Successful tissue repair depends on the precise orchestration of phase-specific cellular responses alongside sustained activity of multifunctional immune regulators. Mast cells, which have primarily been long regarded as effector cells of allergic reactions, have emerged as pivotal modulators of wound repair. Importantly, mast cell activity exhibits a dual nature: while transient activation supports efficient repair and granulation tissue formation, sustained or excessive activation is associated with pathological fibrosis, hypertrophic scarring and keloid formation. Although many experimental studies and clinical evidences implicate a critical role for mast cells in wound repair, several key questions remain. Specifically, the contributions of distinct mast cell subtypes and the precise temporal dynamics of their mediator release, as well as the intricate molecular crosstalk between mast cells, stromal components, and other infiltrating immune cells remans a subject of active investigation. This review highlights current literature on the multifaceted roles of mast cells across the successive phases of wound-healing, and the specific mechanisms by which mast cells support or impair tissue repair, outlining unresolved questions in the field. Through this discussion, we aim to provide a framework for developing new therapeutic strategies to improve healing outcomes and facilitate better scar management.

Mitochondrial DNA (mtDNA) copy number determines the functional state of mitochondria and thus, influences cellular energy production, growth, metabolism, and stress response. Variation in mtDNA copy number has been observed across many cancer types and has been linked to changes in gene expression. However, whether mtDNA copy number has any link to mutation accumulation in cancer is unknown. Further, how mtDNA copy number variation alters expression of cancer-associated pathways and thereby influences cancer progression remains unclear. Here, through an analysis of whole genome data in multiple cancer types, we show that mtDNA copy number increases with an increase in mutational load in cancer samples and the increase in mtDNA copy number bears a signature of compensation for mitochondrial function. We also show that the samples with low-mtDNA generally have increased expression of cancer-promoting genes, including genes involved in cell migration and epithelial-mesenchymal transition (EMT). Taken together, these results reveal a close association of mtDNA copy number with mutational load and disease progression in cancer. These findings provide a way forward toward a better understanding of the role of mtDNA copy number and mitochondrial functional state in cancer progression.

Ovarian cancer (OC) is typically associated with poor prognosis and high mortality. Chimeric antigen receptor (CAR) T-cell therapy offers a promising strategy, yet its application in solid tumours remains constrained by limited efficacy and on-target/off-tumour toxicities. We previously developed K101CAR T cells targeting CA125, the cleaved extracellular domain of MUC16, and demonstrated potent antitumour activity against OC. However, because MUC16 exhibits low-level expression in certain normal tissues, safety concerns remain regarding potential off-tumour effects. We designed a combinatorial CAR composed of two single-chain variable fragments (scFvs): (i) TAG-72 targeting the Sialyl-Tn antigen highly expressed on malignant cells, and (ii) the K101 scFv. The first unit is linked to a CD3ζ signalling domain, whereas the second is linked to a 4-1BB costimulatory domain, leading to a combinatorial CAR fully reactive against double-positive targets, Tz-KBBCAR. We demonstrate that Tz-KBBCAR T cells efficiently eliminate MUC16[+]/TAG-72[+]-, while sparing MUC16[+]/TAG-72[-]- cells in vitro and markedly suppress tumour progression in vivo. We also observed that compared to K101CAR T cells, Tz-KBBCAR T cells exhibit enhanced expansion, sustained viability, and a reduced exhaustion phenotype. Overall, our study presents an efficient combinatorial CAR T-cell strategy predicted to be safer than single CAR T-cell therapy for OC.

The apolipoprotein E ε4 (APOE4) allele is the strongest common genetic risk factor for late-onset Alzheimer's disease. However, its incomplete penetrance supports the view that it acts as a modifiable systems-level perturbation of brain homeostasis rather than a deterministic driver. Increasing evidence further positions APOE4 protein within interconnected lipid metabolic pathways, with converging genetic, epidemiological, and translational studies implicating disrupted cholesterol transport, lipoprotein metabolism, and lipid oxidation as upstream mechanisms that promote neurodegeneration. Here, we synthesize currently developing therapeutic strategies targeting APOE4 across domains: small molecules, endogenous protectors, emerging biologics, and systemic lipid modulators. Small molecules include structural correctors and natural compounds, while endogenous protection arises from APOE2, the APOE3-Christchurch variant, and modifiers such as CASP7, KLOTHO, the VHL-HIF axis, fibronectin, and NHE6-mediated endosomal regulation. Biologic platforms enable allele-selective and pathway-specific interventions via siRNA, antisense oligonucleotides, and antibodies targeting pathological APOE conformers. In parallel, cholesteryl ester transfer protein (CETP) inhibition has emerged as a systems-level strategy that restores lipid and redox homeostasis, with early clinical evidence showing reductions in neurodegenerative biomarkers, particularly in APOE4 carriers. These advances support an integrative therapeutic framework to restore brain lipid homeostasis, stress resilience and neural-vascular coupling, positioning APOE4 as a modifiable node within a preventable lipid-vascular-neurodegenerative axis.

