DNA, Volume 5, Issue 1 (March 2025) – 16 articles

Background: Triple-negative breast cancer (TNBC) is a highly aggressive subtype with limited effective treatments available, including targeted therapies, often leading to poor prognosis. Mitotic checkpoint kinase BUB1 is frequently overexpressed in TNBC and correlates with poor survival outcomes suggesting its potential as a therapeutic target. This study explores the cytotoxicity of TNBC cells to BUB1 inhibition, alone or in combination with radiation and demonstrates that ferroptosis, an iron-dependent form of programmed cell death, has a role. Methods: TNBC cell lines (SUM159, MDA-MB-231, and BT-549) were treated with a BUB1 inhibitor BAY1816032 (BUB1i) alone or in combination with the ferroptosis activator RSL3 with or without 4 Gy irradiation. Cell viability assays were conducted to assess treatment effects, qPCR analyses measured expression of key ferroptosis markers including ACSL4, GPX4, PTGS2, SLC7A11, NCOA4, IREB2, NFS1, and TFRC expression, and TBARS assay measured the lipid peroxidation levels. Ferroptosis specificity was confirmed through co-treatment with the ferroptosis inhibitor Ferrostatin-1 (F-1). Results: In all TNBC cell lines studied, BUB1 inhibition significantly induced ferroptosis, marked by increased expression of ACSL4 and PTGS2, decreased expression of GPX4 and SLC7A11, and increased lipid peroxidation levels. The combination of BUB1i with RSL3 further amplified these ferroptotic markers, suggesting at least an additive effect, which was not present with the combination of BUB1i and radiation. Co-treatment with Ferrostatin-1 reversed the expression of ferroptosis markers, suggesting that BUB1i-mediated cell death may involve ferroptotic signaling in TNBC cell lines. Conclusions: This study demonstrates that BUB1 inhibition may independently induce ferroptosis in TNBC cell lines, which is enhanced when combined with a ferroptosis activator. Further research is warranted to delineate the molecular mechanism of BUB1-mediated ferroptosis in TNBC. Full article

Background and Methods: We assessed the prokaryotic and eukaryotic diversity present in non-vegetated and vegetated soils on King George Island, Maritime Antarctic, in combination with measurements of carbon dioxide fluxes. Results: For prokaryotes, 381 amplicon sequence variants (ASVs) were assigned, dominated by the phyla Actinobacteriota, Acidobacteriota, Pseudomonadota, Chloroflexota, and Verrucomicrobiota. A total of 432 eukaryotic ASVs were assigned, including representatives from seven kingdoms and 21 phyla. Fungi dominated the eukaryotic communities, followed by Viridiplantae. Non-vegetated soils had higher diversity indices compared with vegetated soils. The dominant prokaryotic ASV in non-vegetated soils was Pyrinomonadaceae sp., while Pseudarthrobacter sp. dominated vegetated soils. Mortierella antarctica (Fungi) and Meyerella sp. (Viridiplantae) were dominant eukaryotic taxa in the non-vegetated soils, while Lachnum sp. (Fungi) and Polytrichaceae sp. (Viridiplantae) were dominant in the vegetated soils. Measured CO₂ fluxes indicated that the net ecosystem exchange values measured in vegetated soils were lower than ecosystem respiration in non-vegetated soils. However, the total flux values indicated that the region displayed positive ecosystem respiration values, suggesting that the soils may represent a source of CO₂ in the atmosphere. Conclusions: Our study revealed the presence of rich and complex communities of prokaryotic and eukaryotic organisms in both soil types. Although non-vegetated soils demonstrated the highest levels of diversity, they had lower CO₂ fluxes than vegetated soils, likely reflecting the significant biomass of photosynthetically active plants (mainly dense moss carpets) and their resident organisms. The greater diversity detected in exposed soils may influence future changes in CO₂ flux in the studied region, for which comparisons of non-vegetated and vegetated soils with different microbial diversities are needed. This reinforces the necessity for studies to monitor the impact of resident biota on CO₂ flux in different areas of Maritime Antarctica, a region strongly impacted by climatic changes. Full article

