Associations between AT-rich interactive domain 5B gene polymorphisms and risk of childhood acute lymphoblastic leukemia: a meta-analysis

Genome-wide association with footrot in hair and wool sheep

Ovine footrot is an infectious disease with important contributions from Dichelobacter nodosus and Fusobacterium necrophorum. Footrot is characterized by separation of the hoof from underlying tissue, and this causes severe lameness that negatively impacts animal wellbeing, growth, and profitability. Large economic losses result from lost production as well as treatment costs, and improved genetic tools to address footrot are a valuable long-term goal. Prior genetic studies had examined European wool sheep, but hair sheep breeds such as Katahdin and Blackbelly have been reported to have increased resistance to footrot, as well as to intestinal parasites. Thus, footrot condition scores were collected from 251 U.S. sheep including Katahdin, Blackbelly, and European-influenced crossbred sheep with direct and imputed genotypes at OvineHD array (>500,000 single nucleotide polymorphism) density. Genome-wide association was performed with a mixed model accounting for farm and principal components derived from animal genotypes, as well as a random term for the genomic relationship matrix. We identified three genome-wide significant associations, including SNPs in or near GBP6 and TCHH. We also identified 33 additional associated SNPs with genome-wide suggestive evidence, including a cluster of 6 SNPs in a peak near the genome-wide significance threshold located near the glutamine transporter gene SLC38A1. These findings suggest genetic susceptibility to footrot may be influenced by genes involved in divergent biological processes such as immune responses, nutrient availability, and hoof growth and integrity. This is the first genome-wide study to investigate susceptibility to footrot by including hair sheep and also the first study of any kind to identify multiple genome-wide significant associations with ovine footrot. These results provide a foundation for developing genetic tests for marker-assisted selection to improve resistance to ovine footrot once additional steps like fine mapping and validation are complete.

Identification of Potential Treatments for Acute Lymphoblastic Leukemia through Integrated Genomic Network Analysis

The advancement of high-throughput sequencing and genomic analysis revealed that acute lymphoblastic leukemia (ALL) is a genetically heterogeneous disease. The abundance of such genetic data in ALL can also be utilized to identify potential targets for drug discovery and even drug repurposing. We aimed to determine potential genes for drug development and further guide the identification of candidate drugs repurposed for treating ALL through integrated genomic network analysis. Genetic variants associated with ALL were retrieved from the GWAS Catalog. We further applied a genomic-driven drug repurposing approach based on the six functional annotations to prioritize crucial biological ALL-related genes based on the scoring system. Lastly, we identified the potential drugs in which the mechanisms overlapped with the therapeutic targets and prioritized the candidate drugs using Connectivity Map (CMap) analysis. Forty-two genes were considered biological ALL-risk genes with ARID5B topping the list. Based on potentially druggable genes that we identified, palbociclib, sirolimus, and tacrolimus were under clinical trial for ALL. Additionally, chlorprothixene, sirolimus, dihydroergocristine, papaverine, and tamoxifen are the top five drug repositioning candidates for ALL according to the CMap score with dasatinib as a comparator. In conclusion, this study determines the practicability and the potential of integrated genomic network analysis in driving drug discovery in ALL.

The Role of ARID5B in Acute Lymphoblastic Leukemia and Beyond

Acute lymphoblastic leukemia (ALL) is the most common malignancy in children with distinct characteristics among different subtypes. Although the etiology of ALL has not been fully unveiled, initiation of ALL has been demonstrated to partly depend on genetic factors. As indicated by several genome wide association studies (GWASs) and candidate gene analyses, ARID5B, a member of AT-rich interactive domain (ARID) protein family, is associated with the occurrence and prognosis of ALL. However, the mechanisms by which ARID5B genotype impact on the susceptibility and treatment outcome remain vague. In this review, we outline developments in the understanding of ARID5B in the susceptibility of ALL and its therapeutic perspectives, and summarize the underlying mechanisms based on the limited functional studies, hoping to illustrate the possible mechanisms of ARID5B impact and highlight the potential treatment regimens.

