AKIRIN2 Research Articles

Genome-wide meta-analysis and omics integration identifies novel genes associated with diabetic kidney disease

Aims/hypothesisDiabetic kidney disease (DKD) is the leading cause of kidney failure and has a substantial genetic component. Our aim was to identify novel genetic factors and genes contributing to DKD by performing meta-analysis of previous genome-wide association studies (GWAS) on DKD and by integrating the results with renal transcriptomics datasets.MethodsWe performed GWAS meta-analyses using ten phenotypic definitions of DKD, including nearly 27,000 individuals with diabetes. Meta-analysis results were integrated with estimated quantitative trait locus data from human glomerular (N=119) and tubular (N=121) samples to perform transcriptome-wide association study. We also performed gene aggregate tests to jointly test all available common genetic markers within a gene, and combined the results with various kidney omics datasets.ResultsThe meta-analysis identified a novel intronic variant (rs72831309) in the TENM2 gene associated with a lower risk of the combined chronic kidney disease (eGFR<60 ml/min per 1.73 m2) and DKD (microalbuminuria or worse) phenotype (p=9.8×10−9; although not withstanding correction for multiple testing, p>9.3×10−9). Gene-level analysis identified ten genes associated with DKD (COL20A1, DCLK1, EIF4E, PTPRN–RESP18, GPR158, INIP–SNX30, LSM14A and MFF; p<2.7×10−6). Integration of GWAS with human glomerular and tubular expression data demonstrated higher tubular AKIRIN2 gene expression in individuals with vs without DKD (p=1.1×10−6). The lead SNPs within six loci significantly altered DNA methylation of a nearby CpG site in kidneys (p<1.5×10−11). Expression of lead genes in kidney tubules or glomeruli correlated with relevant pathological phenotypes (e.g. TENM2 expression correlated positively with eGFR [p=1.6×10−8] and negatively with tubulointerstitial fibrosis [p=2.0×10−9], tubular DCLK1 expression correlated positively with fibrosis [p=7.4×10−16], and SNX30 expression correlated positively with eGFR [p=5.8×10−14] and negatively with fibrosis [p<2.0×10−16]).Conclusions/interpretationAltogether, the results point to novel genes contributing to the pathogenesis of DKD.Data availabilityThe GWAS meta-analysis results can be accessed via the type 1 and type 2 diabetes (T1D and T2D, respectively) and Common Metabolic Diseases (CMD) Knowledge Portals, and downloaded on their respective download pages (https://t1d.hugeamp.org/downloads.html; https://t2d.hugeamp.org/downloads.html; https://hugeamp.org/downloads.html).Graphical abstract

Effect of Expressions and SNPs of Candidate Genes on Intramuscular Fat Content in Qinchuan Cattle.

Simple SummaryIntramuscular fat (IMF), which characterizes the marbling, is a key meat quality trait in the beef industry. In this study, we validated the effect of the expression levels and single nucleotide polymorphisms (SNPs) of AKIRIN2, TTN, EDG1, and MYBPC1 genes on IMF content in Chinese Qinchuan cattle. The results showed that the expression levels of these genes could affect the IMF content, and the SNP in EGD1 could affect the IMF content in Qinchuan. The information of this study may be applied to effective marker-assisted selection, to increase the levels of marbling in Qinchuan beef production.Marbling is characterized by the amount and distribution of intramuscular fat (IMF). The AKIRIN2, TTN, EDG1, and MYBPC1 genes are well-known marbling-related genes, which were first identified in Japanese Black beef cattle. The objectives of this study were to analyze the correlation of the expression levels of these genes in the longissimus muscle (LM) with IMF content, and the associations between the single nucleotide polymorphisms (SNPs) in these genes and IMF content in Chinese Qinchuan cattle (n = 350). The association analyses showed that the g.42041062G>T SNP in the EDG1 gene was significantly associated with IMF content in Qinchuan (p < 0.05). Further, the expressions of the EDG1 and MYBPC1 were up-regulated (p < 0.05) in LM of Qinchuan cattle group with low IMF content. Down-regulations of the AKIRIN2 and TTN genes (p < 0.05 and p < 0.01, respectively) were observed in the Qinchuan cattle group with high IMF content. These results suggest possible effects of the expression levels of selected genes on IMF content in the LM, and the g.42041062G>T SNP in the EDG1 gene might be useful as a molecular marker for IMF content in Qinchuan.

