Bacillus subtilis bacteriophage SPP1 is a lytic siphovirus first described 50 years ago [1]. Its complete DNA sequence was reported in 1997 [2]. Here we present an updated annotation of the 44,016 bp SPP1 genome and its correlation to different steps of the viral multiplication process. Five early polycistronic transcriptional units encode phage DNA replication proteins and lysis functions together with less characterized, mostly non-^{essential, functions. Late transcription drives synthesis of proteins necessary for SPP1 viral particles assembly and for cell lysis, together with a short set of proteins of unknown function. The extensive genetic, biochemical and structural biology studies on the molecular mechanisms of SPP1 DNA replication and phage particle assembly rendered it a model system for tailed phages research. We propose SPP1} as the reference species for a new SPP1-like viruses genus of the Siphoviridae family.

BACKGROUND

Tympanosclerosis is a pathological process involving the middle ear. The hallmark of this disease is the formation of calcium deposits. In the submucosal layer, as well as in the right layer of the tympanic membrane, the calcium deposits result in a significant increase in the activity of fibroblasts and deposition of collagen fibers.

OBJECTIVE

The aim of our study was to examine the expression level of genes encoding collagen type I, II, III and IV (COL1A1, COL2A1, COL3A1, COL4A1) and osteopontin (SPP1) in the tympanic membrane of patients with tympanosclerosis.

METHODS

The total RNA was isolated from middle ear tissues with tympanosclerosis, received from 25 patients and from 19 normal tympanic membranes. The gene expression level was determined by real-time RT-PCR. The gene expression levels were correlated with clinical Tos classification of tympanosclerosis.

RESULTS

We observed that in the tympanic membrane of patients with tympanosclerosis, the expression of type I collagen is decreased, while the expression of type II and IV collagen and osteopontin is increased. Moreover, mRNA levels of the investigated genes strongly correlated with the clinical stages of tympanosclerosis.

CONCLUSIONS

The strong correlations between the expression of type I, II, IV collagen and osteopontin and the clinical stage of tympanosclerosis indicate the involvement of these proteins in excessive fibrosis and pathological remodeling of the tympanic membrane. In the future, a treatment aiming to modulate these gene expressions and/or regulation of the degradation of their protein products could be used as a new medical approach for patients with tympanosclerosis.

Background & aim: Tumor-microenvironment (TME) factors and cancer stem cells (CSCs) play a critical role in the aggressiveness of pancreatic cancer (PC). However, the degree to which TME factors promote stemness remains unexplored. Here, we examined whether cancer-associated fibroblasts (CAFs) promote CSC features in PC.

Methods: PC cells were treated long-term (30, 60, and 90 days) with conditioned media (CM)-derived from normal human fibroblasts (NFs) and CAFs. The stemness features of tumorsphere formation and stemness populations, along with CSCs markers, were analyzed using 2D and 3D sodium alginate bead-based co-culture models. Immunohistochemistry and immunofluorescence staining were performed for CSCs and fibroblast markers in autochthonous Kras^G12D/+; Trp53^R172H/+; Pdx1-Cre (KPC) mice and human pancreatic tumors. PCR-array and gene knockdown were performed to identify the mechanism of stemness enrichment.

Results: Long-term treatment of PC cells with CAF-CM enriched stemness, as demonstrated by significantly higher CD44⁺, ALDH⁺, and AF⁺ populations in PC cells. Increased tumorsphere formation and elevated CSC, self-renewal, and drug-resistance markers in CAF-CM-treated PC cells were observed. In addition, CAF co-cultured with PC cells in the 3D model showed a substantial increase in stemness features. CD44 and α-SMA were positively correlated, and their expressions progressively increased from the early to late stages of KPC mice and human pancreatic tumors. OPN/SPP1 was identified as the top-differentially overexpressed gene in CAF-CM-treated PC cells, and knockdown of OPN/SPP1 significantly reduced stemness characteristics in CAF-CM-treated PC cells.

Conclusions: Our data uncover novel insight into the interplay between CAF and enrichment of stemness population through SPP1-CD44 axis in PC.

Keywords: CD44; Cancer-associated Fibroblast; OPN/SPP1; Pancreatic Cancer; cancer stem cells.

