Aberrantly low STAT3 and STAT5 responses are associated with poor outcome and an inflammatory gene expression signature in pediatric acute myeloid leukemia.

The relapse rate for children with acute myeloid leukemia is nearly 40% despite aggressive chemotherapy and often stem cell transplant. We sought to understand how environment-induced signaling responses are associated with clinical response to treatment. We previously reported that patients whose AML cells showed low G-CSF-induced STAT3 activation had inferior event-free survival compared to patients with stronger STAT3 responses. Here, we expanded the paradigm to evaluate multiple signaling parameters induced by a more physiological stimulus. We measured STAT3, STAT5 and ERK1/2 responses to G-CSF and to stromal cell-conditioned medium for 113 patients enrolled on COG trials AAML03P1 and AAML0531. Low inducible STAT3 activity was independently associated with inferior event-free survival in multivariate analyses. For inducible STAT5 activity, those with the lowest and highest responses had inferior event-free survival, compared to patients with intermediate STAT5 responses. Using existing RNA-sequencing data, we compared gene expression profiles for patients with low inducible STAT3/5 activation with those for patients with higher inducible STAT3/5 signaling. Genes encoding hematopoietic factors and mitochondrial respiratory chain subunits were overexpressed in the low STAT3/5 response groups, implicating inflammatory and metabolic pathways as potential mechanisms of chemotherapy resistance. We validated the prognostic relevance of individual genes from the low STAT3/5 response signature in a large independent cohort of pediatric AML patients. These findings provide novel insights into interactions between AML cells and the microenvironment that are associated with treatment failure and could be targeted for therapeutic interventions.

Differential gene expression in the peripheral blood of Chinese Sanhe cattle exposed to severe cold stress.

Livestock is an important food resource for the inhabitants of cold regions, such as northern Asia and alpine regions, where agriculture is limited. In these regions, cold stress largely affects livestock production, thereby reducing the productivity and survival of animals. Despite the importance of breeding cold-tolerant animals, few studies have investigated the effects of cold stress on cattle. Furthermore, whether severe cold stress alters gene expression or affects molecular genetic mechanisms remains unknown. Thus, we investigated gene expression changes in the peripheral blood samples of the Chinese Sanhe cattle exposed to severe cold. A total of 193 genes were found to exhibit significant alteration in expression (P < 0.05; fold change > 1.3), with 107 genes showing upregulation and 86 showing downregulation after cold exposure. The differences in the expression of 10 selected genes were further validated by real-time qRT-PCR. Further analyses showed that these differentially expressed genes (DEGs) were predominantly associated with important biological pathways and gene networks, such as lipid metabolism and cell death and survival, which are potentially associated with severe cold-stress resistance. Identification and description of these cold stress-induced DEGs might lead to the discovery of novel blood biomarkers that could be used to assess cold-stress resistance in cattle. To our knowledge, this is the first genomic evidence of differences in the transcript expression pattern in cattle exposed to severe cold stress. Our findings provide insights on the potential molecular mechanisms underlying cold-stress response in cattle.

Orthogonal design in the optimization of a start codon targeted (SCoT) PCR system in Roegneria kamoji Ohwi.

Roegneria kamoji Ohwi is an excellent forage grass due to its high feeding value and high resistance to some biotic and abiotic stresses. However, the start codon targeted (SCoT) polymorphism has not been conducted on R. kamoji. In this study, an orthogonal L16 (45) design was employed to investigate the effects of five factors (Mg2+, dNTPs, Taq DNA polymerase, primer, and template DNA) on the polymerase chain reaction (PCR) to determine the optimal SCoT-PCR system for R. kamoji. The results showed that the most suitable conditions for SCoT-PCR in R. kamoji included 1.5 mM Mg2+, 0.15 mM dNTPs, 1.0 U Taq DNA polymerase, 0.4 pM primer, and 40 ng template DNA. SCoT primers 39 and 41 were used to verify the stability of the optimal reaction system, and amplification bands obtained from diverse samples were found to be clear, rich, and stable in polymorphisms, indicating that this reaction system can be used for SCoT-PCR analysis of R. kamoji. We have developed a simple and rapid way to study the mutual effects of factors and to obtain positive results through the use of an orthogonal design L16 (45) to optimize the SCoT-PCR system. This method may provide basic information for molecular marker-assisted breeding and analyses of genetic diversity in R. kamoji.