PARP proteins are enzymes catalyzing ADP-ribosylation, a well-conserved post-translational modification. In addition to the catalytic domain present in all PARPs, these proteins have a wide variety of other domains possessing different functions. Additional domains present in human PARP15 are macrodomains, capable of binding ADP-ribose. PARP15 is the least studied of the macrodomain-containing human PARPs, and it is linked to different diseases from infections to cancer. We show that the full-length canonical isoform 1 of PARP15 auto-ADP-ribosylates robustly on glutamate and aspartate residues, from which the modification can be hydrolyzed by known ADP-ribosylhydrolases. We have been able to locate several modification sites in the region of tandem macrodomains. Consistent with previous findings that the catalytic domain dimerization is necessary for enzymatic activity, we confirm this in the full-length context with the recombinant isoform 1 of PARP15. We show that dimerization is required for the efficient substrate NAD[+] binding, and we provide structural basis for this requirement with the help of a co-crystal structure of the catalytic domain dimer with an unhydrolyzable substrate analog.

GRF transcription factors (GRF) are pivotal regulators of plant development and stress tolerance, but their functional repertoire in the rubber crop Taraxacum kok-saghyz (Russian dandelion) remains entirely uncharacterized. Genome-wide analysis of the T. kok-saghyz genome identified 10 TkGRF members, unevenly distributed across eight chromosomes and phylogenetically resolved into five clades. All TkGRFs contained the canonical QLQ and WRC domains, confirming their identity as bona fide GRF transcription factors. Synteny analysis further established close evolutionary conservation of these 10 TkGRF members with Asteraceae relatives, while promoter profiling revealed pervasive cis-regulatory elements linked to hormonal and stress signaling, pointing to a broad regulatory potential. Integrated RNA-seq and qRT-PCR analyses confirmed the tissue-specific expression profiles of TkGRFs under salt stress. Notably, TkGRF1, a nucleus-localized transcription factor displaying transcriptional activation activity, exhibited the most robust response to stress. Overexpression of TkGRF1 in Arabidopsis resulted in elevated Malondialdehyde (MDA) and reactive oxygen accumulation, while lowering antioxidant enzyme activities, confirming its negative role in salt tolerance. RNA-seq further uncovered salt-triggered transcriptional reprogramming of hormone signaling, energy metabolism and stomatal development pathways. This study lays a theoretical basis and offers a potential target for the molecular breeding of salt-tolerant T. kok-saghyz.

Cation-π interactions are widely considered key contributors to protein structure and molecular recognition, with quantum chemical studies often predicting substantial stabilization energies. However, their actual prevalence and strength in protein environments remain debated. Here, we combine high-level quantum chemical calculations with large-scale statistical analyses of high-resolution protein structures to reassess the role of lysine-π interactions. While gas-phase calculations confirm strong cation-π binding for idealized geometries, with corresponding energies of -19.0 kcal·mol[-1] and -16.0 kcal·mol[-1] for Lys-Phe and Arg-Phe pairs respectively, we demonstrate that even small geometric distortions and the inclusion of dielectric screening significantly reduce interaction energies to respective values of -5.9 kcal·mol[-1] and -6.5 kcal·mol[-1] at a dielectric constant of 6 and to -3.7 kcal·mol[-1] and -4.7 kcal·mol[-1] at a dielectric constant of 78. By leveraging the current size of the Protein Data Bank, we analyzed a much larger set of high-resolution protein structures than previously feasible, enabling a more rigorous evaluation of the structural prevalence of lysine-π interactions. Our statistical analysis reveals a low occurrence of geometries consistent with optimal cation-π interactions. By bridging quantum chemical results with structural data, this work reconciles the discrepancy between strong intrinsic interaction energies and their limited manifestation in proteins. These findings highlight the importance of geometric and environmental effects and suggest that Lys-π interactions in proteins are context-dependent and likely contribute less to protein structure than previously assumed.

