USP14 modulates cell pyroptosis and ameliorates doxorubicin-induced cardiotoxicity by deubiquitinating and stabilizing SIRT3.

This study investigates the role of the deubiquitinating enzyme USP14 in alleviating doxorubicin (DOX)-induced cardiotoxicity (DIC), particularly concerning its mechanism of regulating pyroptosis through the stabilization of the mitochondrial protein SIRT3. Using in vivo and in vitro models, the research demonstrated that USP14 overexpression protects against DOX-induced cardiac damage by modulating pyroptosis. Silencing SIRT3 via siRNA revealed that SIRT3 is a key intermediary molecule in USP14-mediated regulation of pyroptosis. Notably, DOX exposure resulted in decreased USP14 expression, while its overexpression preserved mitochondrial function and reduced oxidative stress by stabilizing SIRT3. Immunoprecipitation confirmed that USP14 stabilizes SIRT3 through deubiquitination. These findings position USP14 as a promising therapeutic target for mitigating DOX-induced cardiotoxicity by stabilizing SIRT3 and maintaining mitochondrial integrity, suggesting potential novel strategies for cardio-protection in chemotherapy.

Correction to Vaterite Dissolution: Mechanism and Kinetics.

[This corrects the article DOI: 10.1021/acs.jpcc.4c02074.].

Ferroptosis and myocardial ischemia-reperfusion: mechanistic insights and new therapeutic perspectives.

Myocardial ischemia-reperfusion injury (MIRI) is a significant factor in the development of cardiac dysfunction following a myocardial infarction. Ferroptosis, a type of regulated cell death driven by iron and marked by lipid peroxidation, has garnered growing interest for its crucial involvement in the pathogenesis of MIRI.This review comprehensively examines the mechanisms of ferroptosis, focusing on its regulation through iron metabolism, lipid peroxidation, VDAC signaling, and antioxidant system dysregulation. We also compare ferroptosis with other forms of cell death to highlight its distinct characteristics. Furthermore, the involvement of ferroptosis in MIRI is examined with a focus on recent discoveries concerning ROS generation, mitochondrial impairment, autophagic processes, ER stress, and non-coding RNA regulation. Lastly, emerging therapeutic strategies that inhibit ferroptosis to mitigate MIRI are reviewed, providing new insights into potential clinical applications.

Early evolutionary branching across spatial domains predisposes to clonal replacement under chemotherapy in neuroblastoma.

Neuroblastoma (NB) is one of the most lethal childhood cancers due to its propensity to become treatment resistant. By spatial mapping of subclone geographies before and after chemotherapy across 89 tumor regions from 12 NBs, we find that densely packed territories of closely related subclones present at diagnosis are replaced under effective treatment by islands of distantly related survivor subclones, originating from a different most recent ancestor compared to lineages dominating before treatment. Conversely, in tumors that progressed under treatment, ancestors of subclones dominating later in disease are present already at diagnosis. Chemotherapy treated xenografts and cell culture models replicate these two contrasting scenarios and show branching evolution to be a constant feature of proliferating NB cells. Phylogenies based on whole genome sequencing of 505 individual NB cells indicate that a rich repertoire of parallel subclones emerges already with the first oncogenic mutations and lays the foundation for clonal replacement under treatment.

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.

Overcoming passivation through improved mass transport in dense ionic fluids.

