genotyping Assay. P-selectin Human ELISA Kit was used to determine P-selectin concentration in each extracted plasma samples. CC homozygous subjects had 4-fold higher risk score of being qualified as severely malnourished compared to other genotype carriers (p = 0.015). However, the TT homozygous patients were at lowest risk of severe weight loss >10% during the therapy period (OR = 0.20; p = 0.019). We also noted, that CC genotype carriers had significantly higher risk of early death incidence compared to CT or TT genotype (median survival time: 29 vs 34 months; HR = 3.02; p = 0.0085). Studied SELP -2028 C/T seems to be a novel attractive predictive factor of cancer malnutrition in HNC patients, perhaps in a future, patients carrying unfavorable CC genotype could be earlier scheduled for pharmaceutical intervention with parenterall nutrition, therefore they could be prevented from the development of severe malnutrition or even cachexia.

Comparison of rheumatoid arthritis (RA) and osteoarthritis (OA) based on microarray profiles of human joint fibroblast-like synoviocytes

The purpose of the present study was to investigate the underlying molecular mechanism of osteoarthritis (OA) and rheumatoid arthritis (RA) based on microarray profiles. Three human joint fibroblast-like synoviocytes (FLSs) microarray profiles including 26 OA samples, 33 RA samples, and 20 healthy control (HC) samples were downloaded from the GEO database. Differentially expressed genes (DEGs) between OA and HC (DEGsOA) and RA and HC (DEGsRA) were identified. Co-expressed and specific genes were analysed between DEGsOA and DEGsRA. Gene ontology, KEGG pathway enrichment, PPI network, and GSEA were performed to predict the function of DEGs. Two hundred seventy-six and 410 differential genes in DEGsOA and DEGsRA were observed. One hundred fifty coexpressed genes and 126 OA-specific genes (SELE, SERPINE1, and NFKBIA were the key genes) between DEGsOA and DEGsRA were enriched in the tumour necrosis factor (TNF) signalling pathway. However, 260 RA-specific genes of which the key genes were CCR5, CCR7, CXCR4, CCL5, and CCR4 were enriched in chemokine signalling pathway. Therefore, FLSs might exert an inflammatory effect by regulating TNF signalling pathway, targeting SELE, SERPINE1, and NFKBIA during the process of OA. Although TNF signalling pathway was also involved in the synovitis of RA, chemokine signalling pathway played the key role in RA FLSs mediating cell migration, invasion, and release of chemotaxis. In addition, CCR5, CCR7, CXCR4, CCL5, and CCR4 might be hub genes in RA. The different biomarkers and pathways identified in OA and RA may provide references for further study. SIGNIFICANCE OF THE STUDY: This study revealed the similar and different mechanisms of FLSs and different biomarkers that might with important regulatory effects on RA and OA. In OA, FLSs played an inflammatory role through TNF signalling pathway, targeting SELE, SERPINE1, and NFKBIA. Although TNF signalling pathway was also involved in the synovitis of RA, chemokine signalling pathway was a crucial pathway in mediating FLSs migration, invasion, and release of chemotaxis. CCR5, CCR7, CXCR4, CCL5, and CCR4 might be keys genes in RA. We expect that our results will bring more comprehensively understanding between RA and OA for researchers.

Development and validation of a rapid method for genotyping three P-selectin gene polymorphisms based on high resolution melting analysis

BACKGROUND

High resolution melting (HRM) analysis is one of the newer, reliable, and sensitive genotyping techniques, which offers considerable time and cost savings. P-selectin is an adhesion molecule that has a role in the initial phases of leukocyte adhesion to stimulated platelets and endothelial cells in inflammation. Multiple polymorphisms in P-selectin gene (SELP) that affect the protein sequence have been described. The aim of this study was to design, optimize, and validate a simple and rapid in-house HRM-based method for genotyping the NM_003005.3:c.992G>A (c.992G>A), NM_003005.3:c.1918G>T (c.1918G>T), and NM_003005.3:c.2266A>C (c.2266A>C) SELP polymorphisms.

METHODS

Initial genotyping of three SELP polymorphisms was performed by applying polymerase chain reaction (PCR) with sequence-specific primers (SSP), which was used as a reference method for determination of analytical sensitivity. PCR-HRM was performed with primers for c.2266A>C reported in the literature. Primers for the remaining two polymorphisms were designed using Primer-BLAST. Precision testing was performed using three samples with different genotypes. For accuracy, analytical sensitivity and specificity testing, 20 wild type, 10 heterozygous, and 10 homozygous samples were chosen per polymorphism. Results were expressed as percentage of concordance with the acceptability criterion ≥95%.

RESULTS

Agreement of results was 100% for all validation parameters except for analytical sensitivity for c.1918G>T and c.2266A>C, with agreement of 90%. Repeated analysis using both methods revealed an error in initial genotyping and correct genotyping by PCR-HRM, which was confirmed by Sanger sequencing.

CONCLUSION

The validation confirmed PCR-HRM as a precise, accurate, and specific method for genotyping the c.992G>A, c.1918G>T, and c.2266A>C SELP polymorphisms.

RETRACTED: Effects of Artesunate on chondrocyte proliferation, apoptosis and autophagy through the PI3K/AKT/mTOR signaling pathway in rat models with rheumatoid arthritis

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Editor-in-Chief. Concern was raised about the reliability of the Western blot results in Figure 5D and 5F, which appear to have a similar phenotype as contained within another publication, as detailed here: https://pubpeer.com/publications/CD4DF7B6DCA28182EC6809846F3653; and here: https://docs.google.com/spreadsheets/d/1r0MyIYpagBc58BRF9c3luWNlCX8VUvUuPyYYXzxWvgY/edit#gid=262337249. Concerns were also raised about the provenance of the flow cytometry data in Figure 7A. In addition, suspected duplications were detected in Western blots contained within Figure 5E and 5F. The journal requested the corresponding author comment on these concerns and provide raw data. The corresponding author communicated that the raw data was not available and some of the results were not repeatable and therefore not solid enough to support the conclusions. The authors requested retraction of this article. The Editor-in-Chief assessed this case and decided to retract the article.

Structural and functional impact of SNPs in P-selectin gene: A comprehensive in silico analysis

P-selectin is an adhesion molecule which plays an important role in the development of inflammation. It is encoded by the SELP gene located on chromosome 1q21-q24. Various single nucleotide polymorphisms (SNPs) ofSELPhave been reported to be associated with various inflammatory disease conditions. The genetics behind these diseases could be better understood by knowing the structural and functional impact of various genetic determinants ofSELP. So far, this is the first comprehensive and systematicin silicoanalysis of SNPs inSELP. A total of 2780 SNPs ofSELPwere retrieved from NCBI dbSNP. Only conserved and validated SNPs with minor allele frequency (MAF) ≥ 0.05 were subjected to further analysis. Based on these criteria, we selected 4 non-synonymous SNPs (nsSNPs) and 119 non-coding SNPs (ncSNPs). The nsSNPs were analyzed for deleterious effects using SIFT, Polyphen-2, nsSNPAnalyzer, SNP & Go, SNPs3, Mutperd and I-mutant web tools. The template prediction for variant structure modeling was performed using MUSTER and SWISS-MODEL. The functional impact of ncSNPs was analyzed by SNPinfo and RegulomeDB. Thein silicoanalysis predicted 3 nsSNPs and 21 ncSNPs as potential candidates for future case-control association studies and functional analysis ofSELP.