Background: Walleye (Sander vitreus), a valuable sportfish and an important ecological apex predator, exhibits genetic structuring across their range and localized structuring as a result of stocking. Methods: Walleye from 17 sampling locations across West Virginia were sequenced using a ddRAD protocol, generating various SNP datasets to assess population structuring and genomic diversity, with specific emphasis on the native Eastern Highlands strain. Different minor allele frequency filter thresholds were tested to assess impacts on genetic diversity and differentiation metrics. Results: High genetic differentiation was observed between the Eastern Highlands and Great Lakes strains, with further sub-structuring within the Eastern Highlands strain between the Ohio River populations and the other populations. Increasing MAF thresholds generally reduced the distinctiveness of clusters, but the overall inference of the number of clusters was minimally impacted. Genetic diversity metrics indicated some variability among Eastern Highlands walleye populations, with isolated populations, including the New River and Summersville Lake, showing higher inbreeding coefficients. MAF filters generally increased diversity metrics, but the trend of diversity metrics among populations remained relatively consistent. Several SNPs were found to be potentially undergoing selection, with the minor allele frequencies of these SNPs being found to be highest in Summersville Lake, highlighting potential adaptive divergence between the riverine populations and a large lentic system. Conclusions: The use of any MAF filter generated the same trends of population structuring and genomic diversity inferences regardless of the MAF threshold used. Further management of Eastern Highlands walleye in West Virginia needs to emphasize protecting the genetic integrity of the Kanawha River population and ongoing genomic screening of broodstock to conserve native genetic diversity. Full article

Background/Objectives: Estimating carbon content for cells is often necessary but difficult. In many biological, oceanographic, and marine biogeochemical studies, information on phytoplankton species composition and their biomass contribution to the community is essential. However, it is technically challenging to estimate the biomass of individual species in a natural assemblage. DNA analysis has the potential to profile species composition and estimate species-specific carbon biomass simultaneously. However, this requires an established relationship between carbon biomass and DNA content with species resolution using a measurable DNA index such as rDNA. Methods: In this study, DNA, rDNA, and carbon contents were measured for species from major phytoplankton phyla grown in different growth stages and under different nutrient and temperature conditions. Correlations between these parameters were examined. Results: Our data resulted in significant log-log regression equations: Log C = 0.8165 × Log DNA + 2.407 (R² = 0.9577, p < 0.0001), Log rDNA = 0.7472 × Log DNA − 0.0289 (R² = 0.9456, p < 0.0001), and Log C = 1.09 × Log rDNA + 2.41 (R² = 0.9199, p < 0.0001). Furthermore, similar strong regression functions were found when incorporating previously published data on a wide range of organisms including bacteria, plants, and animals. Conclusions: Carbon biomass is significantly correlated with DNA and rDNA abundances in phytoplankton and other organisms. The regression equations we developed offer a tool for estimating phytoplankton carbon biomass using DNA or rDNA and serve as a foundation for establishing similar models for other organisms. Full article

Background/Objectives: Some G-quadruplex (G4)-forming nucleic acid sequences bind a hemin cofactor to enhance its peroxidase-like activity. This has been implemented in a variety of bioanalytical assays benefiting from analyte-dependent peroxidation of a chromogenic organic substrate (e.g., ABTS) to produce a color change. Adenine and cytosine nucleotides in the vicinity of the G4 hemin-binding site promote the peroxidation reaction. In this work, the effect of G4 loop and flanking nucleotides on the colorimetric signal of split hybridization probes utilizing hemin-G4 signal reporters was tested. Methods: G4s varying by loop sequences and flanking nucleotides were tested with hemin for ABTS peroxidation (A₄₂₀), and the signal was compared with that produced by the most catalytically efficient complexes reported in the literature using one-way ANOVA and post hoc pairwise comparison with Tukey’s HSD test. The best G4s were used as signal transducers in the split peroxidase deoxyribozyme (sPDz) probes for sensing two model nucleic acid analytes, as well as in a cascade system, where the analyte-dependent assembly of an RNA-cleaving deoxyribozyme 10–23 results in G4 release. Results: Intramolecular G4s (G₃T)₃G₃TC or G₃T₃G₃ATTG₃T₃G₃ were found to be the most efficient hemin PDzs. When splitting intramolecular G4 for the purpose of sPDz probe design, the addition of a flanking d(TC) sequence at one of the G4 halves or d(ATT) in a loop connecting the second and third G-tracts helps boost analyte-dependent signal intensity. However, for the cascade system, the effect of d(TC) or d(ATT) in the released G4 was not fully consistent with the data reported for intramolecular G4-hemin complexes. Conclusions: Our findings offer guidance on the design of split hybridization probes utilizing the peroxidase-like activity of G4-hemin complexes as a signal transducer. Full article