Identification of single nucleotide polymorphisms in the ASB15 gene and their associations with chicken growth and carcass traits.

ASB15 is a member of the ankyrin repeat and suppressor of cytokine signaling box family, and is predominantly expressed in skeletal muscle. In the present study, an F2 resource population of Gushi chickens crossed with Anka broilers was used to investigate the genetic effects of the chicken ASB15 gene. Two single nucleotide polymorphisms (SNPs) (rs315759231 A>G and rs312619270 T>C) were identified in exon 7 of the ASB15 gene using forced chain reaction-restriction fragment length polymorphism and DNA sequencing. One was a missense SNP (rs315759231 A>G) and the other was a synonymous SNP (rs312619270 T>C). The rs315759231 A>G polymorphism was significantly associated with body weight at birth, 12-week body slanting length, semi-evisceration weight, evisceration weight, leg muscle weight, and carcass weight (P < 0.05). The rs312619270 T>C polymorphism was significantly associated with body weight at birth, 4, 8, and 12-week body weight, 8-week shank length, 12-week breast bone length, 8 and 12-week body slanting length, breast muscle weight, and carcass weight (P < 0.05). Our results suggest that the ASB15 gene profoundly affects chicken growth and carcass traits.

Relationship between zinc finger protein 36 (ZFP36) gene polymorphisms and obstructive sleep apnea.

Recent data have indicated that inflammation may have an important correlation with obstructive sleep apnea (OSA). Studies have indicated a relationship between OSA and TNF-α gene polymorphisms. Zinc finger protein 36 (ZFP36) regulates TNF-α mRNAs. However, ZFP36 gene polymorphisms have not been investigated in OSA. Therefore, we conducted the present case-control study to assess whether variances in ZFP36 gene polymorphisms account for differences in TNF-α levels in patients with moderate-to-severe OSA. This case-control study aims to investigate the relationship between genetic variations in the ZFP36 gene and moderate-to-severe OSA. Three common single nucleotide polymorphisms of the ZFP36 gene (rs251864, rs3746083, and rs17879933) were evaluated in a group of patients with moderate-to-severe OSA (N = 408) and in a control group (N = 394) by using TaqMan polymerase chain reaction analysis. The moderate-to-severe OSA group and the control group exhibited significant differences in the distributions of rs251864 and rs17879933 genotypes and alleles (P < 0.05). TNF-α levels were significantly different not only among the three rs251864 genotypes but also between the II genotype and the DD + ID genotypes of rs17879933. However, no significant differences in sleep apnea parameters in the three ZFP36 gene polymorphisms were observed. Logistic regression analyses demonstrated that TNF-α and the three ZFP36 gene polymorphisms were not independently associated with OSA. ZFP36 might be involved in TNF-α regulation. However, ZFP36 gene variants were not independent risk factors for moderate-to-severe OSA.

Molecular cloning and functional characterization of a novel CBL-interacting protein kinase NtCIPK2 in the halophyte Nitraria tangutorum.

CBL-interacting protein kinases (CIPKs) mediate many plant responses to abiotic stress. However, their functions are poorly understood in halophytes. In this study, we isolated a CIPK gene, NtCIPK2, from the halophyte Nitraria tangutorum. By sequence alignment and the construction of a phylogenetic tree, we found that NtCIPK2 is similar to CIPK2 proteins from other plants, and contains conserved domains and motifs. The promoter of NtCIPK2 harbors many cis-acting elements that might be recognized and bound by transcription factors that are related to hormones and stress responses. NtCIPK2 was ubiquitously and robustly expressed in all tested organs, and was induced by salinity, drought, heat, and cold stress. The overexpression of NtCIPK2 in Escherichia coli caused better growth against high salinity, alkalinity, and osmotic conditions, dehydration, and extreme temperatures (i.e., heat and cold) compared to the control. Thus, NtCIPK2 is a candidate gene that might improve the stress tolerance of crops and herbs through genetic manipulation.

