DNA, Volume 4, Issue 3 (September 2024) – 11 articles

Thyroid gland carcinoma (TGC), though only 1% of all carcinomas, is the most common endocrine neoplasm with an increasing incidence since the 1990s. Of the TGC types, papillary thyroid carcinoma (PTC) is the most common and has the best overall prognosis. Although primarily studied in various neural spectrum disorders, monoamine oxidase A (MAOA) may also contribute to cancer occurrence. This case control study assessed the prevalence of MAOA uVNTR polymorphism in PTC patients, compared its frequency with a healthy control, and assessed the variant’s impact on clinical features. The research participants consisted of 30 PTC patients (20 female, 10 male) over 18 years old who underwent thyroidectomy and radioiodine therapy at a Federal District private clinic and 30 paired and unrelated healthy volunteers (18 female, 12 male). The most frequent MAOA uVNTR alleles were 3R and 4R. Although no significant difference was detected in the genotypic distribution nor the PTC patients’ thyroglobulin, thyroid-stimulating hormone, and antithyroglobulin levels; body mass indexes; administered radiopharmaceutical (131I) doses; or biological sex, the presence of at least one 3R allele was associated with a larger tumor size (T3 + T4 staging). Thus, the 3R allele seems to be associated with PTC pathogenesis severity. Full article

Diffuse large B cell lymphoma, not otherwise specified (DLBCL, NOS) is the most common type of non-Hodgkin lymphoma (NHL). Significant efforts have been focused on utilizing advanced genomic technologies to further subclassify DLBCL, NOS into clinically relevant subtypes. These efforts have led to the implementation of novel algorithms to support optimal risk-oriented therapy and improvement in the overall survival of DLBCL patients. The pathogenesis of DLBCL at the molecular level indicates copy number variation (CNV) as one of the major forms of genetic alterations in the somatic mutational landscape. Random deregulation that results in complex breaks of chromosomes and restructuring of shattered chromosomal segments is called chromothripsis. Gene expression changes influenced by chromothripsis have been reported in cancer and congenital diseases. This chaotic phenomenon results in complex CNV, gene fusions, and amplification and loss of tumor suppressor genes. We present herein a summary of the most clinically relevant genomic aberrations, with particular focus on copy number aberrations in a case that highlights DLBCL, NOS arising from relapsed Hodgkin lymphoma. The focus of our study was to understand the relationship between the clinical, morphological, and genomic abnormalities in DLBCL, NOS through multiple techniques for therapeutic considerations. Full article

DNA-based biosensors have emerged as cutting-edge tools with significant potential to revolutionize medical diagnostics and environmental monitoring. These biosensors leverage the specificity and sensitivity of DNA interactions to detect a wide range of biomolecular targets, making them ideal for early disease detection, genetic analysis, and real-time environmental assessment. Despite their promising applications, several challenges impede their widespread adoption. Key issues include the stability of DNA molecules, which are prone to degradation under environmental conditions, and the need for enhanced specificity and sensitivity to accurately detect target molecules in complex samples. Technological hurdles in miniaturizing and integrating these sensors into portable, user-friendly devices, along with ethical concerns regarding data privacy and the misuse of genetic information, also pose significant barriers. This systematic review examines the current state of DNA-based biosensor technology, highlights the main challenges, and discusses potential strategies to overcome these obstacles. By addressing these multifaceted issues through ongoing research and innovation, DNA-based biosensors can be developed into robust tools for various applications, contributing to improved public health outcomes and environmental sustainability. Full article

The detection of genetic alterations in patients with acute leukemias is essential for the targeting of more specific and effective therapies. Therefore, the aim of this study was to compare the sensitivity of Nested-PCR and RT-qPCR techniques in the detection of genetic alterations in patients with acute leukemias. This study included samples from 117 patients treated at the Fortaleza General Hospital. All samples were submitted to analysis using the Nested-PCR and the RT-qPCR techniques. Acute Myeloid Leukemia (AML) patients’ samples were submitted to the analysis of the following alterations: FLT3-ITD, RUNX1::RUNX1T1, CBFB::MYH11 and PML::RARA; meanwhile, BCR::ABL1, TCF3::PBX1, KMT2A::AFF1, ETV6::RUNX1, and STIL::TAL1 fusions were investigated in the Acute Lymphoblastic Leukemia (ALL) patients’ samples. Throughout the study, 77 patients were diagnosed with AML and 40 with ALL. Among the 77 AML patients, FLT3-ITD, RUNX1::RUNX1T1, PML::RARA, and CBFB::MYH11 were detected in 4, 7, 10 and 8 patients, respectively. Among the 40 ALL patients, the presence of 23 patients with BCR::ABL1 translocation and 9 patients with TCF3::PBX1 translocation was observed through the RT-qPCR methodology. Overall, the present study demonstrated that the RT-qPCR technique presented a higher sensitivity when compared to the Nested-PCR technique at the time of diagnosis of the acute leukemia samples studied. Full article

