Stress granules: Guardians of cellular health and triggers of disease

Stress granules are membraneless organelles that serve as a protective cellular response to external stressors by sequestering non-translating messenger RNAs (mRNAs) and regulating protein synthesis. Stress granules formation mechanism is conserved across species, from yeast to mammals, and they play a critical role in minimizing cellular damage during stress. Composed of heterogeneous ribonucleoprotein complexes, stress granules are enriched not only in mRNAs but also in noncoding RNAs and various proteins, including translation initiation factors and RNA-binding proteins. Genetic mutations affecting stress granule assembly and disassembly can lead to abnormal stress granule accumulation, contributing to the progression of several diseases. Recent research indicates that stress granule dynamics are pivotal in determining their physiological and pathological functions, with acute stress granule formation offering protection and chronic stress granule accumulation being detrimental. This review focuses on the multifaceted roles of stress granules under diverse physiological conditions, such as regulation of mRNA transport, mRNA translation, apoptosis, germ cell development, phase separation processes that govern stress granule formation, and their emerging implications in pathophysiological scenarios, such as viral infections, cancer, neurodevelopmental disorders, neurodegeneration, and neuronal trauma.

Exosomes in neurodegenerative diseases: Therapeutic potential and modification methods

In recent years, exosomes have garnered extensive attention as therapeutic agents and early diagnostic markers in neurodegenerative disease research. Exosomes are small and can effectively cross the blood-brain barrier, allowing them to target deep brain lesions. Recent studies have demonstrated that exosomes derived from different cell types may exert therapeutic effects by regulating the expression of various inflammatory cytokines, mRNAs, and disease-related proteins, thereby halting the progression of neurodegenerative diseases and exhibiting beneficial effects. However, exosomes are composed of lipid bilayer membranes and lack the ability to recognize specific target cells. This limitation can lead to side effects and toxicity when they interact with non-specific cells. Growing evidence suggests that surface-modified exosomes have enhanced targeting capabilities and can be used as targeted drug-delivery vehicles that show promising results in the treatment of neurodegenerative diseases. In this review, we provide an up-to-date overview of existing research aimed at devising approaches to modify exosomes and elucidating their therapeutic potential in neurodegenerative diseases. Our findings indicate that exosomes can efficiently cross the blood-brain barrier to facilitate drug delivery and can also serve as early diagnostic markers for neurodegenerative diseases. We introduce the strategies being used to enhance exosome targeting, including genetic engineering, chemical modifications (both covalent, such as click chemistry and metabolic engineering, and non-covalent, such as polyvalent electrostatic and hydrophobic interactions, ligand-receptor binding, aptamer-based modifications, and the incorporation of CP05-anchored peptides), and nanomaterial modifications. Research into these strategies has confirmed that exosomes have significant therapeutic potential for neurodegenerative diseases. However, several challenges remain in the clinical application of exosomes. Improvements are needed in preparation, characterization, and optimization methods, as well as in reducing the adverse reactions associated with their use. Additionally, the range of applications and the safety of exosomes require further research and evaluation.

Synaptic and synchronic impairments in subcortical brain regions associated with early non-cognitive dysfunction in Alzheimer's disease

For many decades, Alzheimer's disease research has primarily focused on impairments within cortical and hippocampal regions, which are thought to be related to cognitive dysfunctions such as memory and language deficits. The exact cause of Alzheimer's disease is still under debate, making it challenging to establish an effective therapy or early diagnosis. It is widely accepted that the accumulation of amyloid-beta peptide in the brain parenchyma leads to synaptic dysfunction, a critical step in Alzheimer's disease development. The traditional amyloid cascade model is initiated by accumulating extracellular amyloid-beta in brain areas essential for memory and language. However, while it is possible to reduce the presence of amyloid-beta plaques in the brain with newer immunotherapies, cognitive symptoms do not necessarily improve. Interestingly, recent studies support the notion that early alterations in subcortical brain regions also contribute to brain damage and precognitive decline in Alzheimer's disease. A body of recent evidence suggests that early Alzheimer's disease is associated with alterations (e.g., motivation, anxiety, and motor impairment) in subcortical areas, such as the striatum and amygdala, in both human and animal models. Also, recent data indicate that intracellular amyloid-beta appears early in subcortical regions such as the nucleus accumbens, locus coeruleus, and raphe nucleus, even without extracellular amyloid plaques. The reported effects are mainly excitatory, increasing glutamatergic transmission and neuronal excitability. In agreement, data in Alzheimer's disease patients and animal models show an increase in neuronal synchronization that leads to electroencephalogram disturbances and epilepsy. The data indicate that early subcortical brain dysfunctions might be associated with non-cognitive symptoms such as anxiety, irritability, and motivation deficits, which precede memory loss and language alterations. Overall, the evidence reviewed suggests that subcortical brain regions could explain early dysfunctions and perhaps be targets for therapies to slow disease progression. Future research should focus on these non-traditional brain regions to reveal early pathological alterations and underlying mechanisms to advance our understanding of Alzheimer's disease beyond the traditionally studied hippocampal and cortical circuits.

2,5-Dihydroxyphenylethanone: an anti-melanogenic bioactive compound isolated from Ganoderma cochlear

2,5-dihydroxyacetophenone, a natural product from the fruiting bodies of Ganoderma cochlear, can effectively and safely inhibit the production of melanin in zebrafish model. To achieve analogues with more significant inhibition, 9 analogs were synthesised and 13 analogues were purchased commercially. Among them, 14 compounds can inhibit melanin production, of which 5 compounds displayed the most significant inhibitory effects, with inhibitory rates of more than 80%, compared to positive control SymWhite®377 (phenylethyl resorcinol). This study elucidated the melanin-inhibitory effects of 2,5-dihydroxyacetophenone and its analogs, providing a theoretical foundation for their potential applications in anti-melanogenic reagents.

Design and synthesis of novel HDAC6 inhibitor dimer as HDAC6 degrader for cancer treatment by palladium catalysed dimerisation

The enigmatic histone deacetylase 6 (HDAC6) is one of a kind among its family. Recent reports revealed that HDAC6 CD1 exhibits E3 ligase activity. Inspired by these researches, we attempted to develop drugs targeting HDAC6 via novel mechanism. Herein, we report a palladium catalysed transformation and purification method for hydroxamic acid dimers, and series of HDAC6 inhibitor-based dimer showing outstanding biological activities and capability of inducing auto-degradation. Our proof-of-concept was highlighted with 2-amino benzamide-based HDAC6 inhibitor dimers that exhibit great HDAC6 inhibition activity (3.9-15.4 nM), good HDAC1/6 selectivity (95-577), and excellent cytotoxicity against human hormone-resistant prostate cancer (HRPC) PC-3 and non-small cell lung cancer (NSCLC) A549 cell lines (5.9-11.3 and 6.6-17.9 μM, respectively) while simultaneously inducing HDAC6 degradation. These dimers not only induce apoptosis and autophagy but also interfere with kinetochore attachment by the detection of BUBR1 phosphorylation at S670.

Genomic islands and molecular mechanisms relating to drug-resistance in Clostridioides (Clostridium) difficile PCR ribotype 176

OBJECTIVES

To analyse characteristics of Clostridioides difficile PCR ribotype 176 clinical isolates from Poland, the Czech Republic and Slovakia with regard to the differences in its epidemiology.

METHODS

Antimicrobial susceptibility testing and whole genome sequencing were performed on a selected group of 22 clonally related isolates as determined by multilocus variable-number tandem repeat analysis (n = 509). Heterologous expression and functional analysis of the newly identified methyltransferase were performed.