Multipotentporcine mesenchymal stem cells (pMSC) are invaluable for research and therapeutic use in regenerative medicine. Media used for derivation and expansion of pMSC may play an important role for the selection of MSC subpopulation at an early stage and thereby, the specific basal medium may also affect differentiation potential of these cells. The present study was undertaken to evaluate the effects of αMEM, aDMEM, M199, αMEM/M199, aDMEM/M199 and αMEM/aDMEM mediaon 1) porcine bone marrow MSC derivation; 2) expression of number of osteogenic markers (ALP, COL1A1, SPP1 and BGLAP) at 5^th and 10^th passage in pMSC before differentiation; and 3) differentiation of pMSC (at 5^th passage) to osteogenic lineage. Morphological changes and matrix formation in osteogenic cells were evaluated by microscopic examination. Calcium deposits in osteocytes were confirmed by Alizarin Red S staining. Based on expression of different markers, it was evident that selection of bone marrow pMSC subpopulations was independent of basal media used. But the differentiation of those pMSCs, specifically to osteogenic lineage, was dependent on the medium used for expansion of pMSC at the pre-differentiation stage. We demonstrated here that the pMSC grown in combined αMEM/aDMEM (1:1) medium expressed number of osteogenic markers and these pMSC underwent osteogenic differentiation most efficiently, in comparison to porcine mesenchymal stem cells grown in other media. In conclusion, osteogenic differentiation potential of pMSC maintained in αMEM/aDMEM medium was observed significantly higher compared to cells cultivated in other media and therefore, the combined medium αMEM/aDMEM (1:1) may preferentially be used for expansion of porcine mesenchymal stem cells, if needed for osteogenic differentiation.

Keywords: Basal media; Bone marrow; Mesenchymal stem cells; Osteogenic differentiation; Porcines.

Introduction and objectives: Non-alcoholic fatty liver disease (NAFLD) is multistage with heterogeneous outcomes. We studied the influence of insulin resistance (IR) on the hepatic transcriptome of early NAFLD stages, to understand disease development.

Materials and methods: In this cross-sectional study, possible clinicopathological risk factors were compared between mild-NAFL (N = 72) and Non-alcoholic Steatohepatitis (NASH; N = 51) patients. Liver tissue-transcriptome difference was studied between a subset of 25 mild-NAFL and 20 NASH biopsies and validated on another subset of 12 mild-NAFL and 13 NASH biopsies, using RT-PCR. The relationship between IR driven gene expression changes with fibrosis in NASH was investigated.

Results: Significantly higher weight (p = 0.005) and elevated levels of HbA1c (p = 0.009), FBG (p = 0.03) and HOMA-IR (p = 0.009) were found in NASH patients. Five differentially expressed genes (DEGs, fold change >1.5) were identified in NASH-FABP4, FABP5L2, CD24, PRAP1, and SPP1. The DEGs were positively associated with disease severity and HOMA-IR, and were found to be efficient classifiers of mild-NAFL and NASH. Additional 1218 genes identified related to IR (IrCGs), which can classify NASH-with-fibrosis patients separately from mild-NAFL and NASH patients. IrCGs can promote intra-hepatic fat accumulation, dysregulation of the lipid metabolism, lipotoxicity, and activation of cell survival pathways including activation of cell proliferation and differentiation pathways.

Conclusions: Hepatic expression of genes associated with insulin resistance may drive NAFLD development and progression.

Keywords: HOMA-IR; NASH; fibrosis; insulin-resistance; transcriptome.

Idiopathic pulmonary fibrosis (IPF) and systemic sclerosis-associated interstitial lung disease (SSc-ILD) differ in the predominant demographics and identified genetic risk alleles of effected patients, however both diseases frequently progress to respiratory failure and death. Contrasting advanced SSc-ILD to IPF provides insight to the role dysregulated immunity may play in pulmonary fibrosis. To analyze cell-type specific transcriptome commonalities and differences between IPF and SSc-ILD, we compared single-cell RNA-sequencing (scRNA-seq) of 21 explanted lung tissue specimens from patients with advanced IPF, SSc-ILD, and organ donor controls. Comparison of IPF and SSc-ILD tissue identified divergent patterns of interferon signaling, with interferon-gamma signaling upregulated in the SPP1 ^hi and FABP4 ^hi macrophages, cytotoxic T cells, and natural kill cells of IPF, while type I interferon signaling and production was upregulated in the corresponding SSc-ILD populations. Plasmacytoid dendritic cells were found in diseased lungs only, and exhibited upregulated cellular stress pathways in SSc-ILD compared to IPF. Alveolar type I cells were dramatically decreased in both IPF and SSc-ILD, with a distinct transcriptome signature separating these cells by disease. KRT5^-/KRT17⁺ aberrant basaloid cells exhibiting markers of cellular senescence and epithelial-mesenchymal transition were identified in SSc-ILD for the first time. In summary, our study utilizes the enriched capabilities of scRNA-seq to identify key divergent cell types and pathways between IPF and SSc-ILD, providing new insights into the shared and distinct mechanisms between idiopathic and autoimmune interstitial lung diseases.

