Association of Htra1 gene polymorphisms with the risk of developing AMD in Iranian population

Background:

Half of the cases of vision loss in people under 60 years of age have been attributed to age-related macular degeneration (AMD). This is a multifactorial disease with late onset. It has been demonstrated that many different genetic loci are implicated in the risk of developing AMD in different populations. In the current study, we investigated the association of high-temperature ‎requirement A-1 (HTRA1) gene polymorphisms with the risk of developing AMD in the Iranian population.

Methods:

Genomic DNA samples were extracted from 120 patients with AMD and 120 healthy age- and sex-matched controls. A 385 base-pair fragment of the HTRA1 gene promoter region was amplified using the polymerase chain reaction (PCR) technique and sequenced. The frequencies of the alleles were calculated and statistical analysis was performed using SPSS software.

Results:

Our study demonstrated that the rate of polymorphisms rs11200638 -625 G>A and rs2672598 -487T>C were significantly greater in AMD patients than in healthy controls from the Iranian population.

Conclusions:

The results of our study indicate that HTRA1 gene promoter region polymorphisms are associated with the risk of developing AMD in the Iranian population.Key Words: HTRA1, Single Nucleotide Polymorphisms, Macular Degeneration, Iran     

Development of SNP‐genotyping arrays in two shellfish species

Use of SNPs has been favoured due to their abundance in plant and animal genomes, accompanied by the falling cost and rising throughput capacity for detection and genotyping. Here, we present in vitro (obtained from targeted sequencing) and in silico discovery of SNPs, and the design of medium‐throughput genotyping arrays for two oyster species, the Pacific oyster, Crassostrea gigas, and European flat oyster, Ostrea edulis. Two sets of 384 SNP markers were designed for two Illumina GoldenGate arrays and genotyped on more than 1000 samples for each species. In each case, oyster samples were obtained from wild and selected populations and from three‐generation families segregating for traits of interest in aquaculture. The rate of successfully genotyped polymorphic SNPs was about 60% for each species. Effects of SNP origin and quality on genotyping success (Illumina functionality Score) were analysed and compared with other model and nonmodel species. Furthermore, a simulation was made based on a subset of the C. gigas SNP array with a minor allele frequency of 0.3 and typical crosses used in shellfish hatcheries. This simulation indicated that at least 150 markers were needed to perform an accurate parental assignment. Such panels might provide valuable tools to improve our understanding of the connectivity between wild (and selected) populations and could contribute to future selective breeding programmes.     

Spermatogonial stem cells in the testis of an endangered bovid: Indian black buck (Antilope cervicapra L.)

Numerous wild bovids are facing threat of extinction owing to the loss of habitat and various other reasons. Spermatogonial stem cells (SSCs) represent the only germline stem cells in adult body that are capable of self-renewal and that can undergo differentiation to produce haploid germ cells. SSCs can, therefore, serve as a useful resource for preservation of germplasm of threatened and endangered mammals. The Indian black buck (Antilope cervicapra L.) is a small Indian antelope that is listed as endangered by the Indian Wildlife Protection Act, 1972. Immunohistochemical analysis of testes tissues of black buck revealed the presence of spermatogonia that were specifically stained by lectin-Dolichos biflorus agglutinin (DBA). The expression of pluripotent cell-specific markers, NANOG and stage-specific embryonic antigen-1 (SSEA-1), was detected in spermatogonia. Interestingly, the expression of POU5F1 (OCT3/4) was absent from spermatogonia, however, it was detected in differentiating cells such as spermatocytes and round spermatids but not in elongated spermatids. The expression of NANOG protein was also present in spermatocytes but absent in round and elongated spermatids. Using the testis transplantation assay, stem cell potential of black buck spermatogonia was confirmed as indicated by the presence of colonized DBA-stained cells in the basal membrane of seminiferous tubules of xenotransplanted mice testis. The findings from this study suggest the presence of SSCs in the testis of an endangered bovid for the first time and open new possibility to explore the use of SSCs in conservation.     