The global prevalence of obesity among adults, adolescents, and children has increased to alarming levels, making this disease a serious public health problem. The etiology of obesity is complex and multifactorial. Currently, epigenetic alterations are being investigated to understand the mechanisms of interaction between genes and environmental and behavioral risk factors involved in the genesis of obesity. In this study, we examined the association of the DNA methyltransferase 3 (DNMT3B) gene-149 C>T variant (rs2424913) genotypes with global DNA methylation and the changes in anthropometric parameters in a cohort of 171 children followed from birth to 12 years old. Genotypes were obtained using real-time polymerase chain reaction, and global DNA methylation was measured in blood samples collected at 4 years old through enzyme-linked immunosorbent assays. Our results showed that the TT genotype is associated with an increase in global methylation levels at 4 years old and higher changes in body mass index, waist circumference, subscapular subcutaneous fat, body fat mass, body lean mass, and basal metabolic rate from 4 to 12 years. Our results suggest that this promoter DNMT3B gene variant and DNA methylation can be factors relevant to the increased risk of children developing obesity at an early age. Full article

The three 31 nucleotide minihelix tRNA evolution theorem describes the evolution of type I and type II tRNAs to the last nucleotide. In databases, type I and type II tRNA V loops (V for variable) were improperly aligned, but alignment based on the theorem is accurate. Type II tRNA V arms were a 3′-acceptor stem (initially CCGCCGC) ligated to a 5′-acceptor stem (initially GCGGCGG). The type II V arm evolved to form a stem–loop–stem. In Archaea, tRNA^Leu and tRNA^Ser are type II. In Bacteria, tRNA^Leu, tRNA^Ser, and tRNA^Tyr are type II. The trajectory of the type II V arm is determined by the number of unpaired bases just 5′ of the Levitt base (V_max). For Archaea, tRNA^Leu has two unpaired bases, and tRNA^Ser has one unpaired base. For Bacteria, tRNA^Tyr has two unpaired bases, tRNA^Leu has one unpaired base, and tRNA^Ser has zero unpaired bases. Thus, the number of synonymous type II tRNA sets is limited by the possible trajectory set points of the arm. From the analysis of aminoacyl-tRNA synthetase structures, contacts to type II V arms appear to adjust allosteric tension communicated primarily via tRNA to aminoacylating and editing active sites. To enhance allostery, it appears that type II V arm end loop contacts may tend to evolve to V arm stem contacts. Full article

This study begins by examining phenotypic variations in field growth among four parental Vietnamese rice lines, consisting of two Indica (PD211/GL37) and two Japonica (J23/SRA2-1) cultivars, which differ in life-cycle durations. Their phenotypic observations revealed both similarities and differences in growth patterns and field responses, setting the stage for further genomic investigation. We then focused on the sequencing and de novo genome assembly of these lines using high-coverage Illumina sequencing and achieving pseudochromosome assemblies ranging between 379 Mbp and 384 Mbp. The assemblies were further enhanced by annotation processes, designating between 44,427 and 48,704 gene models/genome. A comparative genomic analysis revealed that the Japonica varieties (J23/SRA2-1) exhibited more genetic similarity than the Indica varieties (PD211/GL37). From this, a phylogenetic analysis on the phytochrome C (phyC) gene distinctly positions the Indica and Japonica lines within their respective clades, affirming their genetic diversity and lineage accuracy. These genomic resources will pave the way for identifying quantitative trait loci (QTLs) critical for developing rice cultivars with shorter life cycles, thus enhancing resilience to adverse climatic impacts in Vietnam. This study provides a foundational step towards leveraging genomic data for rice breeding programs aimed at ensuring food security in the face of climate change. Full article