Keywords: idiopathic pulmonary fibrosis; interstitial lung disease (ILD); single-cell RNA-sequencing (scRNA-seq); systemic sclerosis; systemic sclerosis (scleroderma).

Background: Stanford type A aortic dissection (AAD) is a catastrophic disease. An immune infiltrate has been found within the aortic wall of dissected aortic specimens. The recall and activation of macrophages are key events in the early phases of AAD. Herein, the immune filtration profile of AAD was uncovered. Methods: Gene expression data from the GSE52093, GSE98770 and GSE153434 datasets were downloaded from the Gene Expression Omnibus (GEO). The differentially expressed genes (DEGs) of each dataset were calculated and then integrated. A protein-protein interaction (PPI) network was established with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), and the hub genes were identified in Cytoscape. Furthermore, gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of hub genes were performed. Finally, we set GSE52093 and GSE98770 as the training set and GSE153434 as the validation set to assess immune infiltration in AAD using CIBERSORTx and analyzed the correlations between immune cells and hub genes in both the training and validation sets. Results: Sixty-one integrated DEGs were identified. The top 10 hub genes were selected from the PPI network, and 140 biological process (BP) terms and 12 pathways were enriched among the top 10 hub genes. The proportions of monocytes and macrophages were significantly higher in AAD tissues than in normal tissues. Notably, this result was consistent in the training set and the validation set. In addition, we found that among the hub genes, CA9, CXCL5, GDF15, VEGFA, CCL20, HMOX1, and SPP1 were positively correlated with CD14, a cell marker of monocytes, while CA9, CXCL5, GDF15, and VEGFA were positively correlated with CD68, a cell marker of macrophages in the training set. Finally, according to the results of the GO and KEGG analysis of hub genes, we found that the monocyte/macrophage-related genes were involved in immune-inflammatory responses through degradation of the extracellular matrix, endothelial cell apoptosis, hypoxia and the interaction of cytokines and chemokines. Conclusion: The monocyte-macrophage system plays a major role in immune-inflammatory responses in the development of AAD. Several hub genes are involved in this process via diverse mechanisms.

Keywords: aortic dissection; bioinformactics; hub gene; immune infiltration; monocyte—macrophage.

Background: Lung adenocarcinoma (LUAD) is a common lung cancer with a high mortality, for which microRNAs (miRNAs) play a vital role in its regulation. Multiple messenger RNAs (mRNAs) may be regulated by miRNAs, involved in LUAD tumorigenesis and progression. However, the miRNA-mRNA regulatory network involved in LUAD has not been fully elucidated.

Methods: Differentially expressed miRNAs and mRNA were derived from the Cancer Genome Atlas (TCGA) dataset in tissue samples and from our microarray data in plasma (GSE151963). Then, common differentially expressed (Co-DE) miRNAs were obtained through intersected analyses between the above two datasets. An overlap was applied to confirm the Co-DEmRNAs identified both in targeted mRNAs and DEmRNAs in TCGA. A miRNA-mRNA regulatory network was constructed using Cytoscape. The top five miRNA were identified as hub miRNA by degrees in the network. The functions and signaling pathways associated with the hub miRNA-targeted genes were revealed through Gene Ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The key mRNAs in the protein-protein interaction (PPI) network were identified using the STRING database and CytoHubba. Survival analyses were performed using Gene Expression Profiling Interactive Analysis (GEPIA).