High-density lipoprotein functionality and breast cancer: A potential therapeutic target

Breast cancer is a major cause of death globally, and particularly in developed countries. Breast cancer is influenced by cholesterol membrane content, by affecting the signaling pathways modulating cell growth, adherence, and migration. Furthermore, steroid hormones are derived from cholesterol and these play a key role in the pathogenesis of breast cancer. Although most findings have reported an inverse association between serum high-density lipoprotein (HDL)-cholesterol level and the risk of breast cancer, there have been some reports of the opposite, and the association therefore remains unclear. HDL is principally known for participating in reverse cholesterol transport and has an inverse relationship with the cardiovascular risk. HDL is heterogeneous, with particles varying in composition, size, and structure, which can be altered under different circumstances, such as inflammation, aging, and certain diseases. It has also been proposed that HDL functionality might have a bearing on the breast cancer. Owing to the potential role of cholesterol in cancer, its reduction using statins, and particularly as an adjuvant during chemotherapy may be useful in the anticancer treatment, and may also be related to the decline in cancer mortality. Reconstituted HDLs have the ability to release chemotherapeutic drugs inside the cell. As a consequence, this may be a novel way to improve therapeutic targeting for the breast cancer on the basis of detrimental impacts of oxidized HDL on cancer development.     

IPS-1 differentially induces TRAIL,BCL2, BIRC3 and PRKCE in type I interferons-dependent and -independent anticancer activity

RIG-I-like receptors are the key cytosolic sensors for RNA viruses and induce the production of type I interferons (IFN) and pro-inflammatory cytokines through a sole adaptor IFN-β promoter stimulator-1 (IPS-1) (also known as Cardif, MAVS and VISA) in antiviral innate immunity. These sensors also have a pivotal role in anticancer activity through induction of apoptosis. However, the mechanism for their anticancer activity is poorly understood. Here, we show that anticancer vaccine adjuvant, PolyIC (primarily sensed by MDA5) and the oncolytic virus, Newcastle disease virus (NDV) (sensed by RIG-I), induce anticancer activity. The ectopic expression of IPS-1 into type I IFN-responsive and non-responsive cancer cells induces anticancer activity. PolyIC transfection and NDV infection upregulate pro-apoptotic gene TRAIL and downregulate the anti-apoptotic genes BCL2, BIRC3 and PRKCE. Furthermore, stable knockdown of IPS-1, IRF3 or IRF7 in IFN-non-responsive cancer cells show reduced anticancer activity by suppressing apoptosis via TRAIL and anti-apoptotic genes. Collectively, our study shows that IPS-1 induces anticancer activity through upregulation of pro-apoptotic gene TRAIL and downregulation of the anti-apoptotic genes BCL2, BIRC3 and PRKCE via IRF3 and IRF7 in type I IFN-dependent and -independent manners.The primary protection of the host from various pathogens is ensured by the innate immune system, which consists of families of sensors such as the Toll-like receptors (TLRs), RIG-I-like receptors (RLRs) and NOD-like receptors. These sensors recognize the diverse range of pathogens in various cellular compartments and lead to the activation of innate immunity, including the production of various cytokines that create an anti-pathogenic environment to limit the pathogen. RLRs are cytosolic sensors that recognize the viral RNA and recruit an adaptor, Interferon (IFN)-β promoter stimulator-1 (IPS-1), also known as CARDIF, MAVS or VISA. IPS-1, a protein that contains a caspase activation and -recruitment domain (CARD), is localized to the mitochondria for its antiviral function.^{1, 2, 3, 4} Mice lacking IPS-1 show severely impaired antiviral innate immunity.⁵ The RLRs/IPS-1 signaling axis activates a cascade of signals that predominantly induces the production of the type I IFN and pro-inflammatory cytokines through IRFs and NF-κB, respectively, to establish an antiviral state.In addition to the pivotal role that host immunity has against numerous pathogen challenges, it is crucial in immune surveillance against altered-self cells. Immune mediators such as cytokines, chemokines and type I IFN initiate a complex network of signals to induce an anti-tumor state by triggering various biochemical processes such as cell cycle arrest and apoptosis. Additionally, these immune mediators facilitate cytotoxicity to the tumor cells through the recruitment of immunocompetent cells. The cytotoxic activity is mediated through the upregulation of pro-apoptotic genes and the downregulation of anti-apoptotic genes. These changes are critical for cancer cell death.⁶ Various innate and adaptive cytokines are used for treatment of several types of cancer.^{7, 8} The type I IFN are essential for antiviral immunity and induce pleiotropic effects such as the inhibition of malignant growth and apoptosis of altered-self cells.In addition, pathogen-associated molecular patterns such as polyinosinic:polycytidylic acid (polyIC), a synthetic analog of double-stranded RNA and viruses known as oncolytic viruses such as Vesicular stomatitis virus, Newcastle disease virus (NDV) and Sendai virus induce anticancer activity.⁹ However, the molecular mechanisms for these agents are poorly understood.Here, we showed that treatment of cancer cells with polyIC transfection or NDV infection initiates RIG-I- and MDA5-dependent anticancer activity through recruitment of an adaptor, IPS-1. Using IFN α/β receptor1 (IFNAR1)-sufficient and IFNAR1-deficient cancer cells, we showed that these anticancer activities require the RLR signaling pathway. However, type I IFN are dispensable for the anticancer activity. The RLR pathway induces anticancer activity through the selective induction of cell death or apoptosis via upregulation of the pro-apoptotic gene TRAIL and downregulation of the anti-apoptotic genes BCL2, BIRC3 and PRKCE. These changes lead to post-translational activation of caspases −3 and −9 and PARP-1 in cancer cells. Furthermore, our study reveals that IFN regulatory factors (IRF)3 and IRF7 are indispensable for the RLR-mediated anticancer activity.     