Polyisoprenoid quinones such as ubiquinone (UQ) play an essential role in cellular physiology, acting as membrane-bound electron and proton carriers in respiratory chains and other biological processes across all domains of life. In Escherichia coli, the canonical UQ biosynthesis pathway is well characterized. It involves 12 proteins (UbiA-UbiK and UbiX), most of which catalyze one of the eight modifications of the aromatic ring derived from 4-hydroxybenzoic acid (4-HB), while others (UbiB, UbiJ, UbiK) act as accessory factors ensuring efficient UQ production. Following prenylation by UbiA and subsequent decarboxylation by the UbiX/UbiD system, the final six reactions are catalyzed within a soluble Ubi-complex. UbiB, an atypical protein kinase-like enzyme, was proposed to extract decarboxylated intermediates from the membrane and mediate their delivery to the Ubi-complex. In this study, we demonstrate the existence of an alternative decarboxylation system in E. coli, as UQ biosynthesis can proceed in the absence of the UbiX/UbiD system. Our results show that this alternative decarboxylation activity depends on UbiB and requires its adenosine triphosphatase activity. Bioinformatic analyses further revealed that approximately 27% of Pseudomonadota species lack UbiX/UbiD homologs, and we found that UbiB proteins from two such species enhance the alternative decarboxylation activity when expressed in E. coli. In addition, we identified conserved residues in UbiB that are specifically required for decarboxylation but dispensable for the delivery of UQ intermediates to the Ubi-complex. Taken together, our findings support a model in which UbiB acts as an ATP-dependent decarboxylase, thereby broadening the functional scope of this poorly characterized protein.

Porcine induced pluripotent stem cells (piPSCs) generated via standard reprogramming factors typically remain dependent on exogenous transgene expression to maintain pluripotency and exhibit limited differentiation potential. Improving these limitations is essential for both regenerative medicine and agricultural biotechnology. To enhance the quality of piPSCs, we introduced an episomal plasmid encoding TBX3 in addition to the standard reprogramming factors with transgene-free piPSC lines established via WNT pathway inhibition. Furthermore, we developed optimized differentiation protocols to efficiently generate smooth muscle cells (SMCs), endothelial cells (ECs), hepatocyte-like cells (HLCs), and cardiomyocytes from piPSCs. TBX3-reprogrammed piPSCs (TBX3-piPSC) expressed both SSEA-1 and SSEA-4 surface markers, in contrast to standard piPSCs, which expressed only SSEA-1. TBX3-piPSC rapidly silenced exogenous reprogramming factors and formed teratomas containing well-differentiated tissues from all three germ layers. In contrast, standard piPSCs formed poorly differentiated teratomas composed mainly of mesenchymal and neuroectodermal tissues, consistent with previous reports of transgene-dependent piPSCs. TBX3-piPSC also formed embryoid bodies that demonstrated broader differentiation capacity. Under directed differentiation conditions, TBX3-piPSC efficiently gave rise to SMCs, ECs, HLCs, and beating cardiomyocytes. Thus, we conclude that the addition of TBX3 as a reprogramming factor promotes the generation of transgene-free piPSCs with enhanced differentiation potential. These findings provide a significant advancement in porcine stem cell biology and expand the potential applications of piPSCs.

The long noncoding RNA H19 has been widely attested as a promoter of breast cancer by favoring proliferation, migration, invasion, and tumor growth. In this study, we attempted to decipher molecular mechanisms underlying oncogenic activities of H19. Transcriptomic analyses revealed that H19 overexpression correlates with increased BST2 expression at both transcriptional and protein levels in breast cancer cell lines. Functional assays demonstrated that BST2 overexpression mimics H19 oncogenic effects by enhancing tumor cell aggressiveness in vitro and tumor growth in vivo. Interestingly, we also observed a reciprocal regulation, where BST2 expression modulates H19 levels, suggesting a cross-regulatory mechanism. Further mechanistic studies identified miR-760 as a key post-transcriptional regulator orchestrating this interplay. Using luciferase reporter assays and miRNA modulation strategies, we found that miR-760 directly targets both H19 and BST2, thereby regulating their expression in a coordinated manner. Our findings uncover a novel H19/miR-760/BST2 regulatory axis that enhances breast cancer progression and suggest that this axis could be studied to identify potential targets for therapeutic intervention.