The The favorable alleles of AKIRIN2:c.*188G&gt;A, EDG1:c.-312A&gt;G and TTN:g.231054C&gt;T as candidate markers for high-marbling are very low in Bali cattle

Abstract. Anwar S, Wulandari AS, Putra WPB, Said S. 2019. The favorable alleles of AKIRIN2:c.*188G&gt;A, EDG1:c.-312A&gt;G and TTN:g.231054C&gt;T as candidate markers for high-marbling are very low in Bali cattle. Biodiversitas 20: 965-970. Marbling is one of primary factors influencing the palatability of beef. The AKIRIN2, EDG1 and TTN genes are considered as the three candidate genes responsible for high-marbling in beef cattle. This study aimed to investigate the genetic polymorphism of the SNPs of AKIRIN2:c.*188G&gt;A, EDG1:c.-312A&gt;G and TTN g.231054C&gt;T in Bali cattle. A total of 125 DNA samples of Bali cattle were genotyped for AKIRIN2 and TTN gene and 82 DNA samples for EDG1 gene using PCR-RFLP method. In the present study, it was found that the A allele of AKIRIN2:c.*188G&gt;A, the G allele of EDG1:c.-312A&gt;G and the T allele of TTN g.231054C&gt;T that considered as the favorable alleles were found to be very low in Bali cattle (0.004, 0.000, and 0.004, respectively). This results indicated that the polymorphism of AKIRIN2:c.*188G&gt;A, EDG1:c.-312A&gt;G and TTN g.231054C&gt;T were very low and can be considered as monomorphic in Bali cattle. These findings suggested that Bali cattle may not genetically potential as a high-marbling cattle breed. However, the other specific genes for high-marbling still needs to be investigated in Bali cattle.

Expression analysis of Akirin-2, NFκB-p65 and β-catenin proteins in imatinib resistance of chronic myeloid leukemia

ABSTRACTObjective: Chronic myleoid leukemia (CML) is a myeloproliferative disorder characterized with the constitutive activation of Bcr-Abl tyrosine kinase which is a target for imatinib, the first line treatment option for CML. Constitutive activation of NFκB and β-catenin signaling promotes cellular proliferation and survival and resistance to Imatinib therapy in CML. Akirin-2 is a nuclear protein which is required for NFκB dependent gene expression as a cofactor and has been linked to Wnt/beta-catenin pathway. The purpose of this study is to examine Akirin-2, NFκB and β-catenin in imatinib resistance of CML and to test if any direct physical protein–protein interaction exists between NFkB and both β-catenin and Akirin-2.Methods: RT–PCR and western blot were performed to determine Akirin-2, NFκB-p65 and β-catenin gene and protein expressions, Co-immunoprecipitation and chromatin immunoprecipitation analysis were carried out to detect the direct physical interactions and binding of NFκB-p65 and β-catenin proteins to MDR1 promoter region, respectively.Results: β-catenin and NFκB-p65 proteins bound to DNA promoter regions of MDR1 in imatinib-sensitive and resistant CML cells, whereas any direct protein–protein interaction could not be found between NFκB-p65 and Akirin-2 or β-catenin proteins. Nuclear β-catenin and NFκB-p65 levels increased in imatinib resistance. Moreover, increased Akirin-2 protein accumulation in the nucleus was shown for the first time in imatinib resistant CML cells.Discussion: We show for the first time that Akirin-2 can be a novel biomarker in imatinib resistance. Targeting Akirin-2, NFκB and β-catenin genes may provide an opportunity to overcome imatinib resistance in CML.