Background: Despite increased attention to double-jointedness or joint hypermobility as seen in connective tissue dysplasias like Ehlers–Danlos syndrome, improved clinical DNA correlations are needed to reduce decadal delays in diagnosis. Methods: To this end, patterns of history (among 80) and physical (among 40) findings are compared for 121 Ehlers–Danlos syndrome patients with recurring variants in collagen type I, II, III, V, VI, VII, IX, XI, and XII genes and novel ones in type XV, XVII, XVIII, and XXVII. Results: A recognizable tissue laxity–dysautonomia profile that transcended collagen biochemical class, triple helix component, mutation type, or presence of accessory DNA variants was defined with a few exceptions. Patients with novel variations experienced severe symptoms at younger ages (6–10 versus 14–18 years) and those with collagen type III variations had more than one significant difference in finding frequencies (spinal disk issues 75% versus 49%; bloating-reflux 100% versus 69%; migraines or menorrhagia 92% versus 53%). Conclusions: These results suggest that collagen DNA variants of diverse gene and molecular type can demonstrate EDS disposition and hasten its diagnosis when distress and disease become manifest. Full article

The advancement of modern genomics has led to the large-scale industrial production of molecular data and scientific outcomes. Simultaneously, conventional DNA character alignments (sequence alignments) are utilized for DNA-based phylogenetic analyses without further recoding procedures or any a priori determination of character polarity, contrary to the requirements of foundations of phylogenetic systematics. These factors are the primary reasons why the binary perspective has not been implemented in modern molecular phylogenetics. In this study, we demonstrate how to recode conventional DNA data into various types of binary matrices, either unpolarized or with established polarity. Despite its historical foundation, our analytical approach to DNA sequence data has not been adequately explored since the inception of the molecular age. Binary representations of conventional DNA alignments allow for the analysis of molecular data from a purely comparative or static perspective. Furthermore, we show that the binarization of DNA data possesses broad mathematical and cultural connotations, making them intriguing regardless of their applications to different phylogenetic procedures. Full article

Background: Exon 1 of the gene encoding for the androgen receptor (AR) contains a polymorphic sequence of variably repeated CAG triplets ranging from 11 to 36. The number of triplets appears to inversely correlate with receptor transcriptional activity, conditioning the peripheral effects of testosterone. Methods: We conducted a narrative review to explore the current evidence regarding the relationship between the number of CAG repeats and the human reproductive system. Results: We found several articles that investigate the relationship between CAG polymorphism and the male reproductive system, suggesting a possible modulatory effect on spermatogenesis, sexual function, prostate cancer, and testicular cancer. Similarly, in women, evidence has emerged to support a possible relationship between CAG repeat number and breast cancer, polycystic ovary syndrome (PCOS), and recurrent spontaneous abortions (RSAs). Unfortunately, the data in the current literature are largely discordant, largely due to an important influence of ethnicity on the variability of the CAG polymorphism, and partly due to the quality of the available studies. Conclusions: In the current state of the art, the study of CAG polymorphism does not have a sufficient literature base to allow its use in common clinical practice. However, it represents an interesting research target and, in the future, as new evidence emerges, it could help to elucidate some pathogenetic aspects of human reproductive disorders. Full article

Background: The pyrrolobenzodiazepine (PBD) dimer SJG-136 reached Phase II clinical trials in ovarian cancer and leukaemia in the UK and USA in the 2000s. Several structural analogues of SJG-136 are currently in clinical development as payloads for Antibody-Drug Conjugates (ADCs). There is growing evidence that PBDs exert their pharmacological effects through inhibition of transcription factors (TFs) in addition to arrest at the replication fork, DNA strand breakage, and inhibition of enzymes including endonucleases and RNA polymerases. Hence, PBDs can be used to target specific DNA sequences to inhibit TFs as a novel anticancer therapy. Objective: To explore the ability of SJG-136 to bind to the cognate sequences of transcription factors using a previously described HPLC/MS method, to obtain preliminary mechanistic evidence of its ability to inhibit transcription factors (TF), and to determine its effect on TF-dependent gene expression. Methods: An HPLC/MS method was used to assess the kinetics and thermodynamics of adduct formation between the PBD dimer SJG-136 and the cognate recognition sequence of the TFs NF-κB, EGR-1, AP-1, and STAT3. CD spectroscopy, molecular dynamics simulations, and gene expression analyses were used to rationalize the findings of the HPLC/MS study. Results: Notable differences in the rate and extent of adduct formation were observed with different DNA sequences, which might explain the variations in cytotoxicity of SJG-136 observed across different tumour cell lines. The differences in adduct formation result in variable downregulation of several STAT3-dependent genes in the human colon carcinoma cell line HT-29 and the human breast cancer cell line MDA-MB-231. Conclusions: SJG-136 can disrupt transcription factor-mediated gene expression, which contributes to its exceptional cytotoxicity in addition to the DNA-strand cleavage initiated by its ability to crosslink DNA. Full article