Results: The miRNA-mRNA regulatory network consists of 19 Co-DEmiRNAs and 760 Co-DEmRNAs. The five miRNAs (miR-539-5p, miR-656-3p, miR-2110, let-7b-5p, and miR-92b-3p) in the network were identified as hub miRNAs by degrees (>100). The 677 Co-DEmRNAs were targeted mRNAs from the five hub miRNAs, showing the roles in the functional analyses of the GO analysis and KEGG pathways (inclusion criteria: 836 and 48, respectively). The PPI network and Cytoscape analyses revealed that the top ten key mRNAs were NOTCH1, MMP2, IGF1, KDR, SPP1, FLT1, HGF, TEK, ANGPT1, and PDGFB. SPP1 and HGF emerged as hub genes through survival analysis. A high SPP1 expression indicated a poor survival, whereas HGF positively associated with survival outcomes in LUAD.

Conclusion: This study investigated a miRNA-mRNA regulatory network associated with LUAD, exploring the hub miRNAs and potential functions of mRNA in the network. These findings contribute to identify new prognostic markers and therapeutic targets for LUAD patients in clinical settings.

Keywords: bioinformatics; hub genes; lung adenocarcinoma; microRNAs; prognostic marker.

Polylactide, polyglycolide materials or devices have been utilized routinely during maxillofacial, craniofacial, and orthopaedic reconstructive surgical procedures.(1) These materials combine the benefits of rigid fixation with the advantages of biodegradation, avoiding the need for implant removal and minimizing the risk of other complications.(2) To study how polylactide, polyglycolide acids plates (PLPG plates) can induce osteoblast differentiation and proliferation in mesenchymal stem cells, the expression levels of bone related genes (RUNX2, SP7, ALPL, SPP1, COL1A1, COL3A1 and FOSL1) and mesenchymal stem cells marker (ENG) were measured in adipose derived stem cells (ADSCs) and normal osteoblast (NO) cultivated on PLPG plates after 15 and 30 days of treatment using real time Reverse Transcription-Polymerase Chain Reaction. Significantly differentially expressed genes among ADSCs and NO were SP7, ENG, FOSL1, RUNX, ALPL and SPP1 in the first 15 days of treatment and SP7, ENG FOSL1, COL3A1 COL1A1, SPP1 and ALPL after 30 days. The present study demonstrated that PLPG plates strongly influences the behavior of ADSCs in vitro by enhancing proliferation, differentiation and deposition of matrix.

Vascular smooth muscle cell (VSMC) migration is implicated in atherosclerosis and restenosis. Nuclear receptor subfamily 6, group A, member 1 (NR6A1) is involved in regulating embryonic stem cell differentiation, reproduction, neuronal differentiation. Functional cooperation between cAMP response element modulator tau (CREMtau) and NR6A1 can direct gene expression in cells. cAMP response element binding protein (CREB) plays a key role in VSMC migration. In this study, we sought to determine whether CREB involved in NR6A1-modulated VSMC migration. VSMCs treated with platelet-derived growth factor-BB (PDGF-BB) displayed reduced mRNA and protein levels of NR6A1. Adenovirus-mediated expression of NR6A1 (Ad-NR6A1) could inhibit PDGF-BB- and serum-induced VSMC migration. The mRNA and protein expressions of secreted phosphoprotein 1 (SPP1) were down-regulated by NR6A1 overexpression. SPP1 promoter reporter activity was repressed by NR6A1. NR6A1 was found to physically couple with nuclear actin and the large subunit of RNA polymerase II. Furthermore, we showed that CREB interacted with NR6A1 in VSMCs. NR6A1 overexpression repressed cAMP response element (CRE) activity. ChIP assay revealed that NR6A1 bind to SPP1 promoter. Luciferase reporter assay showed that NR6A1 regulated SPP1 promoter activity via a putative CRE site. Adenovirus mediated local NR6A1 gene transfer attenuated stenosis after balloon-induced arterial injury in Sprague-Dawley rats. Taken together, this study provided experimental evidence that NR6A1 modulated SPP1 expression via its binding with CREB protein in VSMCs. We also revealed a NR6A1-CREB-SPP1 axis that serves as a regulatory mechanism for atherosclerosis and restenosis.