Converging findings point to brain- and body-wide energetic dysregulation in psychotic disorders, implicating metabolic abnormalities across different levels of investigation, including genetic, cellular, postmortem, and in vivo neuroimaging studies. The present review synthesizes this literature documenting aberrant energy production and use, specifically related to mitochondrial and redox dysregulation, in psychotic disorders. Mitochondrial DNA, copy number variants, polygenic risk, and candidate genes involved in metabolic pathways converge on glycolytic, mitochondrial, redox, and oxidative stress mechanisms. Consistent with these findings, cell studies, primarily from ex vivo brain tissue samples and induced pluripotent stem cells (iPSC), show misdistribution and structural fragmentation of mitochondrial networks and dysregulation in the expression of proteins involved in several metabolic processes. Inherent dysregulations, at the genetic and cellular level, may affect both neuronal and glial health, as observed at the tissue level. Neuroimaging studies demonstrate metabolic dysregulations in vivo, including central insulin resistance and redox and bioenergetic aberrations that are associated with cognitive impairment and altered brain networks. We also consider the effects of antipsychotic medications on energy metabolism. Finally, we propose a framework for future work and treatment approaches to target energetic dysregulations, including existing metabolic treatments. The metabolic mechanisms that interact to produce and perpetuate aberrant neuronal health and functioning in psychotic disorders are complex. Nevertheless, the findings highlight pathways that might be targeted for the development of novel treatments, providing an opportunity to develop more efficacious and better-tolerated interventions.

While proteins are built from 20 canonical amino acids, it is interesting to explore whether proteins can be formed from significantly reduced amino acid alphabets. Our bioinformatics survey of UniProt (more than 250 m sequences) revealed that proteins composed of reduced amino acid alphabets are extremely rare among existing proteins. Next, we used computational protein design to design proteins 100 amino acid residues in length composed of all 1013 possible alphabets of 2-10 early amino acids (Ala, Asp, Glu, Gly, Ile, Leu, Pro, Ser, Thr, and Val). Our findings show that small amino acid alphabets preferred simple helices or helix bundles, while larger amino acid alphabets allowed for the design of more complex structures. We verified a protein composed of 8 amino acid types (Ala, Asp, Gly, Leu, Val, Ser, Thr, and Pro) finding it adopts the β-sheet-rich fibronectin type III domain architecture. However, attempts to experimentally verify designs composed of 6 and 4 amino acid types were unsuccessful. Furthermore, we show by computational experiment with experimental validation that inverse folding models, namely ProteinMPNNsol, can stabilize a designed protein within the same eight-amino-acid alphabet. Ultimately, our results show that globular proteins may have formed early in evolution using a minimal amino acid alphabet and that it is possible to design such proteins with interesting properties for biotechnology and synthetic biology.

Phosphate is central to modern bioenergetics and to all theories for the origin of life. How phosphate entered metabolism is unknown, though microbial physiology and geochemical environments can provide important clues. Some bacteria obtain electrons and energy from phosphite (HPO3 [2-]), a reduced form of phosphate (HPO4 [2-]), that naturally occurs in serpentinizing (H2-producing) hydrothermal systems. Here we show that the insoluble, solid-state catalyst native palladium, which is naturally deposited in serpentinizing hydrothermal systems, catalyzes the oxidation of phosphite to phosphate and H2 in water at 25-100 °C in a highly exergonic reaction. Palladium awaruite (PdxNi3Fe), a common form of Pd[0] in serpentinizing vents, also catalyzes phosphite-dependent phosphorylation. Phosphite oxidation over Pd[0] generates a reactive but so far unidentified chemical intermediate, possibly metaphosphate, [PO3][-], that readily phosphorylates hydroxyl moieties in glycerol, ribose, glucose, serine, and cytidine at 25-100 °C in 2-72 h. The same conditions also generate (i) phosphoanhydride bonds in pyrophosphate, polyphosphates, and ADP, (ii) the phosphoramidate bond in phosphocreatine, (iii) and the acyl phosphate bond in acetyl phosphate, which is obtained overnight at 25 °C with 8% yield. The reactions proceed without sulfur, excluding thioester or metal sulfide intermediates. Phosphite-dependent phosphorylations under serpentinizing hydrothermal vent conditions are facile. They identify a natural, geochemical source of prebiotic phosphorylation and a novel source of metabolic energy at origins. The central role of phosphate in bioenergetics, metabolism, and nucleic acids could reflect metal-catalyzed, redox chemistry of phosphorus in the environment where metabolism (and life) arose.