RESULTS

Core genome multilocus sequence typing found 10-37 allele differences. All isolates were resistant to fluoroquinolones (gyrA_p. T82I), aminoglycosides with aac(6')-Ie-aph(2'')-Ia in six isolates. Erythromycin resistance was detected in 21/22 isolates and 15 were also resistant to clindamycin with ermB gene. Fourteen isolates were resistant to rifampicin with rpoB_p. R505K or p. R505K/H502N, and five to imipenem with pbp1_p. P491L and pbp3_p. N537K. PnimBG together with nimB_p. L155I were detected in all isolates but only five were resistant to metronidazole on chocolate agar. The cfrE, vanZ1 and cat-like genes were not associated with linezolid, teicoplanin and chloramphenicol resistance, respectively. The genome comparison identified six transposons carrying antimicrobial resistance genes. The ermB gene was carried by new Tn7808, Tn6189 and Tn6218-like. The aac(6')-Ie-aph(2'')-Ia were carried by Tn6218-like and new Tn7806 together with cfrE gene. New Tn7807 carried a cat-like gene. Tn6110 and new Tn7806 contained an RlmN-type 23S rRNA methyltransferase, designated MrmA, associated with high-level macrolide resistance in isolates without ermB gene.

CONCLUSIONS

Multidrug-resistant C. difficile PCR ribotype 176 isolates carry already described and unique transposons. A novel mechanism for erythromycin resistance in C. difficile was identified.

Cell-specific ferroptosis targeting tumors while sparing immune cells

Ferroptosis serves as a pivotal mechanism in diverse clinical chemotherapeutics and physiological processes, profoundly impacting tumor metabolism and the tumor microenvironment. Recently, the immunosuppression induced by ferroptosis has raised major concerns regarding tumor recurrence upon ferroptosis-based antitumor therapies. However, due to the lack of cell specificity, the antitumor and immunosuppressive effects in ferroptosis are inherently intertwined. Herein, we address the conflicting challenges between immunosuppression and antitumor efficacy in ferroptosis-based therapy by enabling cell-specific ferroptosis, thereby targeting tumors while sparing immune cells. By employing a specially designed nanoagent, i.e., ferrous selenide half-shell-covered gold, we induce notable upregulation of glutathione peroxidase 4 (GPX4) and downregulation of prostaglandin E2, leading to an increase in CD4+ and CD8+ T cell populations and intense antitumor immune responses. Despite the elevated level of GPX4, significant tumor cell ferroptosis is achieved, which is further promoted by the agent's photothermal and photocatalytic effects. Consequently, long-term immunological memory is established, yielding a long-lasting and recurrence-free antitumor efficacy spanning at least 200 days post-treatment. This work unlocks an avenue to balance immunosuppression reversal with tumor inhibition in ferroptosis-based therapies, providing promising prospects for antitumor therapies facing immunological hurdles in the tumor microenvironment.

Human gut commensal Alistipes timonensis modulates the host lipidome and delivers anti-inflammatory outer membrane vesicles to suppress colitis in an Il10-deficient mouse model

Correlative studies have linked human gut microbes to specific health conditions. Alistipes is one such microbial genus negatively linked to inflammatory bowel disease (IBD). However, the protective role of Alistipes in IBD is understudied, and the underlying molecular mechanisms remain unknown. In this study, colonization of Il10-deficient mice with Alistipes timonensis DSM 27924 delays colitis development. Colonization does not significantly alter the gut microbiome composition, but instead shifts the host plasma lipidome, increasing phosphatidic acids while decreasing triglycerides. Outer membrane vesicles (OMVs) derived from Alistipes are detected in the plasma of colonized mice, carrying potentially immunomodulatory metabolites into the host circulatory system. Fractions of A. timonensis OMVs suppress LPS-induced Il6, Il1b, and Tnfa expression in vitro in murine macrophages. We detect putative bioactive lipids in the OMVs, including immunomodulatory sulfonolipids (SoLs) in the active fraction, which are also increased in the blood of colonized mice. Treating Il10-deficient mice with purified SoL B, a representative SoL, suppresses colitis development, suggesting its contribution to the anti-inflammatory phenotype observed with A. timonensis colonization. Thus, A. timonensis OMVs represent a potential mechanism for Alistipes-mediated delay of colitis in Il10-deficient mice via delivery of immunomodulatory lipids and modulation of the host plasma lipidome.

Indirubin-3'-oxime as a dual-action agent: mitigating heat-induced male infertility in Drosophila melanogaster and inhibiting soluble epoxide hydrolase

This study investigated the potential of the indirubin-3'-oxime (I3O) compound to mitigate temperature-induced male infertility in Drosophila melanogaster. Elevated temperatures significantly reduced egg-hatching rates, but I3O supplementation improved these rates, suggesting it can partially restore fertility under heat stress. Additionally, I3O was found to inhibit soluble epoxide hydrolase (sEH), an enzyme involved in the metabolism of epoxyeicosatrienoic acids, which are vital for reproductive health. I3O exhibited sEH inhibitions with an IC50 value of 59.74 ± 0.41 µM. Enzyme kinetics revealed that I3O acts as a non-competitive inhibitor of sEH with a Ki value of 78.88 µM. Molecular docking showed strong interactions between I3O and key residues in the allosteric regions within the sEH enzyme, with a binding affinity of -9.2 kcal/mol. These interactions were supported by 100 ns molecular dynamics simulations, which confirmed the stability of the sEH-I3O complex.

PEGylation technology: addressing concerns, moving forward

PEGylation technology, that is grafting of poly(ethylene glycol)(PEG) to biologics, vaccines and nanopharmaceuticals, has become a cornerstone of modern medicines with over thirty products used in the clinic. PEGylation of therapeutic proteins, nucleic acids and nanopharmaceuticals improves their stability, pharmacokinetic and biodistribution. While PEGylated medicines are safe in the majority of patients, there are growing concerns about the emergence of anti-PEG antibodies and their impact on the therapeutic efficacy of PEGylated medicines as well as broader immune responses, particularly in complement activation and hypersensitivity reactions. These concerns are beginning to scrutinize the future viability of PEGylation technology in medicine design. Here, we outline these concerns, encourage more efforts into looking for comprehensive scientific evidence on the role of anti-PEG antibodies in hypersensitivity reactions, discuss alternatives to PEG and propose strategies for moving PEGylation technology forward.

TET-mediated 5hmC in breast cancer: mechanism and clinical potential

Breast cancer is the most common cancer among women, with differences in clinical features due to its distinct molecular subtypes. Current studies have demonstrated that epigenetic modifications play a crucial role in regulating the progression of breast cancer. Among these mechanisms, DNA demethylation and its reverse process have been studied extensively for their roles in activating or silencing cancer related gene expression. Specifically, Ten-Eleven Translocation (TET) enzymes are involved in the conversion process from 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), which results in a significant difference in the global level of 5hmC in breast cancer compared with normal tissues. In this review, we summarize the functions of TET proteins and the regulated 5hmC levels in the pathogenesis of breast cancer. Discussions on the clinical values of 5hmC in early diagnosis and the prediction of prognosis are also mentioned.

Ophthalmic formulation of methotrexate: a strategy of using the self-assembled LacAC4A nanoparticles for non-invasive drug delivery to the ocular posterior segment

Drug delivery to ocular posterior segment remains difficult due to the challenges imposed by dynamic and static ocular barriers, lesion point targeting, and off-target effect. In this study, a novel approach is demonstrated for non-invasive drug delivery to the ocular posterior segments using lactose-modified azocalix[4] arene (LacAC4A) as a supramolecular ocular drug delivery platform. LacAC4A contains azo groups and is covalently modified by lactose groups, which confers active targeting to the retina, and induces a hypoxic response. The immunomodulator methotrexate (MTX), which is commonly used in ophthalmology to treat immune system diseases such as uveitis, was also selected as a guest to prepare MTX@LacAC4A. The prepared LacAC4A and MTX@LacAC4A systems were characterized, then the internalization mechanisms and hypoxia response abilities were determined through flow cytometry and fluorescence imaging, respectively. Besides, the delivery route and efficiency were verified, and the safety profile of MTX@LacAC4A was evaluated in multiple dimensions. Importantly, it was found that the prepared MTX@LacAC4A exhibits good biocompatibility, can effectively reach the posterior segment, and demonstrates potential ophthalmic applications. These findings lay the grounds for the future development of non-invasive ocular posterior segment disease treatments based on the advanced use of LacAC4A as a drug delivery platform.