The dynamics of the expression of genes encoding adhesion molecules, molecules of the connective tissue matrix, and its remodeling enzymes was studied in multipotent mesenchymal stromal cells (MSCs) from human adipose tissue after interaction with cord blood hematopoietic progenitors (HSPCs). An upregulation of ICAM1 and VCAM1, directly proportional to the coculture time (24-72 h), was found. After 72 h of culturing, a downregulation of the genes encoding the majority of matrix molecules (SPP1; COL6A2,7A1; MMP1,3; TIMP1,3; and HAS1) and cell-matrix adhesion molecules (ITGs) was revealed. The detected changes may ensure the realization of the stromal MSC function due to improvement of adhesion and transmigration of HSPCs into the subcellular space.

BACKGROUND

Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spores resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. pumilus SAFR-032, and the draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. pumilus ATCC7061T. Additional comparisons were made to 61 draft genomes that have been mostly identified as strains of B. pumilus or B. safensis.

RESULTS

The FO-36b gene order is essentially the same as that in SAFR-032 and other B. pumilus strains. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by MERTA and ATCC7061T. The FO-36b genome has ten unique open reading frames and two phage-like regions, homologous to the Bacillus bacteriophage SPP1 and Brevibacillus phage Jimmer1. Differing remnants of the Jimmer1 phage are found in essentially all B. safensis / B. pumilus strains. Seven unique genes are part of these phage elements. Whole Genome Phylogenetic Analysis of the B. pumilus, B. safensis and other Firmicutes genomes, separate them into three distinct clusters. Two clusters are subgroups of B. pumilus while one houses all the B. safensis strains. The Genome-genome distance analysis and a phylogenetic analysis of gyrA sequences corroborated these results.

CONCLUSIONS

It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism's resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. Multiple genome comparison indicates that many strains named as B. pumilus likely belong to the B. safensis group.

Classical Ehlers-Danlos syndrome (cEDS) is a dominant inherited connective tissue disorder mainly caused by mutations in the COL5A1 and COL5A2 genes encoding type V collagen (COLLV), which is a fibrillar COLL widely distributed in a variety of connective tissues. cEDS patients suffer from skin hyperextensibility, abnormal wound healing/atrophic scars, and joint hypermobility. Most of the causative variants result in a non-functional COL5A1 allele and COLLV haploinsufficiency, whilst COL5A2 mutations affect its structural integrity. To shed light into disease mechanisms involved in cEDS, we performed gene expression profiling in skin fibroblasts from four patients harboring haploinsufficient and structural mutations in both disease genes. Transcriptome profiling revealed significant changes in the expression levels of different extracellular matrix (ECM)-related genes, such as SPP1, POSTN, EDIL3, IGFBP2, and C3, which encode both matricellular and soluble proteins that are mainly involved in cell proliferation and migration, and cutaneous wound healing. These gene expression changes are consistent with our previous protein findings on in vitro fibroblasts from other cEDS patients, which exhibited reduced migration and poor wound repair owing to COLLV disorganization, altered deposition of fibronectin into ECM, and an abnormal integrin pattern. Microarray analysis also indicated the decreased expression of DNAJB7, VIPAS39, CCPG1, ATG10, SVIP, which encode molecular chaperones facilitating protein folding, enzymes regulating post-Golgi COLLs processing, and proteins acting as cargo receptors required for endoplasmic reticulum (ER) proteostasis and implicated in the autophagy process. Patients' cells also showed altered mRNA levels of many cell cycle regulating genes including CCNE2, KIF4A, MKI67, DTL, and DDIAS. Protein studies showed that aberrant COLLV expression causes the disassembly of itself and many structural ECM constituents including COLLI, COLLIII, fibronectin, and fibrillins. Our findings provide the first molecular evidence of significant gene expression changes in cEDS skin fibroblasts highlighting that defective ECM remodeling, ER homeostasis and autophagy might play a role in the pathogenesis of this connective tissue disorder.