Background/Objectives: Lung cancer ranks as the leading cause of cancer-related deaths globally and is highly associated with cisplatin resistance due to both intrinsic and extrinsic mechanisms. Proliferating Cell Nuclear Antigen (PCNA) plays a critical role in molecular processes, such as DNA replication and repair, chromatin structure maintenance, and cell cycle progression. PCNA is known as a molecular marker for proliferation and an excellent inhibition target to shut down highly proliferative cells. One of the mechanisms of cisplatin resistance is the increase in DNA repair, and studies have reported an association between PCNA, lung cancer, and cisplatin treatment. The present study aimed to characterize the absence of PCNA in A549 lung adenocarcinoma cells. Methods: Employing a CRISPR/Cas9 gene-editing approach, we generated a monoclonal cell culture, termed PKO (PCNA knockout). Results: PKO cells exhibited a residual PCNA expression, significantly decreased clonogenic potential and ubiquitylation at K164 residue. IC50 assay suggested that PKO cells could not acquire cisplatin resistance when compared to PX. After cisplatin treatment, PKO cells presented impaired ubiquitylation and did not have increased STAT3 phosphorylation (Tyr705), a previously characterized mechanism of cisplatin resistance. Conclusions: We suggest that PCNA participates in cisplatin resistance in A549, partially by DNA damage tolerance through failure on PCNA monoubiquitylation, and its inhibition may be an approach to circumvent cisplatin resistance. Full article

Epigenetic modifications affecting DNA, RNA, and proteins can alter the functional state of a gene and heavily interfere with gene expression. These processes are typically transient, and the predominant form of inheritance is mitotic, with a small fraction of transgenerational modifications. It is therefore reasonable to ask what forces drive this acquisition in living beings, where certain variations in phenotype do not correspond to changes in the DNA sequence. Full article

In this research, we induced acute kidney injury (AKI) by ischemia-reperfusion injury (IRI), one of its main causes. Then, we assessed kidney dysfunction by CRE (creatinine)/BUN (serum blood urea nitrogen) levels and histological analysis. Surprisingly, kidney macrophages, initially not expressing MafB and c-Maf, expressed both of them 48 h after bilateral ischemia renal disease (double IRD; dIRD), supporting their possible roles in the disease. We speculated that the M2 macrophages involved in AKI repair might be the source of MafB and c-Maf after injury and that these two transcription factors could have a significant role in the disease. Considering that IL-4/IL-13-induced M2a is the main contributor to AKI recovery and that MafB is upregulated under the effect of these two cytokines combined, we chose to focus on MafB analysis and aimed to examine its potential role in IRD. Previous studies have not examined the role of MafB in ischemic renal disease (IRD). In this study, we demonstrated a significant loss of brush borders, accumulation of intraluminal debris, and extensive damage to the anatomical structure of the MafB^f/f::Lys-Cre mice kidneys compared to their littermates, MafB^f/f, which are considered as a negative control in the entire paper. This was marked by the enlarged tubules, a significant decrease in mature macrophages (F4/80⁺ cells), and, therefore, worsening of the disease in the absence of MafB and delay/failure of the early signs of ischemia recovery. Importantly, these MafB cKO mice presented higher mortality, caused by the abrogation of the intraluminal debris clearance, and died after 48 h from IRD, suggesting the involvement of MafB in the signaling pathway of this pathology. Therefore, we found evidence that MafB attenuates IRD. Full article

Background: Colorectal cancer (CRC) is the third most diagnosed cancer globally and the second leading cause of cancer-related deaths. Despite advancements, metastatic CRC (mCRC) has a five-year survival rate below 20%. Next-generation sequencing (NGS) is recommended nowadays to guide mCRC treatment; however, its clinical utility when compared with traditional molecular testing in mCRC is debated due to limited survival improvement and cost-effectiveness concerns. Methods: This retrospective study included mCRC patients (≥18 years) treated at a single oncology centre who underwent NGS during treatment planning. Tumour samples were analysed using either a 52-gene Oncomine™ Focus Assay or a 500+-gene Oncomine™ Comprehensive Assay Plus. Variants were classified by clinical significance (ESMO ESCAT) and potential benefit (ESMO-MCBS and OncoKBTM). The Mann–Whitney and Chi square tests were used to compare characteristics of different groups, with significance at p < 0.05. Results: Eighty-six metastatic colorectal cancer (mCRC) patients were analysed, all being MMR proficient. Most cases (73.3%) underwent sequencing at diagnosis of metastatic disease, using primary tumour samples (74.4%) and a focused NGS assay (75.6%). A total of 206 somatic variants were detected in 86.0% of patients, 31.1% of which were classified as clinically significant, predominantly KRAS mutations (76.6%), with G12D and G12V variants as the most frequent. Among 33.7% RAS/BRAF wild-type patients, 65.5% received anti-EGFR therapies. Eleven patients (12.8%) had other actionable variants which were ESCAT level I-II, including four identified as TMB-high, four KRAS G12C, two BRAF V600E, and one HER2 amplification. Four received therapies classified as OncoKbTM level 1–2 and ESMO-MCBS score 4, leading to disease control in three cases. Conclusions: NGS enables the detection of rare variants, supports personalised treatments, and expands therapeutic options. As new drugs emerge and genomic data integration improves, NGS is poised to enhance real-world mCRC management. Full article