Stable intermolecular charge-transfer nanocrystals as efficient immunogenic cell death adjuvants for photoimmunotherapy against trophoblastic and recurrent tumors

Organic photothermal agents (PTAs) with high-performance near-infrared properties hold great promise for precision phototherapy and bioimaging. The development of efficient PTAs depends mainly on advancements in molecular synthesis. However, synthetic approaches for organic PTAs typically involve tedious processes and the consumption of noble metal catalysts, which could leave residues affecting the products' biosafety. In the past few years, a handful of charge transfer complex (CTC) PTAs have been reported. Unfortunately, typical CTCs disintegrate into their donor and acceptor components in water because of their stronger hydrogen bonds with water. To address this issue, facile and synthesis-free super-stable interfacial charge-transfer nanocrystals (H-CTC NPs) have been reported for increasing immunogenic cell death and efficient photoimmunotherapy against tumor recurrence. Water-dispersible H-CTC NPs between pyrene-4,5,9,10-tetrone (PT, acceptor) and indolo[2,3-alpha]carbazole (IC, donor) were prepared with strong intermolecular hydrogen bonds. With this approach, H-CTC NPs are the first examples of stable CTC NPs in water, achieving record-high stability with preferable photothermal conversion efficiency. H-CTC NPs typically cause immunogenic cell death (ICD) and photothermal tumor ablation in vivo. Moreover, distal recurrent tumors are inhibited through the immune synergism between ICD and immune checkpoint therapy. This work developed superstable CTC nanocrystals and explored new pathways for high-performance photoimmunotherapy against recurrent tumors.

Structural comparison of substrate-binding pockets of serine β-lactamases in classes A, C, and D

β-lactams have been the most successful antibiotics, but the rise of multi-drug resistant (MDR) bacteria threatens their effectiveness. Serine β-lactamases (SBLs), among the most common causes of resistance, are classified as A, C, and D, with numerous variants complicating structural and substrate spectrum comparisons. This study compares representative SBLs of these classes, focusing on the substrate-binding pocket (SBP). SBP is kidney bean-shaped on the indented surface, formed mainly by loops L1, L2, and L3, and an additional loop Lc in class C. β-lactams bind in a conserved orientation, with the β-lactam ring towards L2 and additional rings towards the space between L1 and L3. Structural comparison shows each class has distinct SBP structures, but subclasses share a conserved scaffold. The SBP structure, accommodating complimentary β-lactams, determines the substrate spectrum of SBLs. The systematic comparison of SBLs, including structural compatibility between β-lactams and SBPs, will help understand their substrate spectrum.

Development and application of an uncapped mRNA platform

BACKGROUND

A novel uncapped mRNA platform was developed.

METHODS

Five lipid nanoparticle (LNP)-encapsulated mRNA constructs were made to evaluate several aspects of our platform, including transfection efficiency and durability in vitro and in vivo and the activation of humoral and cellular immunity in several animal models. The constructs were eGFP-mRNA-LNP (for enhanced green fluorescence mRNA), Fluc-mRNA-LNP (for firefly luciferase mRNA), SδT-mRNA-LNP (for Delta strain SARS-CoV-2 spike protein trimer mRNA), gDED-mRNA-LNP (for truncated glycoprotein D mRNA coding ectodomain from herpes simplex virus type 2 (HSV2)) and gDFR-mRNA-LNP (for truncated HSV2 glycoprotein D mRNA coding amino acids 1-400).

RESULTS

Quantifiable target protein expression was achieved in vitro and in vivo with eGFP- and Fluc-mRNA-LNP. SδT-mRNA-LNP, gDED-mRNA-LNP and gDFR-mRNA-LNP induced both humoral and cellular immune responses comparable to those obtained by previously reported capped mRNA-LNP constructs. Notably, SδT-mRNA-LNP elicited neutralizing antibodies in hamsters against the Omicron and Delta strains. Additionally, gDED-mRNA-LNP and gDFR-mRNA-LNP induced potent neutralizing antibodies in rabbits and mice. The mRNA constructs with uridine triphosphate (UTP) outperformed those with N1-methylpseudouridine triphosphate (N1mψTP) in the induction of antibodies via SδT-mRNA-LNP.

CONCLUSIONS

Our uncapped, process-simplified and economical mRNA platform may have broad utility in vaccines and protein replacement drugs.KEY MESSAGESThe mRNA platform described in our paper uses internal ribosome entry site (IRES) (Rapid, Amplified, Capless and Economical, RACE; Register as BH-RACE platform) instead of caps and uridine triphosphate (UTP) instead of N1-methylpseudouridine triphosphate (N1mψTP) to synthesize mRNA.Through the self-developed packaging instrument and lipid nanoparticle (LNP) delivery system, mRNA can be expressed in cells more efficiently, quickly and economically.Particularly exciting is that potent neutralizing antibodies against Delta and Omicron real viruses were induced with the new coronavirus S protein mRNA vaccine from the BH-RACE platform.

Protein nanocages: A new frontier in mucosal vaccine delivery and immune activation

Mucosal infectious diseases represent a significant global health burden, impacting millions of people worldwide through pathogens that invade the respiratory, gastrointestinal, and urogenital tracts. Mucosal vaccines provide a promising strategy to combat these diseases by preventing pathogens from entering through the portals as well as within the systemic response compartment. However, challenges such as antigen instability, inefficient delivery, suboptimal immune activation, and the complex biology of mucosal barriers hinder their development. These limitations require integrating specialized adjuvants and delivery systems. Protein nanocages, self-assembling nanoscale structures that can be engineered, may provide an innovative solution for co-delivering antigens and adjuvants. With their remarkable stability, biocompatibility, and design versatility, protein nanocages can potentially overcome existing challenges in mucosal vaccine delivery and enhance protective immune responses. This review highlights the potential of protein nanocages to revolutionize mucosal vaccine development by addressing these challenges.

Exploring covalent inhibitors of SARS-CoV-2 main protease: from peptidomimetics to novel scaffolds

Peptidomimetic inhibitors mimic natural peptide substrates, employing electrophilic warheads to covalently interact with the catalytic Cys145 of Mpro. Examples include aldehydes, α-ketoamides, and aza-peptides, with discussions on their mechanisms of action, potency, and structural insights. Non-peptidomimetic inhibitors utilise diverse scaffolds and mechanisms, achieving covalent modification of Mpro.

Antimicrobial capping agents on silver nanoparticles made via green method using natural products from banana plant waste

Herein, we investigated the phytochemical composition and antibacterial activities of the organic layers from biosynthesized silver nanoparticles (AgNPs). AgNPs were synthesized using Musa paradisiaca and Musa sapientum extracts. UV-vis absorption in the 400-450 nm range indicated surface plasmonic resonance peak of AgNPs. Samples analyses using dynamic light scattering and transmission electron microscopy revealed the presence of particles within nanometric ranges, with sizes of 30-140 nm and 8-40 nm, respectively. Fourier transform infrared (FTIR) unveiled the presence of several organic functional groups on the surface of AgNPs, indicating the presence of phytochemicals from plant extracts. Thin layer chromatography (TLC) of the phytochemicals (capping agents) from AgNPs identified multiple groups of secondary metabolites. These phytochemical capping agents exhibited antibacterial activities against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa, with minimum inhibitory concentrations ranging from 62.5 to 1000 µg/mL. Regardless of the bacterial species or plant parts (leaves or pseudo-stems), capping agents from M. sapientum nanoparticles displayed significantly enhanced antibacterial effectiveness compared to all other samples, including the raw plant extracts and biosynthesized capped and uncapped AgNPs. These results suggest the presence of antimicrobial phytochemicals on biosynthesized AgNPs, highlighting the promise of green nanoparticle synthesis as a valuable approach in bioprospecting antimicrobial agents.