Prolific breeds of domestic sheep (Ovis aries) are important genetic resources due to their reproductive performance, which is characterized by multiple lambs per birth and out-of-season breeding. However, the lack of a comprehensive understanding of the genetic mechanisms underlying the important reproductive traits, particularly from the evolutionary genomics perspective, has impeded the efficient advancement of sheep breeding. Here, for the first time, by performing RNA-sequencing we built a de novo transcriptome assembly of ovarian and endometrial tissues in European mouflon (Ovis musimon) and performed an mRNA-miRNA integrated expression profiling analysis of the wild species and a highly prolific domestic sheep breed, the Finnsheep. We identified several novel genes with differentially expressed mRNAs (e.g., EREG, INHBA, SPP1, AMH, TDRD5, and ZP2) between the wild and domestic sheep, which are functionally involved in oocyte and follicle development and fertilization, and are significantly (adjusted P-value < 0.05) enriched in the Gene Ontology (GO) terms of various reproductive process, including the regulation of fertilization, oogenesis, ovarian follicle development, and sperm-egg recognition. Additionally, we characterized 58 differentially expressed miRNAs and 210 associated target genes that are essential for the regulation of female reproduction cycles through specific regulatory networks [e.g., (miR-136, miR-374a, miR-9-5p)-(EREG, INHBA)]. Furthermore, our integrated mRNA and miRNA expression profiling analysis elucidated novel direct and indirect miRNA/mRNA causal regulatory relationships related to the reproductive traits of the Ovis species. This study provides in-depth insights into the genomic evolution underlying the reproductive traits of the Ovis species and valuable resources for ovine genomics.

The tail apparatus of the bacteriophage SPP1 is an extraordinary approximately 1600-A-long molecular machine. The tail mediates attachment of the virus to the host surface receptor, as well-as ejection of the viral genome into the host. The distal tip of the tail binds the extracellular ectodomain of the Bacillus subtilis receptor YueB, while the tail tube provides a conduit to funnel the viral genome into the host. This process, which culminates with the ejection of the approximately 44 kb of viral DNA across the thick, cell envelope of the Gram-positive bacterial cell, takes place in a time scale of seconds to minutes and represents a remarkable example of biotransformation. In this issue of Molecular Microbiology, Auzat et al. provide compelling evidence that the two major structural proteins of the SPP1 tail, gp17.1 (approximately 19.1 kDa) and gp17.1* (approximately 28 kDa), share a common N-terminal sequence, and that gp17.1* is generated by a translational frameshift in the gene 17.1. The extra domain fused to gp17.1* is synthesized by a +1 programmed translational frameshift at the end of gene 17.1, which leads to the synthesis of approximately one gp17.1* for every three equivalents of gp17.1. This finding extends our current knowledge of translational frameshifts and provides a framework to understand how Siphoviridae phages like SPP1 have developed long-tail machines using only two major structural proteins.

OBJECTIVE

To analyze three kinds of genotype hepatitis C virus (HCV) core protein expressed in human hepatoma (Huh-7) cell line and to recognize HCV core proteins biological function and its pathogenic mechanism.

METHODS

The Huh-7 cell expressed three kinds of core proteins were established respectively. Affymetrix human gene chip was used for identifying the gene expression dependently on Affymetrix's protocol. All genes changed by 3 or 1.5 folds between the transfected cells and a control cells were further analyzed, and annotated by using NetAffx analysis through Affymetrix website and were categorized based on their biological processes.

RESULTS

The HCV-1b core protein caused 16 genes up/down-regulated expression, of which the immune response genes of PF4V1 and SPP1 were up-regulated 3.4 or 4.4 folds respectively. The HCV-2a core protein had caused the immune response gene CXCL5 and apoptosis gene BTF a down-regulated expression of 3.4 and 3.1 folds respectively, but caused the apoptosis genes of HRK and LZTS1 an up-regulated expression of 3.2 and 3.4 folds respectively. As compared with HCV 1b or 2a core protein, HCV-4b core protein caused 111 genes expression changing and it had more obvious effects on gene expression. If we applied 1.5 fold change for a comparison gene expression, a few of the same gene expression profiles might be caused by these two core proteins.

CONCLUSIONS

The three kinds of HCV core protein should have its own expression character and be mainly shown in immune responses, signal transduction, apoptosis, etc. It should be helpful for our recognizing the HCV core protein biological function and its pathogenic mechanism.

OBJECTIVE

The T-helper 1 (TH1) immune reaction is essential for the eradication of hepatitis C virus (HCV) during pegylated interferon α (PEG-IFN-α)- and ribavirin (RBV)-based therapy in chronic HCV patients. Secreted phosphoprotein 1 (SPP1) was shown to be a crucial cytokine for the initiation of a TH1 immune response. We aimed to investigate whether SPP1 single nucleotide polymorphisms (SNPs) may influence sustained virological response (SVR) rates.

