Genome-wide integrated analysis reveals functions of lncRNA-miRNA-mRNA interactions in Atlantic salmon challenged by Aeromonas salmonicida

Hypertension is one of the major risk factors for chronic kidney disease (CKD), and the coexistence of hypertension and CKD increases morbidity and mortality. Although many genetic factors have been identified separately for hypertension and kidney disease, studies specifically focused on hypertensive kidney disease (HKD) have been rare. Therefore, this study aimed to identify loci or genes associated with HKD. A genome-wide association study (GWAS) was conducted using two Korean cohorts, the Health Examinee (HEXA) and Korean Association REsource (KARE). Consequently, 19 single nucleotide polymorphisms (SNPs) were found to be significantly associated with HKD in the discovery and replication phases (p < 5 × 10−8, p < 0.05, respectively). We further analyzed HKD-related traits such as the estimated glomerular filtration rate (eGFR), creatinine, blood urea nitrogen (BUN), systolic blood pressure (SBP) and diastolic blood pressure (DBP) at the 14q21.2 locus, which showed a strong linkage disequilibrium (LD). Expression quantitative trait loci (eQTL) analysis was also performed to determine whether HKD-related SNPs affect gene expression changes in glomerular and arterial tissues. The results suggested that the FANCM gene may affect the development of HKD through an integrated analysis of eQTL and GWAS and was the most significantly associated candidate gene. Taken together, this study indicated that the FANCM gene is involved in the pathogenesis of HKD. Additionally, our results will be useful in prioritizing other genes for further experiments.

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Chimeric Protein IPath® with Chelating Activity Improves Atlantic Salmon’s Immunity against Infectious Diseases

Vaccines ◽

10.3390/vaccines9040361 ◽

2021 ◽

Vol 9 (4) ◽

pp. 361

Author(s):

Valentina Valenzuela-Muñoz ◽

Bárbara P. Benavente ◽

Antonio Casuso ◽

Yeny Leal ◽

Cristian Gallardo-Escárate

Keyword(s):

Immune Response ◽

Atlantic Salmon ◽

Iron Metabolism ◽

Iron Transport ◽

Aeromonas Salmonicida ◽

Transcriptional Analysis ◽

Control Fish ◽

Control Group ◽

Commercial Fish ◽

Chelating Activity

Infection processes displayed by pathogens require the acquisition of essential inorganic nutrients and trace elements from the host to survive and proliferate. Without a doubt, iron is a crucial trace metal for all living organisms and also a pivotal component in the host–parasite interactions. In particular, the host reduces the iron available to face the infectious disease, increasing iron transport proteins’ expression and activating the heme synthesis and degradation pathways. Moreover, recent findings have suggested that iron metabolism modulation in fish promotes the immune response by reducing cellular iron toxicity. We hypothesized that recombinant proteins related to iron metabolism could modulate the fish’s immune system through iron metabolism and iron-responsive genes. Here a chimeric iron transport protein (IPath®) was bioinformatically designed and then expressed in a recombinant bacterial system. The IPath® protein showed a significant chelating activity under in vitro conditions and biological activity. Taking this evidence, a vaccine candidate based on IPath® was evaluated in Atlantic salmon challenged with three different fish pathogens. Experimental trials were conducted using two fish groups: one immunized with IPath® and another injected with adjutant as the control group. After 400 accumulated thermal units (ATUs), two different infection trials were performed. In the first one, fish were infected with the bacterium Aeromonas salmonicida, and in a second trial, fish were exposed to the ectoparasite Caligus rogercresseyi and subsequently infected with the intracellular bacterium Piscirickettsia salmonis. Fish immunized with IPath® showed a significant delay in the mortality curve in response to A. salmonicida and P. salmonis infections. However, no significant differences between infected and control fish groups were observed at the end of the experiment. Notably, sea lice burden reduction was observed in vaccinated Atlantic salmon. Transcriptional analysis evidenced a high modulation of iron-homeostasis-related genes in fish vaccinated with IPath® compared to the control group during the infection. Moreover, increasing expression of Atlantic salmon IgT was associated with IPath® immunization. This study provides evidence that the IPath® protein could be used as an antigen or booster in commercial fish vaccines, improving the immune response against relevant pathogens for salmon aquaculture.