Fundamental knowledge and research regarding the role of immunity in triple-negative breast cancer from 2014-2024: A bibliometric analysis

Immunity has vital research value and promising applications in triple-negative breast cancer (TNBC). Nevertheless, few bibliometric analyses have systematically investigated this area. This study aimed to comprehensively review the collaboration and impact of countries, institutions, authors, and journals on the role of immunity in TNBC from a bibliometric perspective, evaluate the keyword co-occurrence of the knowledge structure, and identify hot trends and emerging topics. Articles and reviews related to immunity in TNBC were retrieved from the Web of Science core collection using subject search. A bibliometric study was conducted primarily using CiteSpace and VOSviewer. A total of 3,104 articles and reviews were included from January 1, 2014, through December 31, 2024. The number of articles on immunization in TNBC is rising. These publications are mainly from 415 institutions in 82 countries, led by China and the USA. Among these publications, Lajos Pusztai published the most papers, while Peter Schmid was co-cited the most. The most productive journals focused on molecular biology, biological immunology, and clinical medicine. Furthermore, co-citation analysis revealed that tumor microenvironment, biomarkers, and immune checkpoint inhibitors are current and developing research areas. The keywords "immunotherapy" and "nanoparticles" are also likely to be new trends and focal points for future research. This study adopted bibliometric and visualization methods to provide a comprehensive review of the research on immunization in TNBC. This article will help researchers better understand the dynamic evolution of the role of immunity in TNBC and identify areas for future research.

Light-triggered nanocarriers for nucleic acid delivery

Gene therapy has evolved into a clinically viable strategy, with several approved products demonstrating its therapeutic potential for genetic disorders, cancer, and infectious diseases, and it has ample applications in regenerative medicine. Its success depends on the ability to efficiently and specifically deliver therapeutic nucleic acids (NAs) into target cells. Although viral or chemical carriers have been used in pioneering applications, safety concerns, and variable delivery efficiencies have prompted the search for alternative delivery vehicles. Light-mediated strategies have gained particular interest due to their biocompatibility and ability to improve the intracellular delivery efficiency. In this review, we focus on recent advancements in the development of light-triggered NA delivery carriers and discuss how they can be designed to overcome specific intracellular barriers. Additionally, we discuss notable therapeutic applications and highlight challenges and opportunities for translating this technology to a clinical setting.

tRNA modifications: greasing the wheels of translation and beyond

Transfer RNA (tRNA) is one of the most abundant RNA types in cells, acting as an adaptor to bridge the genetic information in mRNAs with the amino acid sequence in proteins. Both tRNAs and small fragments processed from them play many nonconventional roles in addition to translation. tRNA molecules undergo various types of chemical modifications to ensure the accuracy and efficiency of translation and regulate their diverse functions beyond translation. In this review, we discuss the biogenesis and molecular mechanisms of tRNA modifications, including major tRNA modifications, writer enzymes, and their dynamic regulation. We also summarize the state-of-the-art technologies for measuring tRNA modification, with a particular focus on 2'-O-methylation (Nm), and discuss their limitations and remaining challenges. Finally, we highlight recent discoveries linking dysregulation of tRNA modifications with genetic diseases.

Mature biofilm-sensitive lysozyme-grafted Bi-guanidine backbone porphyrin nanorods for deep penetration and double phototherapy

The efficacy of antibacterial therapy was largely vitiated because of the shield of bacteria by the intricate architecture of biofilms. For emerging phototherapy strategies like photothermal therapy (PTT) and photodynamic therapy (PDT), dense biofilms can substantially impede the permeation of photo-agents, ultimately compromising the thermal conductivity and reactive oxygen species (ROS) diffusion. To address these challenges, we have proposed a biofilm-sensitive MT nanorod with dual phototherapy, based on the ordered directional assembly of photosensitizer meso-tetra(4-carboxyphenyl) porphine (TCPP) molecules by metformin hydrochloride (MET) as functional backbone. The formed MT nanorod avoids the uncontrollable aggregation of TCPP, producing pleased water-solubility with efficient fluorescent emission and allowing simultaneous PTT-PDT effects under a single laser. The grafted MT-LYZ by conjugation of lysozyme (LYZ) to MT nanorods can be used for acidic environment guided deep biofilm penetration and LYZ-assisted dual phototherapy for effective elimination of mature biofilm, with MT-LYZ acquires adaptive conversion from negative to positive charges in biofilm. Because of effective bacterial ablation within biofilms and gene regulation in bacterial quorum, MT-LYZ was successfully utilized for the treatment of deep-seated MRSA biofilm infections with minimized side effects, which promotes the repair of the MRSA biofilm infected wounds in mice and displays anti-inflammatory features, providing an alternative approach for effectively combating biofilm infections.

Is uric acid a true antioxidant? Identification of uric acid oxidation products and their biological effects

Uric acid (UA), the final product of purine metabolism in humans, exhibits a dual role as an anti or pro-oxidant, depending on the microenvironment. The two-electron oxidation of UA by biological oxidants can neutralize such harmful molecules. Additionally, UA chelates metals and can activate adaptive response against oxidation. However, some products of the reaction between UA and oxidants are not inert and, therefore, do not confer the anticipated antioxidant protection. A direct pro-oxidant effect is favoured in the one-electron oxidation of UA by heme-peroxidases yielding free radical intermediates that can initiate or propagate a radical-chain reaction. Additionally, an indirect pro-oxidant effect has been proposed by eliciting the expression or activation of enzymes that catalyse oxidant production, e.g. NADPH oxidase (NOX). This review brings together fundamental concepts and the molecular mechanisms of the redox reactions involving UA. The signature metabolites from these reactions are discussed to give valuable insights on whether these intermediates are being formed and what role they may play in disease pathogenesis. It proposes that, through identifying specific products, it may be possible to elucidate whether a harmful or protective action is linked to downstream bioactivities.

Small molecules targeting the eubacterial β-sliding clamp discovered by combined in silico and in vitro screening approaches

Antibiotic resistance stands as the foremost post-pandemic threat to public health. The urgent need for new, effective antibacterial treatments is evident. Protein-protein interactions (PPIs), owing to their pivotal role in microbial physiology, emerge as novel and attractive targets. Particularly promising is the α-subunit/β-sliding clamp interaction, crucial for the replicative competence of bacterial DNA polymerase III holoenzyme. Through pharmacophore-based virtual screening, we identified 4,000 candidate small molecule inhibitors targeting the β-clamp binding pocket. Subsequently, these candidates underwent evaluation using the BRET assay in yeast cells. Following this, three hits and 28 analogues were validated via Protein Thermal Shift and competitive ELISA assays. Among them, thiazolo[4,5-d]-pyrimidinedione and benzanilide derivatives exhibited micromolar potency in displacing the β-clamp protein partner and inhibiting DNA replication. This screening campaign unveiled new chemical classes of α/β-clamp PPI disruptors capable of inhibiting DNA polymerase III activity, which lend themselves for further optimisation to improve their antibacterial efficacy.