METHODS

Two SNPs in the promoter region of SPP1 at the -443 C>T and -1748 G>A loci were genotyped in 100 patients with chronic HCV genotype 4 infection using a TaqMan SNP genotyping assay.

RESULTS

Sixty-seven patients achieved a SVR, and 33 patients showed no SVR. Patients carrying the T/T genotype at the -443 locus showed a significantly higher SVR rate than those carrying the C/T or C/C genotype (83.67% vs. 50.98%, p<0.001). At the -1748 locus, the SVR rate was significantly higher in patients with the G/G genotype than in those with the A/A genotype (88.89% vs. 52.63%, p=0.028) and in patients with the G/A genotype than in those with the A/A genotype (85.29% vs. 52.63%, p=0.001).

CONCLUSIONS

SPP1 SNPs at -443 C>T and -1748 G>A loci may be useful markers for predicting the response to PEG-IFN-α-2b plus RBV therapy in Egyptian patients with chronic HCV genotype 4 infection.

OBJECTIVE

To investigate the association between SPP1 gene polymorphisms and nephrolithiasis.

METHODS

A total of 65 pediatric patients and 50 healthy controls were enrolled in this study. Two known polymorphisms of the SPP1 gene, c.240T>> C and c.708C>> T nucleotide substitutions, both of which were also known as synonymous aminoacid polymorphisms, D80D and A236A, respectively, at SPP1 gene cDNA level were investigated. SPP1 gene polymorphism was evaluated using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism method.

RESULTS

In c.240T>> C polymorphism, C allele frequency [Odds Ratio (OR), 2.13; 95% Confidence Interval (CI), 1.170 to 3.880; P = .013] and CC genotype distribution (OR, 2.946; 95% CI, 0.832 to 10.431; P = .094) and in c.708C>> T polymorphism, T allele frequency (OR, 2.183; 95% CI, 1.197 to 3.980; P = .011) and TT genotype distribution (OR, 3.056; 95% CI, 0.861 to 10.839; P = .084) were found to be higher in the patient group.

CONCLUSIONS

SPP1 polymorphisms were found to be associated with nephrolithiasis and it may be suggested that SPP1 gene polymorphism could be a useful marker for evaluation of the early genetic risk factor in childhood nephrolithiasis.

Despite increasing evidence for the involvement of bone marrow (BM) hematopoietic stem cell niche in leukemogenesis, how BM mesenchymal stem and progenitor cells (MSPCs) contribute to leukemia niche formation and progression remains unclear. Using an MLL-AF9 acute myeloid leukemia (AML) mouse model, we demonstrate dynamic alterations of BM cellular niche components, including MSPCs and endothelial cells during AML development and its association with AML engraftment. Primary patient AML cells also induced similar niche alterations in xenografted mice. AML cell infiltration in BM causes an expansion of early B-cell factor 2+ (Ebf2+) MSPCs with reduced Cxcl12 expression and enhanced generation of more differentiated mesenchymal progenitor cells. Importantly, in vivo fate-mapping indicates that Ebf2+ MSPCs participated in AML niche formation. Ebf2+ cell deletion accelerated the AML development. These data suggest that native BM MSPCs may suppress AML. However, they can be remodeled by AML cells to form leukemic niche that might contribute to AML progression. AML induced dysregulation of hematopoietic niche factors like Angptl1, Cxcl12, Kitl, Il6, Nov, and Spp1 in AML BM MSPCs, which was associated with AML engraftment and partially appeared before the massive expansion of AML cells, indicating the possible involvement of the niche factors in AML progression. Our study demonstrates distinct dynamic features and roles of BM MSPCs during AML development.

Background: Lung adenocarcinoma (LUAD) comprises around 40% of all lung cancers, and in about 70% of patients, it has spread locally or systemically when first detected leading to a worse prognosis.

Methods: We filtered out differentially expressed genes (DEGs) based on the RNA sequencing data in the Gene Expression Omnibus database and verified and deeply analyzed screened DEGs using a combined bioinformatics approach.