Molecular genetics and bioinformatics analysis of EDG1 and AKIRIN2 genes in Iranian fat-tailed and nonfat-tailed sheep breeds

This study was conducted to detect different allelic forms and its association with fat-tail traits, and also investigation of domains variants in 5/- and 3/-UTR regions of EDG1 and AKIRIN2 genes in Iranian fat-tailed (Lori-Bakhtiari) and nonfat-tailed (Zel) sheep breeds. Blood samples were randomly collected from 300 sheep (150 samples per each breed) and genomic DNA was extracted by modified salting out method. Two primer pairs were designed by oligo7 software for amplification of fragments with the length of 516 and 454bp from EDG1 and AKIRIN2 genes, respectively. The results of genotyping by SSCP assay and silver nitrate staining showed that, in both breeds, there was no incidence of mutation in AKIRIN2 gene. But, the EDG1 was highly polymorph in studied sheep breeds, so that, six banding patterns with different frequencies of A (36.73 and 31.19%), B (8.84 and 21.6%), C (7.48 and 41.12%), D (29.93 and 34.50%), E (13.61 and 34.10%) and F (3.40 and 38.1%) were observed for Zel and Lori-Bakhtiari breeds, respectively. Comparison of banding pattern frequencies by Chi-square test showed significant difference between two breeds (P<0.01). One sample from each banding patterns were sequenced. The alignment and motif analysis of sequences by BioEdit and DNASIS MAX software showed incidence of 11 single nucleotide polymorphism (SNP) and 18 DNA motifs in EDG1 marker site. According to different SNPs, the paternal and maternal haplotypes were determined by phase software. The association study showed significant association between EDG1 gene haplotypes and banding patterns with fat-tail traits in Lori-Bakhtiari sheep except for height of fat-tail. This study was the first effort for evaluate of these genes in sheep. Therefore, more studies on other breeds of sheep and on coding sequence of these genes are recommended.

Evolution of akirin family in gene and genome levels and coexpressed patterns among family members and rel gene in croaker

Akirins, which are highly conserved nuclear proteins, are present throughout the metazoan and regulate innate immunity, embryogenesis, myogenesis, and carcinogenesis. This study reports all akirin genes from miiuy croaker and analyzes comprehensively the akirin gene family combined with akirin genes from other species. A second nuclear localization signal (NLS) is observed in akirin2 homologues, which is not in akirin1 homologues in all teleosts and most other vertebrates. Thus, we deduced that the loss of second NLS in akirin1 homologues in teleosts likely occurred in an ancestor to all Osteichthyes after splitting with cartilaginous fish. Significantly, the akirin2(2) gene included six exons interrupted by five introns in the miiuy croaker, which may be caused by the intron insertion event as a novel evidence for the variation of akirin gene structure in some species. In addition, comparison of the genomic neighborhood genes of akirin1, akirin2(1), and akirin2(2) demonstrates a strong level of conserved synteny across the teleost classes, which further proved the deduction of Macqueen and Johnston 2009 that the produce of akirin paralogues can be attributed to whole-genome duplications and the loss of some akirin paralogues after genome duplications. Furthermore, akirin gene family members and relish gene are ubiquitously expressed across all tissues, and their expression levels are increased in three immune tissues after infection with Vibrio anguillarum. Combined with the expression patterns of LEAP-1 and LEAP-2 from miiuy croaker, an intricate network of co-regulation among family members is established. Thus, it is further proved that akirins acted in concert with the relish protein to induce the expression of a subset of downstream pathway elements in the NF-kB dependent signaling pathway.

A Novel SNP in the Coding Region of the Akirin2 Gene and Its Association with Marbling Score in Hanwoo (Korean Cattle)

A Novel SNP in the Coding Region of the Akirin2 Gene and Its Association with Marbling Score in Hanwoo (Korean Cattle)

Akirin2 expression in response to vaccine-induced immunity in chicken.