TRIP13 is a member of the large AAA+ ATPase protein superfamily that plays a crucial role in the precise segregation of chromosomes during mitosis. The abnormal function of TRIP13 has diverse functions, including mitotic processes, DNA repair pathways, and spindle assembly checkpoints, which may contribute to chromosomal instability (CIN). Emerging evidence suggests that the overexpression of TRIP13, observed in many cancers, plays a significant role in drug resistance, autophagy, and immune invasion. Recently, significant advances have been made in identifying TRIP13-associated signaling pathways that have been implicated in cancer progression. Several small molecules that specifically inhibit TRIP13 function and reduce cancer cell growth have been developed. Combination treatments, including TRIP13 inhibitors and other anticancer drugs, have shown promising results. While these findings are promising, TRIP13 inhibitors are awaiting clinical trials. This review discusses recent progress in understanding the oncogenic function of TRIP13 and its possible therapeutic targets, which could be exploited as an attractive option for cancer management. Full article

Background/Objectives: One of the significant challenges in forensic casework is the analysis of samples with degraded or poorly concentrated genetic material. The utilisation of the GlobalFiler™ and Yfiler Plus™ kits has unquestionably enhanced the efficacy of genetic profiling in challenging samples, facilitating the analysis of alleles that were previously undetectable with alternative kits. Therefore, the main objective of this work was to verify the efficiency of these kits in analysing forensic samples, progressively reducing the amplification volumes. To further optimise genetic profiling, it was essential not only to assess the behaviour of the alleles but also to prevent allelic loss. Methods: A series of reaction volume reduction studies were conducted, evaluating the performance of genetic profiles in both controlled samples (positive controls) and low template DNA samples (0.01 ng/µL). Results: The results demonstrate that it is effective to obtain complete genetic profiles from the amplification of optimal samples in reduced volumes of 12, 6 or 3 µL with GlobalFiler™ and Yfiler™ Plus. Conclusions: The limiting factor in obtaining complete genetic profiles is the amount of DNA available, rather than the amplification volume. Furthermore, reducing the amplification volume from DNA extracts of low template DNA samples proportionally increases the number of allelic dropouts. Full article

Background/Objectives: Culex species mosquitoes are globally distributed and transmit several pathogens that impact animal and public health, including West Nile virus, Usutu virus, and Plasmodium relictum. Despite their relevance, Culex species are less widely studied than Aedes and Anopheles mosquitoes. To expand the genetic tools used to study Culex mosquitoes, we previously developed an optimized plasmid for transient Cas9 and single-guide RNA (sgRNA) expression in Culex quinquefasciatus cells to generate gene knockouts. Here, we established a monoclonal cell line that consistently expresses Cas9 and can be used for screens to determine gene function or antiviral activity. Methods: We used this system to perform the successful gene editing of seven genes and subsequent testing for potential antiviral effects, using a simple single-guide RNA (sgRNA) transfection and subsequent virus infection. Results: We were able to show antiviral effects for the Cx. quinquefasciatus genes dicer-2, argonaute-2b, vago, piwi5, piwi6a, and cullin4a. In comparison to the RNAi-mediated gene silencing of dicer-2, argonaute-2b, and piwi5, our Cas9/sgRNA approach showed an enhanced ability to detect antiviral effects. Conclusions: We propose that this cell line offers a new tool for studying gene function in Cx. quinquefasciatus mosquitoes that avoids the use of RNAi. This short study also serves as a proof-of-concept for future gene knock-ins in these cells. Our cell line expands the molecular resources available for vector competence research and will support the design of future research strategies to reduce the transmission of mosquito-borne diseases. Full article