Results: Expressions of 11,143 genes in 694 nontumor lung tissues and LUAD cases from 8 independent laboratories were analyzed; 188 mRNAs were identified as differentially expressed genes (DEGs). A PPI network constructed with 188 DEGs screened out 8 hub DEGs (CDH5, PECAM1, VWF, CLDN5, COL1A1, MMP9, SPP1, and IL6) which highly interconnected with other nodes. The expression levels of 8 hub genes in LUAD and control were assessed in the Oncomine database, and the results were consistent. The survival curves of 8 hub genes showed that their expressions are significantly related to the prognosis of lung cancer and LUAD patients except for IL6. Since the expression of IL6 is nonspecific and highly sensitive, we choose the other 7 hub genes we had verified to do the next analysis. Mutual exclusivity or cooccurrence analysis of 7 hub genes identified a tendency towards cooccurrence between CDH5, PECAM1, and VWF in LUAD. The coexpression profiles of CDH5 in LUAD were identified, and we found that PECAM1 and VWF coexpressed with CDH5. Immunohistochemistry and RT-PCR analysis showed that higher levels of CDH5, PECAM1, and VWF were expressed in normal lung tissues but a low or undetectable level was found in LUAD tissues.

Conclusions: Taken together, we speculate that CDH5, PECAM1, and VWF played an important role in LUAD.

Many studies focus on the identification of genomic regions that undergo selective processes, where evidence of selection is revealed and positional candidate genes are identified. The aim of the research was to evaluate the association between positional candidate genes, namely secreted phosphoprotein 1 (SPP1, sheep chromosome Ovis aries OAR6, 36.651-36.658 Mb), protein O-fucosyltransferase 1 (POFUT1, OAR13, 61.006-61.027 Mb) and prolactin receptor (PRLR, OAR16, 38.969-39.028 Mb) with milk yield, composition and coagulation traits. Eight single nucleotide polymorphisms (SNPs) mapping to the three genes were genotyped in 380 Sarda dairy sheep. Statistical analysis revealed an association between SNP rs161844011 at SPP1 (chromosome position Oar_v3 OAR6:36651870, gene region exon 7) and somatic cell score, while POFUT1 SNP rs424501869 (OAR13:61007495, intron 1) was associated with curd firmness both 45 and 60 min after rennet addition (p = 0.015 and p = 0.007, respectively). SNP rs400874750 at PRLR gene (OAR16:39004070, intron 2) had a significant association with lactose content (p = 0.020), somatic cell score (p = 0.038), rennet coagulation time (p = 0.018) and curd firming time (p = 0.047). The outcome of this research confirmed predictions based on genomic studies, producing new information regarding the SPP1, POFUT1 and PRLR genes, which may be useful for future breeding schemes.

Keywords: POFUT1; PRLR; SPP1; coagulation traits; sheep milk.

OBJECTIVE

Most color vision tests require a high level of cognitive ability and as such are problematic for preschool children and multiply challenged individuals. Our goal was to design a color vision test for these groups and evaluate the clinical utility for preschool children.

METHODS

The University of Waterloo Colored Dot Test (UWCDot) for Color Vision Testing requires the subject to distinguish a colored disc from seven gray discs. The target disc was a Munsell color along the deutan, protan, or tritan confusion line with gray. The first phase estimated the sensitivity and specificity of the test for adults. Thirty-one adults with normal color vision and 21 adults with congenital red-green defects participated. In the second phase, the utility of the UWCDot test for screening preschool children was determined. Subjects were 281 males and 269 females aged 2.5 to 5 years with normal vision. Their color vision was also assessed with the Standard Pseudoisochromatic Plates, Part 1 (SPP1).

RESULTS

The sensitivity and specificity of UWCDot for adults approached the values for the desaturated D-15 when subjective responses were scored. Monitoring fixational eye movements produced sensitivity and specificity values that were similar to the anomaloscope. After adjusting the scoring criterion for the preschool children by using the females as a control, 2.9% of the males were identified as red-green deficient, 1.8% were blue-yellow deficient, and 3.2% had an unclassified deficiency. By definition, 1% of the females failed the test. Counting fixational eye movements was not a useful scoring method in the preschool children. Comparisons with SPP1 indicated that the UWCDot uncovers approximately 35% of the individuals with definite red-green color vision defects.

CONCLUSIONS

Our results indicate that the UWCDot is capable of detecting approximately 35% of the preschool children who have a congenital red-green color vision defect. These individuals are likely to have a more severe deficiency.