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The color change and stress response of Atlantic salmon (Salmo salar L.) infected with Aeromonas salmonicida

Aquaculture Reports ◽

10.1016/j.aqrep.2021.100664 ◽

2021 ◽

Vol 20 ◽

pp. 100664

Author(s):

Mengmeng Yi ◽

Huanda Lu ◽

Yishuai Du ◽

Guoxiang Sun ◽

Ce Shi ◽

...

Keyword(s):

Stress Response ◽

Atlantic Salmon ◽

Salmo Salar ◽

Color Change ◽

Aeromonas Salmonicida ◽

Atlantic Salmon Salmo Salar

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Infectious load of Aeromonas salmonicida subsp. salmonicida during the initial phase of a cohabitant infection experiment with Atlantic salmon, Salmo salar L.

Journal of Fish Diseases ◽

10.1111/j.1365-2761.1992.tb01242.x ◽

1992 ◽

Vol 15 (5) ◽

pp. 425-430 ◽

Cited By ~ 14

Author(s):

O. ENGER ◽

B. GUNNLAUGSDOTTIR ◽

B. K. THORSEN ◽

B. HJELTNES

Keyword(s):

Atlantic Salmon ◽

Salmo Salar ◽

Initial Phase ◽

Aeromonas Salmonicida ◽

Infection Experiment ◽

Atlantic Salmon Salmo Salar

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Identification of gene expression and DNA methylation of SERPINA5 and TIMP1 as novel prognostic markers in lower-grade gliomas

PeerJ ◽

10.7717/peerj.9262 ◽

2020 ◽

Vol 8 ◽

pp. e9262

Author(s):

Wen-Jing Zeng ◽

Yong-Long Yang ◽

Zhi-Peng Wen ◽

Peng Chen ◽

Xiao-Ping Chen ◽

...

Keyword(s):

Gene Expression ◽

Classification System ◽

Differentially Expressed ◽

Integrated Analysis ◽

Lower Grade ◽

Kaplan Meier ◽

Genome Wide ◽

Genes Expression ◽

Tumors Classification ◽

Long Term Survivors

Background Lower-grade gliomas (LGGs) is characteristic with great difference in prognosis. Due to limited prognostic biomarkers, it is urgent to identify more molecular markers to provide a more objective and accurate tumor classification system for LGGs. Methods In the current study, we performed an integrated analysis of gene expression data and genome-wide methylation data to determine novel prognostic genes and methylation sites in LGGs. Results To determine genes that differentially expressed between 44 short-term survivors (<2 years) and 48 long-term survivors (≥2 years), we searched LGGs TCGA RNA-seq dataset and identified 106 differentially expressed genes. SERPINA5 and TIMP1 were selected for further study. Kaplan–Meier plots showed that SERPINA5 and TIMP1 expression were significantly correlated with overall survival (OS) and relapse-free survival (RFS) in TCGA LGGs patients. We next validated the correlation between the candidate genes expression and clinical outcome in CGGA LGGs patients. Multivariate analysis showed that TIMP1 mRNA expression had a significant prognostic value independent of other variables (HR = 4.825, 95% CI = 1.370–17.000, P = 0.014). Then, differential methylation sites were identified from differentially candidate gene expression groups, and all four methylation sites were significantly negatively correlated with gene expression (spearman r < − 0.5, P < 0.0001). Moreover, hyper-methylation of four methylation sites indicated better OS (P < 0.05), and three of them also shown statistical significantly association with better RFS, except for SERPINA5 cg15509705 (P = 0.0762). Conclusion Taken together, these findings indicated that the gene expression and methylation of SERPINA5 and TIMP1 may serve as prognostic predictors in LGGs and may help to precise the current histology-based tumors classification system and to provide better stratification for future clinical trials.

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