Genetic polymorphisms of ARID5B rs7089424 and rs10994982 are associated with B-lineage ALL susceptibility in Chinese pediatric population

BACKGROUND

Several ARID5B single nucleotide polymorphisms (SNPs) were confirmed to be significantly associated with the susceptibility of childhood acute lymphoblastic leukemia (ALL) based on Caucasian populations in previous studies. Similar investigations in Asian populations were less. The aim of this study is to explore the relationship between ARID5B SNPs rs7089424, rs10994982, and the risk of ALL in Chinese pediatric population.

METHODS

A total of 190 pediatric ALL patients and 270 controls were enrolled in this study. PCR amplification combined with mass spectrometry were used to evaluate the genotypes of ARID5B rs7089424 and rs10994982. χ test was used in allele frequencies and genotype distributions of the SNPs for analyzing statistical differences between patients and controls.

RESULTS

There were significant differences in the risk allele frequencies of ARID5B rs7089424 and rs10994982 between B-lineage ALL (B-ALL) patients and controls (rs7089424, G allele: p = 0.001; rs10994982, A allele: p = 0.000). The genotype distributions of ARID5B rs7089424 and rs10994982 were also statistically different in B-ALL patients compared with controls (rs7089424, p = 0.004; rs10994982, p = 0.001). Further analyzing the relevance of ARID5B rs7089424 and rs10994982 genotypes to clinical risk classification of ALL showed GG genotype of rs7089424 and AA genotype of rs10994982 were strikingly correlated with the medium-risk and low-risk groups of B-ALL. Finally, GG and GT genotypes of rs7089424 and AA genotype of rs10994982 seemed to be responsible for the hyperdiploid subtype susceptibility of childhood B-ALL.

CONCLUSION

ARID5B rs7089424 and rs10994982 might serve as genetic susceptibility markers for B-ALL in Chinese pediatric population. Moreover, the two ARID5B SNPs are associated with the risk of B-hyperdiploid ALL, which had a better therapeutic response than other ALL subtypes.

ARID5B gene polymorphisms and the risk of childhood acute lymphoblastic leukemia: a meta-analysis

Genome-wide association studies have implicated several single-nucleotide polymorphisms (SNPs) in the AT-rich interactive domain 5B (ARID5B) gene in children with ALL; however, whether ARID5B variants (rs10821936, rs10994982, rs7089424) are associated with childhood ALL remains controversial. We performed this study to obtain more conclusive results. Eligible studies were searched in PubMed, Web of Science, and EMBASE. Odds ratios and 95% confidence intervals were calculated. A total of 26 studies were included. Analyses stratified by ethnicity revealed that three polymorphisms are significantly associated with the odds of childhood ALL in Caucasians, and rs10994982 and rs7089424 with the odds of childhood ALL in Asian populations. Furthermore, subtype analyses provided strong evidence that the three polymorphisms are highly associated with the risk of B-cell ALL. Our findings indicate that the ARID5B variants (rs10821936, rs10994982, rs7089424) are significantly associated with the risk of childhood ALL.

Regional evaluation of childhood acute lymphoblastic leukemia genetic susceptibility loci among Japanese

Genome-wide association studies (GWAS) performed mostly in populations of European and Hispanic ancestry have confirmed an inherited genetic basis for childhood acute lymphoblastic leukemia (ALL), but these associations are less clear in other races/ethnicities. DNA samples from ALL patients (aged 0–19 years) previously enrolled onto a Tokyo Children’s Cancer Study Group trial were collected during 2013–2015, and underwent single nucleotide polymorphism (SNP) microarray genotyping resulting in 527 B-cell ALL for analysis. Cases and control data for 3,882 samples from the Nagahama Study Group and Aichi Cancer Center Study were combined, and association analyses across 10 previous GWAS-identified regions were performed after targeted SNP imputation. Linkage disequilibrium (LD) patterns in Japanese and other populations were evaluated using the varLD score based on 1000 Genomes data. Risk associations for ARID5B (rs10821936, OR = 1.84, P = 6 × 10⁻¹⁷) and PIP4K2A (rs7088318, OR = 0.76, P = 2 × 10⁻⁴) directly transferred to Japanese, and the IKZF1 association was detected by an alternate SNP (rs1451367, OR = 1.52, P = 2 × 10⁻⁶). Marked regional LD differences between Japanese and Europeans was observed for most of the remaining loci for which associations did not transfer, including CEBPE, CDKN2A, CDKN2B, and ELK3. This study represents a first step towards characterizing the role of genetic susceptibility in childhood ALL risk in Japanese.