LncRNA‐miRNA network analysis across the Th17 cell line reveals biomarker potency of lncRNA NEAT1 and KCNQ1OT1 in multiple sclerosis

Differentiation of CD⁴⁺ T cells into Th17 cells is an important factor in the onset and progression of multiple sclerosis (MS) and Th17/Treg imbalance. Little is known about the role of lncRNAs in the differentiation of CD⁴⁺ cells from Th17 cells. This study aimed to analyse the lncRNA‐miRNAs network involved in MS disease and its role in the differentiation of Th17 cells. The lncRNAs in Th17 differentiation were obtained from {"type":"entrez-geo","attrs":{"text":"GSE66261","term_id":"66261"}}GSE66261 using the GEO datasets. Differential expression of lncRNAs in Th17 primary cells compared to Th17 effector cells was investigated by RNA‐seq analysis. Next, the most highlighted lncRNAs in autoimmune diseases were downloaded from the lncRNAs disease database, and the most critical miRNA was extracted by literature search. Then, the lncRNA‐miRNA interaction was achieved by the Starbase database, and the ceRNA network was designed by Cytoscape. Finally, using the CytoHubba application, two hub lncRNAs with the most interactions with miRNAs were identified by the MCODE plug‐in. The expression level of genes was measured by qPCR, and the plasma level of cytokines was analysed by ELISA kits. The results showed an increase in the expression of NEAT1, KCNQ1OT1 and RORC and a decrease in the expression of FOXP3. In plasma, an upregulation of IL17 and a downregulation of TGFB inflammatory cytokines were detected. The dysregulated expression of these genes could be attributed to relapsing‐remitting MS (RR‐MS) patients and help us understand MS pathogenesis better.     

Isolating plant genomic DNA without liquid nitrogen

DNA was isolated from leaves of 10 plant species (Cuminum cyminum, Vigna aconitifolia, Pennisetum typhoides, Tecoma stans, Lycium barbarum, Anogeissus acuminata, Tecomella undulata, Zizyphus mauritiana, Phoenix dactylifera, andEruca sativa) and a fungus (Fusarium oxysporum) using the CTAB method. Three fixing solutions (alcohol, alcohol and chloroform, alcohol and EDTA) were used to produce high molecular weight DNA (>40 kb). DNA quality and quantity was comparable for the 3 fixing solutions and liquid nitrogen grinding. Adding chloroform or EDTA to fixing solutions offered no advantage over absolute alcohol. Isolated DNA was suitable for RAPD analysis, restriction digestion, and cloning. This method does not require liquid nitrogen for fixation, grinding, or storage at −80°C, making it advantagenous over other common protocols.     

UCHL-1 protein expression specifically marks spermatogonia in wild bovid testis

Spermatogonia are germ cells that initiate spermatogenesis in mammalian testis and they are the only cells in adult body capable of dividing both mitotically and meiotically. Therefore, isolation and preservation of spermatogonia can provide an alternative method for preservation of genetic pool of endangered animals. To achieve this objective, it is essential to identify markers that can specifically distinguish spermatogonia from other cells in the testis. In the present study, anti-ubiquitin C-terminal hydroxylase-1 (UCHL-1/PGP 9.5) antibody specifically recognized spermatogonia in the testis of wild and domestic bovid. The size of the UCHL-1 protein in various species of bovid testes was identical, and similar to that in mice. Furthermore, UCHL-1 staining could be utilized for the identification of spermatogonia in isolated testicular cells from wild bovids suggesting that UCHL-1 protein expression could be used as a specific marker for spermatogonia in bovid family.