Recent advances in nuclear actin research

Actin was first observed in the nucleus more than sixty years ago but research on nuclear actin did not receive significant attention for the next forty years. It only started to accelerate around the year 2000, when the first convincing experimental data emerged indicating that actin participates in essential nuclear processes. Today, we know that actin is involved in transcription, replication, DNA repair, chromatin remodeling, and participates in the determination of nuclear shape and size. In this paper we review the results of the last five years of increasingly intensive research on nuclear actin, because on one hand, the field has expanded with several new directions during this time, and on the other hand, the enrichment of our picture of nuclear actin will certainly provide a more solid foundation and new impetus for its future investigation.

Quantifying antibody binding: techniques and therapeutic implications

The binding kinetics of an antibody for its target antigen represent key determinants of its biological function and success as a novel biotherapeutic. Defining these interactions and kinetics is critical for understanding the pharmacological and pharmacodynamic profiles of antibodies in therapeutic applications, with line of sight to clinical translation. In this review, we discuss the latest developments in approaches to measure and modulate antibody-antigen interactions, including antibody engineering, novel antibody formats, current, and emerging technologies for measuring antibody-antigen binding interactions, and emerging perspectives within the field. We also explore how emerging computational methods are set to become powerful tools for modeling antibody-binding interactions under physiologically relevant conditions. Finally, we consider the therapeutic implications of modulating target engagement in terms of pharmacodynamics and pharmacokinetics.

How has the field of immunogenic cell death in breast cancer evolved and impacted clinical practice over the past eleven years?

This study elucidates the research landscape of immunogenic cell death (ICD) in breast cancer through a bibliometric analysis of 457 Web of Science articles. Contributions from China and the USA are particularly prominent, with notable international collaborations. Core journals such as Biomaterials published influential studies, while researchers like Huang Y made impactful contributions. High-frequency keyword analysis identified key research hotspots, including immunotherapy, the tumor microenvironment, and nanomedicine. The integration of chemotherapy with immunotherapy and the identification of key proteins have driven recent advancements. Fundamental research on immunotherapy, photodynamic therapy (PDT), and triple-negative breast cancer (TNBC) points to future trends and potential breakthroughs. This study offers a strategic overview of ICD in breast cancer, providing insights into clinical practice and guiding future research in the field.

Integrating immune library probing with structure-based computational design to develop potent neutralizing nanobodies against emerging SARS-CoV-2 variants

To generate antibodies (Abs) against SARS-CoV-2 emerging variants, we integrated multiple tools and engineered molecules with excellent neutralizing breadth and potency. Initially, the screening of an immune library identified a nanobody (Nb), termed Nb4, specific to the receptor-binding domain (RBD) of the Omicron BA.1 variant. A Nb4-derived heavy chain antibody (hcAb4) recognized the spike (S) of the Wuhan, Beta, Delta, Omicron BA.1, and BA.5 SARS-CoV-2 variants. A high-resolution crystal structure of the Nb4 variable (VHH) domain in complex with the SARS-CoV-2 RBD (Wuhan) defined the Nb4 binding mode and interface. The Nb4 VHH domain grasped the RBD and covered most of its outer face, including the core and the receptor-binding motif (RBM), which was consistent with hcAb4 blocking RBD binding to the SARS-CoV-2 receptor. In mouse models, a humanized hcAb4 showed therapeutic potential and prevented the replication of SARS-CoV-2 BA.1 virus in the lungs of the animals. In vitro, hcAb4 neutralized Wuhan, Beta, Delta, Omicron BA.1, and BA.5 viral variants, as well as the BQ.1.1 subvariant, but showed poor neutralization against the Omicron XBB.1.5. Structure-based computation of the RBD-Nb4 interface identified three Nb4 residues with a reduced contribution to the interaction with the XBB.1.5 RBD. Site-saturation mutagenesis of these residues resulted in two hcAb4 mutants with enhanced XBB.1.5 S binding and virus neutralization, further improved by mutant Nb4 trimers. This research highlights an approach that combines library screening, Nb engineering, and structure-based computational predictions for the generation of SARS-CoV-2 Omicron-specific Abs and their adaptation to emerging variants.

Mitochondrial dysfunction: the hidden catalyst in chronic kidney disease progression

Chronic kidney disease (CKD) represents a global health epidemic, with approximately one-third of affected individuals ultimately necessitating renal replacement therapy or transplantation. The kidney, characterized by its exceptionally high energy demands, exhibits significant sensitivity to alterations in energy supply and mitochondrial function. In CKD, a compromised capacity for mitochondrial ATP synthesis has been documented. As research advances, the multifaceted roles of mitochondria, extending beyond their traditional functions in oxygen sensing and energy production, are increasingly acknowledged. Empirical studies have demonstrated a strong association between mitochondrial dysfunction and the pathogenesis of fibrosis and cellular apoptosis in CKD. Targeting mitochondrial dysfunction holds substantial therapeutic promise, with emerging insights into its epigenetic regulation in CKD, particularly involving non-coding RNAs and DNA methylation. This article presents a comprehensive review of contemporary research on mitochondrial dysfunction in relation to the onset and progression of CKD. It elucidates the associated molecular mechanisms across various renal cell types and proposes novel research avenues for CKD treatment.

Electron-donor planar extension based on donor-acceptor-donor molecules generates charge transfer-mediated J-aggregates for NIR-II photothermal immunotherapy and bacterial elimination

Second near-infrared photothermal therapy (NIR-II-PTT) has emerged as a promising therapeutic modality in diverse medical aspects. In particular, J-aggregate is a potential strategy to develop high-performance NIR-II-PTT materials, however, it suffers from specific molecular skeletons and complex control conditions. Herein, we presented a simply electron-donor planar extension strategy to develop donor-acceptor-donor (D-A-D) type small molecules with charge-transfer (CT)-mediated J-aggregation for NIR-II PTT. By integrating ring-fused thiophene units in a benzo[1,2-'c:4,5-c']bis[1,2,5]thiadiazole (BBTDT) scaffold, we enabled tunable electrostatic and π-π interactions, promoting CT-mediated J-aggregate formation. The resulting BDTT nanoparticles showed an impressive light-harvesting capability (ɛ1064) of 2.92 × 104 M-1 cm-1 under 1064 nm excitation, yielding an exceptional photothermal performance (ɛ1064 × PCE = 1.99 × 104), which surpasses those of reported D-A-D type NIR-II-absorbing small molecules. This outstanding NIR-II photothermal property induced sufficient immunogenic cell death and amplified the final ablation of deep-seated tumor in conjunction with programmed cell death protein 1 (PD-1). Meanwhile, the fabricated BDTT nanoparticles also facilitated hyperthermia-triggered bacterial death. Together, this study provides valuable insights into developing NIR-II-absorbing J-aggregates based on D-A-D type small molecules, and offers critical potentials to treat malignant tumors and prevents postsurgical infections.

β-amino acid substitution in the SIINFEKL antigen alters immunological recognition

BACKGROUND

Peptide vaccines offer a direct way to initiate an immunogenic response to a defined antigen epitope. However, peptide vaccines are unstable in vivo, subject to rapid enzymatic proteolysis. Replacement of an α-amino acid residue with a homologous β-amino acid residue (native side chain, but backbone extended by a single CH2 unit) impairs proteolysis at nearby amide bonds. Therefore, antigen analogues containing α-to-β replacements have been examined for functional mimicry of native all-α antigens. Another group previously took this approach in the ovalbumin (OVA) antigen model by evaluating single α-to-β analogues of the murine major histocompatibility complex (MHC) I-restricted peptide SIINFEKL.

METHODS

We re-examined this set of α/β SIINFEKL antigens. We tested the susceptibility to proteolysis in mouse serum and their ability to activate OVA-antigen-specific CD8 T cells in vitro. Additionally, we tested the α/β antigens in vivo for their ability to induce an antigen-specific immunogenic response in naïve mice and in OVA-expressing tumor-bearing mice.