ARID5B, CEBPE and PIP4K2A Germline Genetic Polymorphisms and Risk of Childhood Acute Lymphoblastic Leukemia in Mexican Patients: A MIGICCL Study

BACKGROUND AND AIMS

Childhood acute lymphoblastic leukemia (ALL) is the leading cause of childhood cancer-related deaths worldwide. Multiples studies have shown that ALL seems to be originated by an interaction between environmental and genetic susceptibility factors. The ARID5B polymorphisms are among the most reproducible ALL associated-risk alleles in different populations. The aim of the present study was to examine the contribution of ARID5B, CEBPE, and PIP4K2 risk alleles for the development of ALL in children from Mexico City and Yucatan, Mexico.

METHODS

A study was conducted with a total of 761 unrelated subjects. Two hundred eighty five ALL cases (111 from Yucatan and 174 from Mexico City) and 476 healthy subjects. Genotyping included the rs7088318 (PIP4K2A), rs10821936 (ARID5B), rs7089424 (ARID5B) and rs2239633 (CEBPE) polymorphisms.

RESULTS

Associations between ALL and rs10821936 and rs7089424 ARID5B SNPs were found (OR = 1.9, 95% CI (1.5-2.4) and OR = 2.0, 95% CI (1.6-2.5), respectively). Moreover, a higher risk was observed in the homozygous risk genotypes of carriers from Mexico City (OR = 3.1, 95% CI (2.0-4.9) and OR 3.1, CI 95% (2.0-4.8), respectively). Otherwise, the rs7088318 (PIP4K2A) and rs2239633 (CEBPE) polymorphisms were not associated with ALL risk.

CONCLUSIONS

Our analysis suggests that ARID5B confers risk for childhood ALL in a Mexican population.

[Acute lymphoblastic leukemia: a genomic perspective]

In parallel to the human genome sequencing project, several technological platforms have been developed that let us gain insight into the genome structure of human entities, as well as evaluate their usefulness in the clinical approach of the patient. Thus, in acute lymphoblastic leukemia (ALL), the most common pediatric malignancy, genomic tools promise to be useful to detect patients at high risk of relapse, either at diagnosis or during treatment (minimal residual disease), and they also increase the possibility to identify cases at risk of adverse reactions to chemotherapy. Therefore, the physician could offer patient-tailored therapeutic schemes. A clear example of the useful genomic tools is the identification of single nucleotide polymorphisms (SNPs) in the thiopurine methyl transferase (TPMT) gene, where the presence of two null alleles (homozygous or compound heterozygous) indicates the need to reduce the dose of mercaptopurine by up to 90% to avoid toxic effects which could lead to the death of the patient. In this review, we provide an overview of the genomic perspective of ALL, describing some strategies that contribute to the identification of biomarkers with potential clinical application.

Downregulation of SATB1 increases the invasiveness of Jurkat cell via activation of the WNT/β-catenin signaling pathway in vitro

Special AT-rich sequence-binding protein-1 (SATB1) is critical for genome organizer that reprograms chromatin organization and transcription profiles, and associated with tumor growth and metastasis in several cancer types. Many studies suggest that SATB1 overexpression is an indicator of poor prognosis in various cancers, such as breast cancer, malignant cutaneous melanoma, and liver cancer. However, their expression patterns and function values for adult T cell leukemia (ATL) are still largely unknown. The aim of this study is to examine the levels of SATB1 in ATL and to explore its function and mechanisms in Jurkat cell line. Here, we reported that SATB1 expressions were decreased in ATL cells (p < 0.001) compared with normal controls. Knockdown of SATB1 expression significantly enhanced invasion of Jurkat cell in vitro. Furthermore, knockdown of SATB1 gene enhances β-catenin nuclear accumulation and transcriptional activity and thus may increase the invasiveness of Jurkat cell through the activation of Wnt/β-catenin signaling pathway in vitro.