Deep Eutectic Solvents (DESs) have recently been shown to be part of a dense ionic fluid continuum between ionic liquids and concentrated aqueous brines. Charge transport was shown to be governed by fluidity, with no discontinuity between molar conductivity and fluidity irrespective of cation, charge density or ionic radius. By adjusting the activity of water and chloride ions, mass transport, speciation and reactivity can be altered. It has been shown that while brines provide a high chloride content at a lower viscosity than DESs, unlike DESs, brines are unable to prevent metal passivation due to their high water content. This results in the possibility to impart a level of selectivity towards metal dissolution (or passivation) when processing mixed metal materials. Forced convection can be used to avoid the issue of slow mass transport in viscous media, and the use of jets or targeted ultrasound are effective methods for overcoming this issue. High-powered ultrasound was applied to copper, cobalt, and aluminium electrodes undergoing anodic dissolution, and linear sweep voltammetry showed a linear current-voltage response at potentials anodic of the oxidation potential under sonication, with total charge passed being 5 to 134 times greater than under silent conditions. Application of ultrasound to silver and nickel electrodes displayed an initial linear current-voltage response, but the increased water content of the brines resulted in passivation. Mass transport throughout the bulk solution is governed by the forced convection imparted by the ultrasound and ionic species must only migrate across the electrical double layer. It is shown that the anodic dissolution of a range of metals classically expected to passivate, e.g. aluminium, can be significantly accelerated under insonation conditions.

Picosecond laser capture microdissection based on edge catapulting combined with dielectrophoretic force.

The spatial omics information analysis of heterogeneous cells or cell populations is of great importance for biomedical research. Herein, we proposed a picosecond laser capture microdissection boosted by edge catapulting combined with dielectrophoretic force (ps-LMED) that enables fast and non-invasive acquisition of uncontaminated cells and cell populations for downstream molecular assays. The target cells were positioned under a microscope and separated by a focused picosecond pulsed laser. The system employed the plasma expansion force during cutting to lift the target and captured it under dielectrophoretic force from the charged collection cap eventually. The principle of our system has been validated by both theoretical analysis and practical experiments. The results indicated that our system can collect samples ranging from a single cell with a diameter of a few microns to large tissues with a volume of 532,500 µm3 at the moment finishing the cutting, without further operations. The cutting experiments of living cells and ribonucleic acid (RNA) and protein omics analysis results of collected targets demonstrated the advantage of non-destructiveness to the samples and feasibility in omics applications.

Laser axial scanning microdissection for high-efficiency dissection from uneven biological samples.

Fast and efficient separation of target samples is crucial for the application of laser-assisted microdissection in the molecular biology research field. Herein, we developed a laser axial scanning microdissection (LASM) system with an 8.6 times extended depth of focus by using an electrically tunable lens. We showed that the ablation quality of silicon wafers at different depths became homogenous after using our system. More importantly, for those uneven biological tissue sections within a height difference of no more than 19.2 µm, we have demonstrated that the targets with a size of microns at arbitrary positions can be dissected efficiently without additional focusing and dissection operations. Besides, dissection experiments on various biological samples with different embedding methods, which were widely adopted in biological experiments, also have shown the feasibility of our system.

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.

Drug-resilient Cancer Cell Phenotype Is Acquired via Polyploidization Associated with Early Stress Response Coupled to HIF2α Transcriptional Regulation.

Therapeutic resistance and recurrence remain core challenges in cancer therapy. How therapy resistance arises is currently not fully understood with tumors surviving via multiple alternative routes. Here, we demonstrate that a subset of cancer cells survives therapeutic stress by entering a transient state characterized by whole-genome doubling. At the onset of the polyploidization program, we identified an upregulation of key transcriptional regulators, including the early stress-response protein AP-1 and normoxic stabilization of HIF2α. We found altered chromatin accessibility, ablated expression of retinoblastoma protein (RB1), and enrichment of AP-1 motif accessibility. We demonstrate that AP-1 and HIF2α regulate a therapy resilient and survivor phenotype in cancer cells. Consistent with this, genetic or pharmacologic targeting of AP-1 and HIF2α reduced the number of surviving cells following chemotherapy treatment. The role of AP-1 and HIF2α in stress response by polyploidy suggests a novel avenue for tackling chemotherapy-induced resistance in cancer. SIGNIFICANCE: In response to cisplatin treatment, some surviving cancer cells undergo whole-genome duplications without mitosis, which represents a mechanism of drug resistance. This study presents mechanistic data to implicate AP-1 and HIF2α signaling in the formation of this surviving cell phenotype. The results open a new avenue for targeting drug-resistant cells.