Akirin2 is a nuclear factor that plays an important role in the development and regulation of innate immune response. In this study, akirin2 gene expression in several primary immune organs (liver, thymus, and bursa) of Hi-Line Brown chicken administered with the LoSota vaccine was analyzed during the various stages of increase in Newcastle disease virus antibody titer. The results revealed that akirin2 expression was significantly higher in the liver (P < 0.01) and bursa (P < 0.05) of vaccinated chicken 7 and 14 days post-immunization, respectively. These results could serve as a foundation for further studies on the functions of akirin2 in immune response.

The identification of the first molluscan Akirin2 with immune defense function in the Hong Kong oyster Crassostrea hongkongensis

The Akirin protein is a nuclear factor in the innate immune system that is highly conserved from insects to mammals and plays key roles in diverse biological processes, including immunity, myogenesis, development and the cellular stress response. However, the function of Akirins in mollusk, the second most diverse group of animals, is still poorly understood. In this study, we report the discovery of an Akirin2 gene homolog (ChAkirin2) and its biological functions in the Hong Kong oyster Crassostrea hongkongensis. ChAkirin2 is 189 amino acids in length and shares significant homology with invertebrate homologs. Phylogenetic analysis results revealed that ChAkirin2 is clustered with invertebrate Akirin2s. A sequence analysis of the 5' flanking regions of ChAkirin2 indicated that it harbors several potential PAMP-activated transcription factor binding sites (TFB), including sites for NF-κB, C/EBPα, AP-1, SRF, Oct-1 and GATA-1. An RT-PCR analysis showed that ChAkirin2 mRNA was ubiquitously expressed in various tissues and at different embryonic and larval stages. Additionally, upon infection by pathogens (Vibrio alginolyticus, Staphylococcus haemolyticus and Saccharomyces cerevisiae) and pathogen-associated molecular patterns (PAMPs: LPS, PGN and polyI:C), the expression of ChAkirin2 was significantly up-regulated. Moreover, fluorescence microscopy observations show that ChAkirin2 is located in the nuclei of HeLa cells, and the overexpression of ChAkirin2 activated the transcriptional activities of the NF-κB reporter gene in HEK293T cells. Altogether, this report provided the first experimental demonstration that mollusks possess a functional Akirin2 that is involved in the innate defense and embryogenesis processes of the oyster.

Molecular cloning, sequence analysis and tissue-specific expression of Akirin2 gene in Tianfu goat

The Akirin2 gene is a nuclear factor and is considered as a potential functional candidate gene for meat quality. To better understand the structures and functions of Akirin2 gene, the cDNA of the Tianfu goat Akirin2 gene was cloned. Sequence analysis showed that the Tianfu goat Akirin2 cDNA full coding sequence (CDS) contains 579bp nucleotides that encode 192 amino acids. A phylogenic tree of the Akirin2 protein sequence from the Tianfu goat and other species revealed that the Tianfu goat Akirin2 was closely related with cattle and sheep Akirin2. RT-qPCR analysis showed that Akirin2 was expressed in the myocardium, liver, spleen, lung, kidney, leg muscle, abdominal muscle and the longissimus dorsi muscle. Especially, high expression levels of Akirin2 were detected in the spleen, lung, and kidney whereas lower expression levels were seen in the liver, myocardium, leg muscle, abdominal muscle and longissimus dorsi muscle. Temporal mRNA expression showed that Akirin2 expression levels in the longissimus dorsi muscle, first increased then decreased from day 1 to month 12. Western blotting results showed that the Akirin2 protein was only detected in the lung and three skeletal muscle tissues.

Cloning and expression pattern of akirin2 gene in broiler.

Akirin2 is an important nuclear factor which plays functions in innate immune response, myogenesis, muscle development, and carcinogenesis. In this study, akirin2 genes were cloned from 4-day-old Sanhuang and AA(+) broiler, and its expression patterns were analyzed by RT-PCR. The results showed that there were four SNPs in the 5'-terminal region of akirin2 coding sequences. Expression profile analysis showed that the akirin2 transcripts were constitutively expressed in 15 tissues tested, and similar expression patterns were found between the two breeds of broilers. In addition, one of the interesting findings was that the akirin2 gene is highly expressed in blood and lowly expressed in heart, respectively. These data can serve as a foundation for further studying functions of akirin2 gene.