RESULTS

The α/β antigens were comparable to the native antigen in their susceptibility to proteolysis in serum. Each α/β antigen was capable of activating antigen-specific CD8 T cells in vitro. However, antigen-specific CD8 T cells induced against α/β antigens in vivo were not cross-reactive to the native antigen. Moreover, immunization with α/β analogues did not elicit anti-tumor effects in tumor-bearing mice.

CONCLUSIONS

We conclude that even though α/β analogues of the SIINFEKL antigen can elicit a T cell-based response, this class of backbone-modified peptides is not promising from the perspective of antitumor vaccine development.

Discovery and biological evaluation of a novel and highly potent JAK2 inhibitor for the treatment of triple negative breast cancer

Janus kinase 2 (JAK2) is considered an attractive target for the treatment of triple-negative breast cancer (TNBC). Herein, we discovered six JAK2 inhibitors using structure-based virtual screening and molecular docking. Among them, JNN-5 was the best compound. It indicated strong inhibitory effects on JAK2 in the nanomolar range (IC50 = 0.41 ± 0.03 nM), and high selectivity for JAK2 over JAK1 and JAK3 (selectivity index (SI) > 73.17). Moreover, molecular dynamics (MD) simulation exhibited that JNN-5 bound with high stability to JAK2 JH1. Cellular assays revealed that JNN-5 displayed strong antiproliferative activities in the TNBC cell lines (MDA-MB-468, MDA-MB-213, HCC70, MDA-MB-157). JNN-5 significantly reduced the migration of HUVECs with the dose-dependence. JNN-5 had a significant inhibitory effect on multidrug-resistant MDA-MB-231/ADR (IC50 = 0.37 ± 0.02 μM). These data demonstrate that JNN-5 may be a highly effective and selective antitumor compound for the treatment of TNBC.

Indole signaling in Escherichia coli: a target for antivirulence therapy?

Pathogenic Escherichia coli are a major cause of infections in both humans and animals, leading to conditions such as severe diarrheal diseases, urinary tract infections, enteritis, and septicemia. To combat bacterial infections, antibiotics are widely utilized. However, the extensive and inappropriate use of antibiotics has fueled the development and spread of antibiotic resistance, posing a significant challenge to the effective treatment of E. coli. There is consequently an urgent need to explore alternative therapies to control such infections. This review provides an overview of the recent findings concerning indole signaling in E. coli. E. coli uses indole as a quorum sensing molecule, and indole signaling has been reported to decrease various virulence factors in pathogenic E. coli, including motility, biofilm formation, adherence to host cells, expression of the LEE pathogenicity island, and formation of attaching and effacing lesions. This makes indole signaling an interesting target for the development of new therapeutics in the framework of antivirulence therapy. Both natural and synthetic indole analogues have been explored as potential virulence inhibitors. This alternative approach could be advantageous, as it will exert less selective pressure for resistance development than conventional antibiotics.

Biomimetic peptide conjugates as emerging strategies for controlled release from protein-based materials

Biopolymers, such as collagens, elastin, silk fibroin, spider silk, fibrin, keratin, and resilin have gained significant interest for their potential biomedical applications due to their biocompatibility, biodegradability, and mechanical properties. This review focuses on the design and integration of biomimetic peptides into these biopolymer platforms to control the release of bioactive molecules, thereby enhancing their functionality for drug delivery, tissue engineering, and regenerative medicine. Elastin-like polypeptides (ELPs) and silk fibroin repeats, for example, demonstrate how engineered peptides can mimic natural protein domains to modulate material properties and drug release profiles. Recombinant spider silk proteins, fibrin-binding peptides, collagen-mimetic peptides, and keratin-derived structures similarly illustrate the ability to engineer precise interactions and to design controlled release systems. Additionally, the use of resilin-like peptides showcases the potential for creating highly elastic and resilient biomaterials. This review highlights current achievements and future perspectives in the field, emphasizing the potential of biomimetic peptides to transform biopolymer-based biomedical applications.

Microfluidic captured patient-derived circulating endothelial cells identify novel targets of pulmonary arterial hypertension

Endothelial cell (EC) dysfunction and gene expression abnormalities in pulmonary arterial hypertension (PAH) vary among patients. Existing PAH cell sources, often from lung transplant patients, are influenced by drug treatments and are inadequate for identifying early-stage PAH genes. We propose isolating viable circulating endothelial cells (CECs) from the whole blood of PAH patients to evaluate their potential as surrogates for PAH-ECs and discover novel gene expression profiles relevant to PAH. We developed a microfluidic bioengineering system to directly detect and separate CECs from the blood of PAH patients. Viable CECs were isolated and compared with those from healthy individuals and PAH patients. Differentially expressed genes (DEGs) were identified, and the role of the novel gene PRND in PAH was investigated using in vitro, genomic, and in vivo methods. CEC levels were higher in PAH patients and correlated with disease severity. Transcriptomic analysis revealed 138 DEGs when comparing healthy controls with PAH patients of intermediate severity. These DEGs were associated with PAH-specific markers and angiogenesis. The Doppel (PRND) gene, previously unlinked to PAH, was significantly upregulated in PAH-CECs and PAH-ECs. Overexpression of Doppel in human PAH-ECs matched 13-15 % of DEGs related to hypoxia and endothelial-to-mesenchymal transition (EndMT). Doppel blocking or knockdown in ECs activated the BMPRII/pSMAD1/5 pathway and altered EndMT-related gene levels, while Doppel-knockout mice showed reduced right ventricular systolic pressure in Sugen/Hypoxia PH model. Collectively our findings demonstrate that PAH patient-derived CECs are a promising tool for identifying novel genes involved in PAH pathogenesis.

Design, synthesis and biological activity of novel Xuetongsu derivatives as potential anticancer agents by inducing apoptosis

Xuetongsu (XTS, Schisanlactone E) is one of the main active compounds and considered as the star molecule isolated from Kadsura heteroclita (Roxb.) Craib. In order to improve XTS anti-tumour bioactivities, a series of novel XTS derivatives were designed and synthesised by introducing an amide bond at the parent. Anti-proliferative assays on four different human tumour cell lines (BGC-823, HepG-2, HCT-116, and MCF-7) showed that the anti-tumour activities of most derivatives increased greatly compared to the parent XTS, and especially, compounds A-7, A-14, and A-18 exhibited multiple anti-tumour effects. Among them, compound A-7 has the best biological activities on the four tumour cell lines with the IC50 values ranging from 13.86 to 20.71 μM, which could significantly increase the fraction of apoptotic cells according to flow cytometry experience. Further study demonstrated that A-7 could induce apoptosis on HepG-2 cells through influencing the key apoptotic related proteins, such as Bcl-2, Bax, and cleaved Caspase-3.

RNase P cleavage of pseudoknot substrates reveals differences in active site architecture that depend on residue N-1 in the 5' leader

We show that a small biotin-binding RNA aptamer that folds into a pseudoknot structure acts as a substrate for bacterial RNase P RNA (RPR) with and without the RNase P C5 protein. Cleavage in the single-stranded region in loop 1 was shown to depend on the presence of a RCCA-motif at the 3' end of the substrate. The nucleobase and the 2'hydroxyl at the position immediately 5' of the cleavage site contribute to both cleavage efficiency and site selection, where C at this position induces significant cleavage at an alternative site, one base upstream of the main cleavage site. The frequencies of cleavage at these two sites and Mg2+ binding change upon altering the structural topology in the vicinity of the cleavage site as well as by replacing Mg2+ with other divalent metal ions. Modelling studies of RPR in complex with the pseudoknot substrates suggest alternative structural topologies for cleavage at the main and the alternative site and a shift in positioning of Mg2+ that activates the H2O nucleophile. Together, our data are consistent with a model where the organization of the active site structure and positioning of Mg2+ is influenced by the identities of residues at and in the vicinity of the site of cleavage.