The solubility product controls the rate of calcite dissolution in pure water and seawater.

Quantification of calcite dissolution underpins climate and oceanographic modelling. We report the factors controlling the rate at which individual crystals of calcite dissolved. Clear, generic criteria based on the change of calcite particle dimensions measured microscopically with time are established to indicate if dissolution occurs under kinetic or thermodynamic control. The dissolution of calcite crystals into water is unambiguously revealed to be under thermodynamic control such that the rate at which the crystal dissolved is controlled by the rate of diffusion of ions from a saturated surface layer adjacent to the calcite surface. As such the dissolution rate is controlled by the true stoichiometric solubility product which is inferred from the microscopic measurement as a function of the concentration of NaCl. Comparison with accepted literature values shows that the role of ion pairing at high ionic strengths as in seawater, specifically that of CaCO3 and other ion pairs, exerts a significant influence since these equilibria control the amount of dissolved calcium and carbonate ions in the later of solution immediately adjacent to the solid.

Discovering Electrochemistry with an Electrochemistry-Informed Neural Network (ECINN).

Machine learning is increasingly integrated into chemistry research by guiding experimental procedures, correlating structure and function, interpreting large experimental datasets, to distill scientific insights that might be challenging with traditional methods. Such applications, however, largely focus on gaining insights via big data and/or big computation, while neglecting the valuable chemical prior knowledge dwelling in chemists' minds. In this paper, we introduce an Electrochemistry-Informed Neural Network (ECINN) by explicitly embedding electrochemistry priors including the Butler-Volmer (BV), Nernst and diffusion equations on the backbone of neural networks for multi-task discovery of electrochemistry parameters. We applied the ECINN to voltammetry experiments of F e 2 + / F e 3 + ${{\rm F}{{\rm e}}^{2+}/{\rm F}{{\rm e}}^{3+}}$ and R u N H 3 6 2 + / R u N H 3 6 3 + ${{\rm R}{\rm u}{\left({\rm N}{{\rm H}}_{3}\right)}_{6}^{2+{\rm \ }}/{\rm R}{\rm u}{\left({\rm N}{{\rm H}}_{3}\right)}_{6}^{3+{\rm \ }}}$ redox couples to discover electrode kinetics and mass transport parameters. Notably, ECINN seamlessly integrated mass transport with BV to analyze the entire voltammogram to infer transfer coefficients directly, so offering a new approach to Tafel analysis by outdating various mass transport correction methods. In addition, ECINN can help discover the nature of electron transfer and is shown to refute incorrect physics if imposed. This work encourages chemists to embed their domain knowledge into machine learning models to start a new paradigm of chemistry-informed machine learning for better accountability, interpretability, and generalization.

Calcifying Coccolithophore: An Evolutionary Advantage Against Extracellular Oxidative Damage.

The evolutionary advantages afforded by phytoplankton calcification remain enigmatic. In this work, fluoroelectrochemical experiments reveal that the presence of a CaCO3 shell of a naturally calcifying coccolithophore, Coccolithus braarudii, offers protection against extracellular oxidants as measured by the time required for the switch-off in their chlorophyll signal, compared to the deshelled equivalents, suggesting the shift toward calcification offers some advantages for survival in the surface of radical-rich seawater.

AI facilitated fluoro-electrochemical phytoplankton classification.