Oxidative stress-mediated biomolecular damage is a characteristic feature of ionizing radiation (IR) injury, leading to genomic instability and chronic health implications. Specifically, a dose- and linear energy transfer (LET)-dependent persistent increase in oxidative DNA damage has been reported in many tissues and biofluids months after IR exposure. Contrary to low-LET photon radiation, high-LET IR exposure is known to cause significantly higher accumulations of DNA damage, even at sublethal doses, compared to low-LET IR. High-LET IR is prevalent in the deep space environment (i.e., beyond Earth’s magnetosphere), and its exposure could potentially impair astronauts’ health. Therefore, the development of biomarkers to assess and monitor the levels of oxidative DNA damage can aid in the early detection of health risks and would also allow timely intervention. Among the recognized biomarkers of oxidative DNA damage, 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-OxodG) has emerged as a promising candidate, indicative of chronic oxidative stress. It has been reported to exhibit differing levels following equivalent doses of low- and high-LET IR. This review discusses 8-OxodG as a potential biomarker of high-LET radiation-induced chronic stress, with special emphasis on its potential sources, formation, repair mechanisms, and detection methods. Furthermore, this review addresses the pathobiological implications of high-LET IR exposure and its association with 8-OxodG. Understanding the association between high-LET IR exposure-induced chronic oxidative stress, systemic levels of 8-OxodG, and their potential health risks can provide a framework for developing a comprehensive health monitoring biomarker system to safeguard the well-being of astronauts during space missions and optimize long-term health outcomes. Full article

In forensic DNA laboratories, it is important to conduct internal validations of the commercially available kits of short tandem repeat (STR) loci and to investigate their individual and combined effectiveness. This study aims to report on a comparative investigation of the forensic kits used in our laboratory and their combinations in analysing low-copy-number (LCN) human DNA samples. We used five partly overlapping multiplex kits with different marker configurations from different manufacturers: the NGM Select^TM PCR Amplification Kit, NGM Detect^TM, the GlobalFiler^TM Amplification Kit (Applied Biosystem^TM, Foster City, CA, USA), the PowerPlex^® Fusion 6C System (Promega Co., Madison, WI, USA) and the Investigator^® 24plex QS Kit (Qiagen GmbH, Hilden, Germany). The efficacy of the kits was scrutinised by specific criteria, such as allelic dropout rate, the individually calculated Likelihood Ratio (LR) of consensus profiles and the LR value of the composite profile produced by the combined profiles of two kits. According to the results, the pairing of PowerPlex^® Fusion 6C System and Investigator^® 24plex QS produced the lowest, while the pairing of the NGM Detect^TM and GlobalFiler^TM kits provided the highest LR value. In summary, our study is meant to aid the selection of the optimal kit combination for samples of different qualities. Full article

Mammalian cell lines devoid of mitochondrial DNA (mtDNA) are indispensable in studies aimed at elucidating the contribution of mtDNA to various cellular processes or interactions between nuclear and mitochondrial genomes. However, the repertoire of tools for generating such cells (also known as rho-0 or ρ⁰ cells) remains limited, and approaches remain time- and labor-intensive, ultimately limiting their availability. Ethidium bromide (EtBr), which is most commonly used to induce mtDNA loss in mammalian cells, is cytostatic and mutagenic as it affects both nuclear and mitochondrial genomes. Therefore, there is growing interest in new tools for generating ρ⁰ cell lines. Here, we examined the utility of 2′,3′-dideoxycytidine (ddC, zalcitabine) alone or in combination with EtBr for generating ρ⁰ cell lines of mouse and human origin as well as inducing the ρ⁰ state in mouse/human somatic cell hybrids. We report that ddC is superior to EtBr in both immortalized mouse fibroblasts and human 143B cells. Also, unlike EtBr, ddC exhibits no cytostatic effects at the highest concentration tested (200 μM), making it more suitable for general use. We conclude that ddC is a promising new tool for generating mammalian ρ⁰ cell lines. Full article

Quantitative PCR is a molecular technique for DNA quantification that depends on reaction efficiency and the Ct value (“cycle threshold”). However, the results are dependent on laboratory conditions and mathematical approaches. Thus, the data of 16 genes from Pseudomonas aeruginosa strain AG1 were generated using qPCR to assess the effect of DNA concentration and three mathematical methods (a standard curve and two individual-curve-based approaches called exponential and sigmoidal models) on efficiency and DNA quantification. Differences in efficiency were revealed depending on the mathematical method used; the values were 100% in three out of the four standard curves, but estimations of the expected fold change in DNA serial dilutions were not achieved, indicating the possible overestimation of efficiency. Moreover, when efficiency was compared to DNA concentration, a decreasing trend in efficiency as DNA concentration increased in the reaction was observed in most cases, which is probably related to PCR inhibitors. For all 16 genes at a single DNA concentration, the efficiencies for the exponential model were found in the range of 1.5–2.79 (50–79%), and for the sigmoidal approach, the range was 1.52–1.75 (52–75%), with similar impact on normalized expression values, as indicated by the genes for standard curves. Jointly, DNA concentration and mathematical model choice were demonstrated to impact the estimation of reaction efficiency and, subsequently, DNA quantification when using qPCR. Full article