An mRNA vaccine candidate encoding cholera toxin subunit B and conserved antigens of influenza viruses confers cross-protection against influenza a viruses in adult and aged mice

Currently, vaccination with influenza vaccines is still an effective strategy to prevent infection by seasonal influenza virus. However, seasonal influenza vaccines frequently fail to induce effective immune protection against rapidly changing seasonal influenza viruses and emerging zoonotic influenza viruses. In addition, seasonal influenza vaccines may not confer potent protection in elderly and immunocompromised individuals. There is an urgent need to develop potent broad-spectrum influenza vaccines to address this problem. Herein, we designed an mRNA-based broad-spectrum influenza vaccine candidate encoding cholera toxin subunit B and conserved antigens of influenza viruses. In both adult and aged mice, this universal influenza mRNA vaccine candidate stimulated robust T-cell and humoral immune responses and conferred effective protection against broad-spectrum influenza viruses in both adult and aged mice.

Homogeneous antibody-drug conjugates with dual payloads: potential, methods and considerations

The development of site-specific dual-payload antibody-drug conjugates (ADCs) represents a potential advancement in targeted cancer therapy, enabling the simultaneous delivery of two distinct drugs into the same cancer cells to overcome payload resistance and enhance therapeutic efficacy. Here, we examine various methodologies for achieving site-specific dual-payload conjugation, including the use of multi-functional linkers, canonical amino acids, non-canonical amino acids, and enzyme-mediated methods, all of which facilitate precise control over payload attachment while ensuring homogeneity. We explore the implications of different conjugation techniques on drug-to-antibody ratios and the ratios of the two payloads, as well as their impact on process complexity and manufacturability. Additionally, we address the potential advantages of dual-payload ADCs compared to ADCs combined with traditional chemotherapy or single-payload ADC/ADC combinations. By evaluating these innovative methods, we aim to provide a comprehensive understanding of the current landscape in dual-payload ADC development and outline emerging directions necessary for further advancement of this promising therapeutic strategy.

Machine learning-assisted design of immunomodulatory lipid nanoparticles for delivery of mRNA to repolarize hyperactivated microglia

Regulating inflammatory microglia presents a promising strategy for treating neurodegenerative and autoimmune disorders, yet effective therapeutic agents delivery to these cells remains a challenge. This study investigates modified lipid nanoparticles (LNP) for mRNA delivery to hyperactivated microglia, particularly those with pro-inflammatory characteristics, utilizing supervised machine learning (ML) classifiers. We developed and screened a library of 216 LNP formulations with varying lipid compositions, N/P ratios, and hyaluronic acid (HA) modifications. The transfection efficiency of eGFP mRNA was assessed in the BV-2 murine microglia cell line under different immunological states, including resting and activated conditions (LPS-activated and IL4/IL13-activated). ML-guided morphometric analysis tracked the phenotypes of various microglia subtypes before and after transfection. Four supervised ML classifiers were investigated to predict transfection efficiency and phenotypic changes based on LNP design parameters. The Multi-Layer Perceptron (MLP) neural network emerged as the best-performing model, achieving weighted F1-scores ≥0.8. While it accurately predicted responses from LPS-activated and resting cells, it struggled with IL4/IL13-activated cells. The MLP model was validated by predicting the performance of four unseen LNP formulations delivering eGFP mRNA to LPS-activated BV2 cells. HA-LNP2 emerged as optimal formulation for delivering target IL10 mRNA, effectively suppressing inflammatory phenotypes, evidenced by shifts in cell morphology, increased IL10 expression, and reduced TNF-α levels. We also evaluated HA-LNP2 on LPS-activated human iPSC-derived microglia, confirming its efficacy in modulating inflammatory responses. This study highlights the potential of tailored LNP design and ML techniques to enhance mRNA therapy for neuroinflammatory disorders by leveraging carrier's immunogenic properties to modulate microglial responses.

Leveraging strain competition to address antimicrobial resistance with microbiota therapies

The enteric microbiota is an established reservoir for multidrug-resistant organisms that present urgent clinical and public health threats. Observational data and small interventional studies suggest that microbiome interventions, such as fecal microbiota products and characterized live biotherapeutic bacterial strains, could be an effective antibiotic-sparing prevention approach to address these threats. However, bacterial colonization is a complex ecological phenomenon that remains understudied in the context of the human gut. Antibiotic resistance is one among many adaptative strategies that impact long-term colonization. Here we review and synthesize evidence of how bacterial competition and differential fitness in the context of the gut present opportunities to improve mechanistic understanding of colonization resistance, therapeutic development, patient care, and ultimately public health.

Role of iron in brain development, aging, and neurodegenerative diseases

It is now understood that iron crosses the blood-brain barrier via a complex metabolic regulatory network and participates in diverse critical biological processes within the central nervous system, including oxygen transport, energy metabolism, and the synthesis and catabolism of myelin and neurotransmitters. During brain development, iron is distributed throughout the brain, playing a pivotal role in key processes such as neuronal development, myelination, and neurotransmitter synthesis. In physiological aging, iron can selectively accumulate in specific brain regions, impacting cognitive function and leading to intracellular redox imbalance, mitochondrial dysfunction, and lipid peroxidation, thereby accelerating aging and associated pathologies. Furthermore, brain iron accumulation may be a primary contributor to neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Comprehending the role of iron in brain development, aging, and neurodegenerative diseases, utilizing iron-sensitive Magnetic Resonance Imaging (MRI) technology for timely detection or prediction of abnormal neurological states, and implementing appropriate interventions may be instrumental in preserving normal central nervous system function.

A stable GH31 α-glucosidase as a model system for the study of mutations leading to human glycogen storage disease type II

GH31 glycosidases are widespread across organisms, but remarkably, less than 1% of them have been biochemically characterised to date. Among them, human lysosomal acid α-glucosidase (GAA) stands out due to its link to Pompe disease, a rare lysosomal storage disorder caused by its deficiency. This disease results in glycogen accumulation, severe cellular damage, motor impairment, and premature death. Structural and functional studies of GAA mutants are challenging due to their instability and lack of activity, hindering their expression and purification. The GH31 enzyme MalA from a hyperthermophilic archaeon is explored here as a stable homolog of GAA. MalA is highly expressible, easy to purify, and structurally characterised. The R400H mutant in MalA, corresponding to the pathogenic GAA R600H mutation, revealed here a 1200-fold drop in specificity constant and >8 °C reduction in thermal stability. We propose MalA's as a robust model for studying GAA mutations and developing therapeutic chaperones.

Characterization of the binding features between SARS-CoV-2 5'-proximal transcripts of genomic RNA and nucleocapsid proteins

Packaging signals (PSs) of coronaviruses (CoVs) are specific RNA elements recognized by nucleocapsid (N) proteins that direct the selective packaging of genomic RNAs (gRNAs). These signals have been identified in the coding regions of the nonstructural protein 15 (Nsp 15) in CoVs classified under Embecovirus, a subgenus of betacoronaviruses (beta-CoVs). The PSs in other alpha- and beta-CoVs have been proposed to reside in the 5'-proximal regions of gRNAs, supported by comprehensive phylogenetic evidence. However, experimental data remain limited. In this study, we investigated the interactions between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) 5'-proximal gRNA transcripts and N proteins using electrophoretic mobility shift assays (EMSAs). Our findings revealed that the in vitro synthesized 5'-proximal gRNA transcripts of CoVs can shift from a major conformation to alternative conformations. We also observed that the conformer comprising multiple stem-loops (SLs) is preferentially bound by N proteins. Deletions of the 5'-proximal structural elements of CoV gRNA transcripts, SL1 and SL5a/b/c in particular, were found to promote the formation of alternative conformations. Furthermore, we identified RNA-binding peptides from a pool derived from SARS-CoV N protein. These RNA-interacting peptides were shown to preferentially bind to wild-type SL5a RNA. In addition, our observations of N protein condensate formation in vitro demonstrated that liquid-liquid phase separation (LLPS) of N proteins with CoV-5'-UTR transcripts was influenced by the presence of SL5a/b/c. In conclusion, these results collectively reveal previously uncharacterized binding features between the 5'-proximal transcripts of CoV gRNAs and N proteins.

