Genetic Biomarkers and Their Clinical Implications in B-Cell Acute Lymphoblastic Leukemia in Children

Acute lymphoblastic leukemia (ALL) is a heterogeneous group of hematologic malignancies characterized by abnormal proliferation of immature lymphoid cells. It is the most commonly diagnosed childhood cancer with an almost 80% cure rate. Despite favorable survival rates in the pediatric population, a significant number of patients develop resistance to therapy, resulting in poor prognosis. ALL is a heterogeneous disease at the genetic level, but the intensive development of sequencing in the last decade has made it possible to broaden the study of genomic changes. New technologies allow us to detect molecular changes such as point mutations or to characterize epigenetic or proteomic profiles. This process made it possible to identify new subtypes of this disease characterized by constellations of genetic alterations, including chromosome changes, sequence mutations, and DNA copy number alterations. These genetic abnormalities are used as diagnostic, prognostic and predictive biomarkers that play an important role in earlier disease detection, more accurate risk stratification, and treatment. Identification of new ALL biomarkers, and thus a greater understanding of their molecular basis, will lead to better monitoring of the course of the disease. In this article, we provide an overview of the latest information on genomic alterations found in childhood ALL and discuss their impact on patients’ clinical outcomes.     

PCD Genes—From Patients to Model Organisms and Back to Humans

Primary ciliary dyskinesia (PCD) is a hereditary genetic disorder caused by the lack of motile cilia or the assembxly of dysfunctional ones. This rare human disease affects 1 out of 10,000–20,000 individuals and is caused by mutations in at least 50 genes. The past twenty years brought significant progress in the identification of PCD-causative genes and in our understanding of the connections between causative mutations and ciliary defects observed in affected individuals. These scientific advances have been achieved, among others, due to the extensive motile cilia-related research conducted using several model organisms, ranging from protists to mammals. These are unicellular organisms such as the green alga Chlamydomonas, the parasitic protist Trypanosoma, and free-living ciliates, Tetrahymena and Paramecium, the invertebrate Schmidtea, and vertebrates such as zebrafish, Xenopus, and mouse. Establishing such evolutionarily distant experimental models with different levels of cell or body complexity was possible because both basic motile cilia ultrastructure and protein composition are highly conserved throughout evolution. Here, we characterize model organisms commonly used to study PCD-related genes, highlight their pros and cons, and summarize experimental data collected using these models.     

Calcium-induced voltage gating in single conical nanopores

We examine time signals of ion current through single conically shaped nanopores in the presence of sub-millimolar concentrations of calcium ions. We show that calcium induces voltage-dependent ion current fluctuations in time in addition to the previously reported negative incremental resistance (Nano Lett. 2006, 6, 473-477). These current fluctuations occur on the millisecond time scale at voltages at which the effect of negative incremental resistance was observed. We explain the fluctuations as results of transient binding of calcium ions to carboxyl groups on the pore walls that cause transient changes in electric potential inside a conical nanopore. We support this explanation by recordings of ion current in the presence of manganese ions that bind to carboxyl groups 3 orders of magnitude more tightly than calcium ions. The system of a single conical nanopore with calcium ions is compared to a semiconductor device of a unijunction transistor in electronic circuits. A unijunction transistor also exhibits negative incremental resistance and current instabilities.     

Structure and carrier lifetime in LT-GaAs

The relationship between the structural quality of low-temperature GaAs layers and the photoexcited carrier lifetime has been studied. Transmission electron microscopy, x-ray rocking curves, time-resolved reflectance methods, and photoconductive-switch-response measurements were used for this study. For a variety of samples grown at temperatures in the vicinity of 200°C, subpicosecond carrier lifetimes were observed both in as-grown layers, as well as in the same layers after post-annealing and formation of As precipitates. These results suggest that the carrier lifetime, which was found to be shorter in the as-grown layers than in the annealed ones, might be related to the density of As_Ga antisite defects present in the layers. The annealed layers which contained structural defects before annealing appeared to exhibit the longest carrier lifetime due to gettering of As on these defects (and formation of relatively large As precipitates) and depletion of extra As (As_Ga) defects from the layer. It was found as well that the responsivity of detectors fabricated on these layers depended strongly on the structural quality of the layers, with the greatest response obtained not for the layers with the fewest defects, but for the layers with 10⁷–10⁸/cm² of pyramidal defects.     