Marine phytoplankton is extremely diverse. Counting and characterising phytoplankton is essential for understanding climate change and ocean health not least since phytoplankton extensively biomineralize carbon dioxide whilst generating 50% of the planet's oxygen. We report the use of fluoro-electrochemical microscopy to distinguish different taxonomies of phytoplankton by the quenching of their chlorophyll-a fluorescence using chemical species oxidatively electrogenerated in situ in seawater. The rate of chlorophyll-a quenching of each cell is characteristic of the species-specific structural composition and cellular content. But with increasing diversity and extent of phytoplankton species under study, human interpretation and distinction of the resulting fluorescence transients becomes increasingly and prohibitively difficult. Thus, we further report a neural network to analyse these fluorescence transients, with an accuracy >95% classifying 29 phytoplankton strains to their taxonomic orders. This method transcends the state-of-the-art. The success of the fluoro-electrochemical microscopy combined with AI provides a novel, flexible and highly granular solution to phytoplankton classification and is adaptable for autonomous ocean monitoring.

Clonal origin and development of high hyperdiploidy in childhood acute lymphoblastic leukaemia.

High hyperdiploid acute lymphoblastic leukemia (HeH ALL), one of the most common childhood malignancies, is driven by nonrandom aneuploidy (abnormal chromosome numbers) mainly comprising chromosomal gains. In this study, we investigate how aneuploidy in HeH ALL arises. Single cell whole genome sequencing of 2847 cells from nine primary cases and one normal bone marrow reveals that HeH ALL generally display low chromosomal heterogeneity, indicating that they are not characterized by chromosomal instability and showing that aneuploidy-driven malignancies are not necessarily chromosomally heterogeneous. Furthermore, most chromosomal gains are present in all leukemic cells, suggesting that they arose early during leukemogenesis. Copy number data from 577 primary cases reveals selective pressures that were used for in silico modeling of aneuploidy development. This shows that the aneuploidy in HeH ALL likely arises by an initial tripolar mitosis in a diploid cell followed by clonal evolution, in line with a punctuated evolution model.

Quantifying the Extent of Calcification of a Coccolithophore Using a Coulter Counter.

Although, in principle, the Coulter Counter technique yields an absolute measure of particle volume, in practice, calibration is near-universally employed. For regularly shaped and non-biological samples, the use of latex beads for calibration can provide sufficient accuracy. However, this is not the case with particles encased in biogenically formed calcite. To date, there has been no effective route by which a Coulter Counter can be calibrated to enable the calcification of coccolithophores─single cells encrusted with biogenic calcite─to be quantified. Consequently, herein, we seek to answer the following question: to what extent can a Coulter Counter be used to provide accurate information regarding the calcite content of a single-species coccolithophore population? Through the development of a new calibration methodology, based on the measurement and dynamic tracking of the acid-driven calcite dissolution reaction, a route by which the cellular calcite content can be determined is presented. This new method allows, for the first time, a Coulter Counter to be used to yield an absolute measurement of the amount of calcite per cell.

Electrochemical Heterogeneity at the Nanoscale: Diffusion to Partially Active Nanocubes.

How does heterogeneity in activity affect the response of nanoparticles? This problem is key to studying the structure-activity relationship of new electrocatalytic materials. However, addressing this problem theoretically and to a high degree of accuracy requires the use of three-dimensional electrochemical simulations that have, until recently, been challenging to undertake. To start to probe this question, we investigate how the diffusion-limited flux to a cube changes as a function of the number of active faces. Importantly, it is clearly demonstrated how the flux is not linearly proportional to the active surface area of the material due to the faces of the cube not having diffusional independence, meaning that the flux to each face reflects the activity or not of nearby faces. These results have clear and important implications for experimental work that uses a correlation-based approach to evidence changes in activity at the nanoscale.

Calcium Carbonate Dissolution from the Laboratory to the Ocean: Kinetics and Mechanism.

The ultimate fate, over the course of millennia, of nearly all of the carbon dioxide formed by humankind is for it to react with calcium carbonate in the world's oceans. Although, this reaction is of global relevance, aspects of the calcite dissolution reaction remain poorly described with apparent contradictions present throughout the expansive literature. In this perspective we aim to evidence how a lack of appreciation of the role of mass-transport may have hampered developments in this area. These insights have important implications for both idealised experiments performed under laboratory conditions and for the measurement and modelling of oceanic calcite sediment dissolution.