Staphylococcus aureus nt5 gene mutation through CRISPR RNA-guided base editing weakens bacterial virulence and immune evasion

The resistance of commonly used clinical antibiotics, such as daptomycin (DAP), has become increasingly serious in the fight against Staphylococcus aureus (S. aureus) infection. It is essential to explore key pathogenicity-driven genes/proteins in bacterial infection and antibiotics resistance, which contributes to develop novel therapeutic strategies against S. aureus infections. The nt5 gene of S. aureus, encoding 5'-nucleotidase (NT5), is nearly unknown for its function in drug resistance and bacterial infection. Herein, to reveal nt5 gene role in drug resistance and infection ability of S. aureus, we performed nt5C166T gene mutation using a clustered regulatory interspaced short palindromic repeat ribonucleic acid (RNA)-guided base editing system to investigate the lose-of-function of NT5 protein. Subsequent transcriptome sequencing of the mutant strain revealed that nt5 inactivation caused changes in cell membrane integrity and inhibited nucleotide metabolism, suggesting the nt5 gene may be involved in bacterial drug resistance and virulence. The mutant strain exhibited enhanced tolerance to DAP treatment by attenuating cell membrane potential dissipation and slowing deoxyribonucleic acid release. Moreover, the nt5 mutation alleviated abscess degree of mouse kidneys caused by S. aureus infection byreducing the expression of IL-1β, IL-6, and IL-18. The nt5 mutant strain was easily swallowed by host immune cells, resulting in weak bacterial toxicity of the S. aureus mutant in the bacterial infection process. In summary, nt5 gene mutation confers tolerance to DAP and a lower bacterial capacity to form kidney abscesses through phagocytosis of host immune cells, which indicates the targeted inhibition of NT5 protein would offer a potential new therapeutic strategy against S. aureus infection.

Biparatopic binding of ISB 1442 to CD38 in trans enables increased cell antibody density and increased avidity

ISB 1442 is a bispecific biparatopic antibody in clinical development to treat hematological malignancies. It consists of two adjacent anti-CD38 arms targeting non-overlapping epitopes that preferentially drive binding to tumor cells and a low-affinity anti-CD47 arm to enable avidity-induced blocking of proximal CD47 receptors. We previously reported the pharmacology of ISB 1442, designed to reestablish synthetic immunity in CD38+ hematological malignancies. Here, we describe the discovery, optimization and characterization of the ISB 1442 antigen binding fragment (Fab) arms, their assembly to 2 + 1 format, and present the high-resolution co-crystal structures of the two anti-CD38 Fabs, in complex with CD38. This, with biophysical and functional assays, elucidated the underlying mechanism of action of ISB 1442. In solution phase, ISB 1442 forms a 2:2 complex with CD38 as determined by size-exclusion chromatography with multi-angle light scattering and electron microscopy. The predicted antibody-antigen stoichiometries at different CD38 surface densities were experimentally validated by surface plasmon resonance and cell binding assays. The specific design and structural features of ISB 1442 enable: 1) enhanced trans binding to adjacent CD38 molecules to increase Fc density at the cancer cell surface; 2) prevention of avid cis binding to monomeric CD38 to minimize blockade by soluble shed CD38; and 3) greater binding avidity, with a slower off-rate at high CD38 density, for increased specificity. The superior CD38 targeting of ISB 1442, at both high and low receptor densities, by its biparatopic design, will enhance proximal CD47 blockade and thus counteract a major tumor escape mechanism in multiple myeloma patients.

Copper-instigated modulatory cell mortality mechanisms and progress in kidney diseases

Copper is a vital cofactor in various enzymes, plays a pivotal role in maintaining cell homeostasis. When copper metabolism is disordered and mitochondrial dysfunction is impaired, programmed cell death such as apoptosis, paraptosis, pyroptosis, ferroptosis, cuproptosis, autophagy and necroptosis can be induced. In this review, we focus on the metabolic mechanisms of copper. In addition, we discuss the mechanism by which copper induces various programmed cell deaths. Finally, this review examines copper's involvement in prevalent kidney diseases such as acute kidney injury and chronic kidney disease. The findings indicate that the use of copper chelators or plant extracts can mitigate kidney damage by reducing copper accumulation, offering novel insights into the pathogenesis and treatment strategies for kidney diseases.

Assessment for antibiotic resistance in Helicobacter pylori: A practical and interpretable machine learning model based on genome-wide genetic variation

Helicobacter pylori (H. pylori) antibiotic resistance poses a global health threat. Accurate identification of antibiotic resistant strains is essential for the control of infection. In the present study, our goal is to leverage the whole-genome data of H. pylori to develop practical and interpretable machine learning (ML) models for comprehensive antibiotic resistance assessment. A total of 296 H. pylori isolates with genome-wide data were downloaded from the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) and the National Center for Biotechnology Information (NCBI) databases. By training ML models on feature sets of single nucleotide polymorphisms from SNP calling (SNPs-1), antibiotic-resistance SNP annotated by the Comprehensive Antibiotic Resistance Database (SNPs-2), gene presence or absence (GPA), we generated predictive models for four antibiotics and multidrug-resistance (MDR). Among them, the models that combined SNPs-1, SNPs-2, and GPA data demonstrated the best performance, with the eXtreme Gradient Boosting (XGBoost) consistently outperforming others. And then we utilized the SHapley Additive exPlanations (SHAP) method to interpret the ML models. Furthermore, a free web application for the MDR model was deployed to the GitHub repository (https://H.pylori/MDR/App/). Our study demonstrated the promise of employing whole-genome data in conjunction with ML algorithms to forecast H. pylori antibiotic resistance. In the future, the application of this approach for predicting H. pylori antibiotic resistance would hold the potential to mitigate the empiric administration.

Structural and biochemical differences between non-catalytic and catalytic antibodies

A conventional antibody can be converted into its catalytic counterparts by deleting Pro95 in the CDR-3 of human and mice antibody light chains, as previously reported. T99wt is a naturally occurring human antibody light chain that we transformed into its catalytic antibody using Pro95 deletion. In peptidase activity tests, T99wt exhibited a low catalytic activity against a synthetic peptide Arg-pNA and hardly cleaved amyloid-β peptide. In contrast, the engineered variant (T99-Pro95(-)) demonstrated significant catalytic activity, effectively cleaving both Arg-pNA substrate and amyloid-β peptides. In this study, the structural basis for the acquisition of enzymatic function through Pro95 deletion in the CDR-3 region of the light chain was elucidated using X-ray crystallography and molecular dynamics (MD) simulations. X-ray crystallography revealed that Pro95 deletion substantially reduces the distance between Asp1 and His93-key residues for catalytic activity - from 9.56 Å in T99wt to 3.84 Å in T99-Pro95(-). The observed decrease in distance indicates a strong interaction between Asp1(Oδ1) and His93(Nε2), contributing to the formation of an active site in T99-Pro95(-). MD simulations revealed that the entire structure exhibits slight fluctuations and adopts various configurations upon the removal of Pro95. In particular, when His residues in the catalytic region are fully deprotonated, Asp1, His93, and Ser27a transiently come into close proximity, enabling the formation of a functional catalytic triad. Catalytic antibodies can be made starting from just the amino acid sequence of a desired mAb, which may be available in databases such as OAS or IMGT. Therefore, our finding represents a significant technological advancement.