Nanofluidic diode

We present a nanofluidic diode that at voltage range -5 to +5 V rectifies ion current with degrees of rectification reaching several hundreds. The diode is based on a single asymmetric nanopore whose surface was patterned so that a sharp boundary between positively and negatively charged regions is created. This boundary defines a zone that is enriched with positive and negative ions or creates a depletion zone. The principle of operation of the nanofluidic diode is analogous to that of a bipolar semiconductor diode.     

The In Vitro Anti-Pseudomonal Activity of Cu2+, Strawberry Furanone,Gentamicin, and Lytic Phages Alone and in Combination: Pros and Cons

In this study, we investigated the anti-pseudomonal activity of cupric ions (Cu²⁺), strawberry furanone (HDMF), gentamicin (GE), and three lytic Pseudomonas aeruginosa bacteriophages (KT28, KTN4, LUZ19), separately and in combination. HDMF showed an anti-virulent effect but only when applied with Cu²⁺ or GE. GE, at a sub-minimal inhibitory concentration, slowed down phage progeny production due to protein synthesis inhibition. Cu²⁺ significantly reduced both the bacterial cell count and the number of infective phage particles, likely due to its genotoxicity or protein inactivation and cell membrane disruption effects. Furthermore, Cu²⁺‘s probable sequestration by phage particles led to the reduction of free toxic metal ions available in the solution. An additive antibacterial effect was only observed for the combination of GE and Cu²⁺, potentially due to enhanced ROS production or to outer membrane permeabilization. This study indicates that possible interference between antibacterial agents needs to be carefully investigated for the preparation of effective therapeutic cocktails.     

Detecting single porphyrin molecules in a conically shaped synthetic nanopore

We report here the first example of abiotic resistive-pulse sensing of a molecular (as opposed to a particle or macromolecular) analyte. This was accomplished by using a conically shaped nanopore prepared by the track-etch method as the sensing element. It is possible to sense the molecular analyte because the small diameter opening of the conical nanopore (approximately 4.5 nm) is comparable to the diameter of the analyte molecule (approximately 2 nm).     

Minocycline Impact on Redox Homeostasis of Normal Human Melanocytes HEMn-LP Exposed to UVA Radiation and Hydrogen Peroxide

Minocycline is a semisynthetic tetracycline antibiotic. In addition to its antibacterial activity, minocycline shows many non-antibiotic, beneficial effects, including antioxidative action. The property is responsible, e.g., for anti-inflammatory, neuroprotective, and cardioprotective effects of the drug. However, long-term pharmacotherapy with minocycline may lead to hyperpigmentation of the skin. The reasons for the pigmentation disorders include the deposition of the drug and its metabolites in melanin-containing cells and the stimulation of melanogenesis. The adverse drug reaction raises a question about the influence of the drug on melanocyte homeostasis. The study aimed to assess the effect of minocycline on redox balance in human normal melanocytes HEMn-LP exposed to hydrogen peroxide and UVA radiation. The obtained results indicate that minocycline induced oxidative stress in epidermal human melanocytes. The drug inhibited cell proliferation, decreased the level of reduced thiols, and stimulated the activity of superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx). The described changes were accompanied by an increase in the intracellular level of ROS. On the other hand, pretreatment with minocycline at the same concentrations increased cell viability and significantly attenuated the oxidative stress in melanocytes exposed to hydrogen peroxide and UVA radiation. Moreover, the molecular docking analysis revealed that the different influence of minocycline and other tetracyclines on CAT activity can be related to the location of the binding site.     

Ionic selectivity of single nanochannels

There has been an increasing interest in single nanochannel ionic devices, such as ionic filters that control the type of transported ions and ionic diodes that rectify the ionic flow. In this article, we theoretically investigate the importance of the dimensions, surface charge, electrolyte concentration, and applied bias on nanopore performance. We compare numerical solutions of the Poisson, Nernst-Planck (PNP), and Navier-Stokes (NS) equations with their one-dimensional, analytical approximations. We show that by decreasing the length of the nanopore, the ionic current and ionic selectivity become affected by processes outside the nanochannel. The contribution of electroosmosis is noticeable, especially for highly charged nanochannels, but is insignificant, justifying the use of the simple one-dimensional approximation in many cases. Estimates for the critical electric field at which the nanopore selectivity decreases and the ion current starts to saturate are provided.