Aberrant promoter methylation of the CD4 gene in peripheral blood cells of mastitic dairy cows.

Bovine mastitis is the most common and costly disease of dairy cattle. Cluster of differentiation 4 (CD4) is closely related to the immune response in mastitis. We quantified promoter CpG methylation levels of the CD4 gene in Chinese Holsteins with clinical mastitis (CM) and in healthy controls; these levels were quantitatively detected with bisulfite pyrosequencing assays and confirmed by cloning sequencing. We found that the bovine CD4 promoter had 16% more methyl groups in the cows with CM (75.0 ± 5.8%) compared to the controls (59.0 ± 8.5%). The decreased expression level of CD4 in CM cows may be downregulated by the increased DNA methylation levels in the CD4 promoter. Two-dimensional hierarchical clustering analyses showed large differences in promoter CD4 methylation between mastitic and healthy cows; the dendrogram clearly distinguished the cows with clinical mastitis from healthy controls based on methylation levels. The DNA methylation level of the CD4 gene was strongly influenced by mastitis status in all comparisons. We suggest that the DNA methylation level of the CD4 promoter can be used as a molecular marker for clinical mastitis in dairy cows.

Inheritance of cytosine methylation patterns in purebred versus hybrid chicken lines.

We used methylation-sensitive amplified polymorphism to examine DNA methylation levels and CCGG patterns in parents and offsprings of 3 groups of adult chickens, purebred White Leghorn (AA), White Plymouth Rock (EE), and crossbred individuals (EA) using 10 primer combinations. We found that about 66% of the cytosines at CCGG sites were not methylated. Fully methylated sites were less frequent than hemi-methylated sites in the chicken genome; these frequencies were different from those of plants. We observed that the probability that the offspring would inherit the methylation pattern for any given site from the parents was 88%; consequently, unexpected methylation patterns in offspring occurred at a rate of about 12%. The methylation degree in offspring was lower than in parents, and there were more sites with altered methylation patterns in EA crossbreds compared with AA and EE purebreds. Seven differentially methylated fragments between parental lines and their offspring were isolated, sequenced, and characterized, 4 of which were located in the coding regions. We conclude that most of the methylation status is transferred from parents to offspring in chickens, and that there are differences in the inheritance of methylation status in purebred versus crossbred offspring. We also concluded that methylation-sensitive amplified polymorphism is highly efficient for large-scale detection of cytosine methylation in the chicken genome.

Novel single nucleotide polymorphisms of the bovine methyltransferase 3b gene and their association with meat quality traits in beef cattle.

DNA methylation is essential for adipose deposition in mammals. We screened SNPs of the bovine DNA methyltransferase 3b (DNMT3b) gene in Snow Dragon beef, a commercial beef cattle population in China. Nine SNPs were found in the population and three of six novel SNPs were chosen for genotyping and analyzing a possible association with 16 meat quality traits. The frequencies of the alleles and genotypes of the three SNPs in Snow Dragon beef were similar to those in their terminal-paternal breed, Wagyu. Association analysis disclosed that SNP1 was not associated with any of the traits; SNP2 was significantly associated with lean meat color score and chuck short rib score, and SNP3 had a significant effect on dressing percentage and back-fat thickness in the beef population. The individuals with genotype GG for SNP2 had a 25.7% increase in lean meat color score and a 146% increase in chuck short rib score, compared with genotype AA. The cattle with genotype AG for SNP3 had 35.7 and 24% increases in dressing percentage and 28.8 and 29.2% increases in back-fat thickness, compared with genotypes GG and AA, respectively. Genotypic combination analysis revealed significant interactions between SNP1 and SNP2 and between SNP2 and SNP3 for the traits rib-eye area and live weight. We conclude that there is considerable evidence that DNMT3b is a determiner of beef quality traits.