Constitutional and acquired genetic variants in ARID5B in pediatric B-cell precursor acute lymphoblastic leukemia.

Constitutional polymorphisms in ARID5B are associated with an increased risk of developing high hyperdiploid (HeH; 51-67 chromosomes) pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL). Here, we investigated constitutional and somatic ARID5B variants in 1335 BCP ALL cases from five different cohorts, with a particular focus on HeH cases. In 353 HeH ALL that were heterozygous for risk alleles and trisomic for chromosome 10, where ARID5B is located, a significantly higher proportion of risk allele duplication was seen for the SNPs rs7090445 (p = 0.009), rs7089424 (p = 0.005), rs7073837 (p = 0.03), and rs10740055 (p = 0.04). Somatic ARID5B deletions were seen in 16/1335 cases (1.2%), being more common in HeH than in other genetic subtypes (2.2% vs. 0.4%; p = 0.002). The expression of ARID5B in HeH cases with genomic deletions was reduced, consistent with a functional role in leukemogenesis. Whole-genome sequencing and RNA-sequencing in HeH revealed additional somatic events involving ARID5B, resulting in a total frequency of 3.6% of HeH cases displaying a somatic ARID5B aberration. Overall, our results show that both constitutional and somatic events in ARID5B are involved in the leukemogenesis of pediatric BCP ALL, particularly in the HeH subtype.

A hybrid approach to assess the structural impact of long noncoding RNA mutations uncovers key NEAT1 interactions in colorectal cancer.

Long noncoding RNAs (lncRNAs) are emerging players in cancer and they entail potential as prognostic biomarkers or therapeutic targets. Earlier studies have identified somatic mutations in lncRNAs that are associated with tumor relapse after therapy, but the underlying mechanisms behind these associations remain unknown. Given the relevance of secondary structure for the function of some lncRNAs, some of these mutations may have a functional impact through structural disturbance. Here, we examined the potential structural and functional impact of a novel A > G point mutation in NEAT1 that has been recurrently observed in tumors of colorectal cancer patients experiencing relapse after treatment. Here, we used the nextPARS structural probing approach to provide first empirical evidence that this mutation alters NEAT1 structure. We further evaluated the potential effects of this structural alteration using computational tools and found that this mutation likely alters the binding propensities of several NEAT1-interacting miRNAs. Differential expression analysis on these miRNA networks shows upregulation of Vimentin, consistent with previous findings. We propose a hybrid pipeline that can be used to explore the potential functional effects of lncRNA somatic mutations.

Analytical application of flower-shaped nickel nanomaterial for the preconcentration of manganese in domestic wastewater samples.

In this study, detection sensitivity of the conventional flame atomic absorption spectrophotometer (FAAS) for the determination of manganese (Mn2+) was enhanced by employing a preconcentration method from wastewater samples. Flower-shaped Ni(OH)2 nanomaterials were synthesized and used as sorbent material in preconcentration procedure. With the aim of attaining optimum experimental conditions, effective parameters of extraction method were optimized and these included pH of buffer solution, desorption solvent concentration and volume, mixing type and period, nanoflower amount, and sample volume. The detection limit of the optimized method was determined to be 2.2 µg L-1, and this correlated to about 41-fold enhancement in detection power relative to direct FAAS measurement. Domestic wastewater was used to test the feasibility of the proposed method to real samples by performing spike recovery experiments. The wastewater sample was spiked at four different concentrations of manganese, and the percent recoveries determined were in the range of 95-120%.

Characterizing the allele-specific gene expression landscape in high hyperdiploid acute lymphoblastic leukemia with BASE.

Somatic copy number variations (CNVs), including abnormal chromosome numbers and structural changes leading to gain or loss of genetic material, play a crucial role in initiation and progression of cancer. CNVs are believed to cause gene dosage imbalances and modify cis-regulatory elements, leading to allelic expression imbalances in genes that influence cell division and thereby contribute to cancer development. However, the impact of CNVs on allelic gene expression in cancer remains unclear. Allele-specific expression (ASE) analysis, a potent method for investigating genome-wide allelic imbalance profiles in tumors, assesses the relative expression of two alleles using high-throughput sequencing data. However, many existing methods for gene-level ASE detection rely on only RNA sequencing data, which present challenges in interpreting the genetic mechanisms underlying ASE in cancer. To address this issue, we developed a robust framework that integrates allele-specific copy number calls into ASE calling algorithms by leveraging paired genome and transcriptome data from the same sample. This integration enhances the interpretability of the genetic mechanisms driving ASE, thereby facilitating the identification of driver events triggered by CNVs in cancer. In this study, we utilized BASE to conduct a comprehensive analysis of ASE in high hyperdiploid acute lymphoblastic leukemia (HeH ALL), a prevalent childhood malignancy characterized by gains of chromosomes X, 4, 6, 10, 14, 17, 18, and 21. Our analysis unveiled the comprehensive ASE landscape in HeH ALL. Through a multi-perspective examination of HeH ASEs, we offer a systematic understanding of how CNVs impact ASE in HeH, providing valuable insights to guide ASE studies in cancer.

Implementation of simple and effective fine droplet formation-based spray-assisted liquid phase microextraction for the simultaneous determination of twenty-nine endocrine disruptor compounds and pesticides in rock, soil, water, moss, and feces samples from antarctica using gas chromatography-mass spectrometry.

This study established the simultaneous determination of the selected endocrine-disrupting compounds (EDCs) and pesticides in rock, soil, water, moss, and feces samples collected from the Antarctic region. The spray-assisted droplet formation-based liquid phase microextraction (SADF-LPME) coupled to GC-MS system was developed and validated for the screening and monitoring of 29 selected EDCs and pesticides. Binary solvent system, 1:1 (v/v) dichlormethane: 1,2-dichloroethane mixture was employed as an extraction solvent and sprayed onto sample or standard solutions using a straightforward and practical spray apparatus. The factors affecting the extraction process such as extraction solvent type and ratio, extraction solvent volume (spray repetition), vortexing period, and sample pH were properly optimized. Analytical figures of the merit of the method were recorded under the optimal extraction/chromatographic conditions. The LOD, LOQ, and enhancement factor were in the range of 1.0 to 6.6 ng/g, 3.2 to 22.1 ng/g, and 3.7 to 158.9, respectively. The method demonstrated a good linear working range for all the selected analytes with proper coefficients of determination. The usability and reliability of the microextraction strategy was confirmed using seawater, moss, and soil samples, and the %recoveries were within an acceptable range (> 70%) for all examined samples. The environmental samples collected from the Horseshoe and Faure Islands of the Antarctica region were analyzed to assess the potential pollution of EDCs and pesticides. This method has the potential to be employed for the analysis of EDCs in routine analytical laboratories and for controlling and screening the organic pollutant content of different environmental samples.