Identification and molecular characterization of an Akirin2 homolog in Chinese loach (Paramisgurnus dabryanus)

Akirin is a nuclear factor involved in innate immune responses of arthropods and mammals. In this study we have cloned an Akirin2 gene, pdakirin2, from freshwater Chinese loach (Paramisgurnus dabryanus) and characterized its biological functions. Phylogenetic analysis revealed deduced PdAkirin2 had high sequence identities to Akirin2 homologs from fish and mammals (70−91%), it contained two conserved nuclear localization signals (NLSs) with verified sub-cellular localization. Quantitative real-time (qRT)-PCR analysis indicated that PdAkirin2 was present in a wide range of loach tissues and showed up-regulation with challenges of Aeromonas hydrophila NJ-1, LPS and poly I:C. PdAkirin2 as an immune factor had significant effects on the expression of cytokines (TNFα, IFN-α, IFN-γ, IL-4 and IL-1β) and transcription factor NF-κB. This study provides insights into the potential role of PdAkirin2 in the innate immune system.

Molecular Cloning, Tissue Distribution, and Functional Analysis of Porcine Akirin2

Akirin2 is a recently discovered gene that is involved in innate immune response. In this study, the porcine Akirin2 gene was cloned. The full-length coding sequence (CDS) of porcine Akirin2 consists of 612 bp and encodes 203 amino acids with a molecular mass of 22493 kD. The homology tree analysis showed that the pig Akirin2 has closer genetic relationships and distance with the known mammalian Akirin2. Real time quantitative PCR analysis showed that the porcine Akirin2 transcript was most abundant in the lung, followed by the skeletal muscle, heart, liver, fat, thymus, lymph node, small intestine, kidney, and spleen. Overexpression of porcine Akirin2 increased expression of IL-6 in porcine jejunal epithelial cell line IPEC-J2 cells. Our data suggest that porcine Akirin2 could play an important role in intestinal immune regulation.

Retraction Note to: Molecular Cloning, Sequence Characterization, and Tissue Expression Analysis of Hi-Line Brown Chicken Akirin2

Akirins are novel important nuclear proteins able to modulate transcriptional activities in a gene-specific manner. Akirin2 is an important gene related to immune responses, it is necessary to isolate the akirin2 gene from chicken because it may be associated with vaccine and enhancement of immune response. In this study, a Hi-Line Brown chicken homolog of the vertebrate akirin2 gene was cloned, sequenced, and characterized. The akirin2 full-length coding sequence (CDS) consisted of 576nt and encoded 191 amino acids with a molecular weight of 21.58 kD. The COOH-terminal alpha-helix region was well conserved between chicken and other animals. RT-PCR analysis showed that the akirin2 transcripts were constitutively expressed in 16 tissues tested. Several microRNA target sites were predicted in the CDS of chicken akirin2 gene. We presume that Akirin2 protein may be used as a new-type immunopotentiator in poultry immune system in the future.

RETRACTED ARTICLE: Molecular Cloning, Sequence Characterization, and Tissue Expression Analysis of Hi-Line Brown Chicken Akirin2

Akirins are novel important nuclear proteins able to modulate transcriptional activities in a gene-specific manner. Akirin2 is an important gene related to immune responses, it is necessary to isolate the akirin2 gene from chicken because it may be associated with vaccine and enhancement of immune response. In this study, a Hi-Line Brown chicken homolog of the vertebrate akirin2 gene was cloned, sequenced, and characterized. The akirin2 full-length coding sequence (CDS) consisted of 576nt and encoded 191 amino acids with a molecular weight of 21.58 kD. The COOH-terminal alpha-helix region was well conserved between chicken and other animals. RT-PCR analysis showed that the akirin2 transcripts were constitutively expressed in 16 tissues tested. Several microRNA target sites were predicted in the CDS of chicken akirin2 gene. We presume that Akirin2 protein may be used as a new-type immunopotentiator in poultry immune system in the future.