Release and activity of histone in diseases

Quercetin protects red blood cells from aggregation, eryptosis, and delayed hemolysis caused by cell-free histones through sialic acid interaction

Histones are nuclear proteins and play a vital role in regulating gene expression. Cell free histones in the circulation proved as damage-associated molecular patterns and were positively associated with various inflammatory disease conditions. Also, cell-free histones directly induce toxicity toward blood cells and are implicated in vascular dysfunction. However, cell-free histones are known to induce RBCs dysfunction in several histone-associated disorders, leading to hypoxia conditions. In this study, we aimed to understand the mechanism underlying the dysfunction of RBCs induced by histones and explore the protective effect of quercetin. Histone treatment at lower doses induces RBCs aggregation while at higher doses it induces eryptosis and delayed hemolysis. Surprisingly, the removal of negatively charged sialic acid on the RBC membrane prevents histone-induced toxicity, thereby confirming the significance of the interaction between sialic acid and histone. Quercetin (QUE), a flavonoid, significantly inhibits histone-induced RBCs aggregation, eryptosis, and hemolysis. Most importantly, inhibition against the pro-coagulant phenotype of RBCs induced by histones, emphasizes the therapeutic potential of QUE on blood coagulation. Further, spectral and molecular docking studies confirm the interaction between histones and QUE. Collectively, this study highlights the therapeutic value of QUE in protecting the RBCs functions during histones-associated pathological conditions.

A field resource for the glioma cerebrospinal fluid proteome: Impacts of resection and location on biomarker discovery

BACKGROUND

While serial sampling of glioma tissue is rarely performed prior to recurrence, cerebrospinal fluid (CSF) is an underutilized longitudinal source of candidate glioma biomarkers for understanding therapeutic impacts. However, the impact of key variables to consider in longitudinal CSF samples for monitoring biomarker discovery, including anatomical location and post-surgical changes, remains unknown.

METHODS

Aptamer-based proteomics was performed on 147 CSF samples from 74 patients; 71 of whom had grade 2-4 astrocytomas or grade 2-3 oligodendrogliomas. This included pre- versus post-resection intracranial CSF samples obtained at early (1-16 days; n = 20 patients) or delayed (86-153 days; n = 11 patients) time points for patients with glioma. Paired lumbar versus intracranial glioma CSF samples were also obtained (n = 14 patients).

RESULTS

Significant differences were identified in the CSF proteome between lumbar, subarachnoid, and ventricular CSF in patients with gliomas. Importantly, we found that resection had a significant, evolving longitudinal impact on the CSF proteome, with distinct sets of proteins present at different time points since resection. Our analysis of serial intracranial CSF samples suggests the early potential for disease monitoring and evaluation of pharmacodynamic impact of targeted therapies, such as bevacizumab and immunotherapies.

CONCLUSIONS

The intracranial glioma CSF proteome serves as a rich and dynamic reservoir of potential biomarkers that can be used to evaluate the effects of resection and other therapies over time. All data within this study, including detailed individual clinical annotations, are shared as a resource for the neuro-oncology community to collectively address these unanswered questions and further understand glioma biology through CSF proteomics.

Anti-DAMP therapies for acute inflammation

Shock, affecting a third of intensive care patients, remains a highly fatal condition despite advances in critical care, irrespective of its etiology. Cellular injury, central to shock pathophysiology, triggers the release of damage-associated molecular patterns (DAMPs), such as extracellular cold-inducible RNA-binding protein (eCIRP), high-mobility group box 1 (HMGB1), histones 3 and 4, and adenosine triphosphate (ATP). These molecules are confined within cells under normal conditions and perform essential physiological functions. However, upon their extracellular release during cellular injury, they act as alarmins, engaging pattern recognition receptors (PRRs) on immune cells. This interaction triggers a robust inflammatory response, propagating systemic inflammation and exacerbating tissue damage. Excessive DAMP-mediated inflammation is increasingly recognized as a major contributor to morbidity and mortality in a wide range of critical illnesses, including trauma, hemorrhagic shock, sepsis, and organ ischemia/reperfusion (I/R) injury. These pathologies are characterized by uncontrolled inflammatory cascades driven by the deleterious effects of DAMPs, underscoring the urgent need for targeted therapeutic interventions. This review explores the pivotal role of DAMPs in the pathogenesis of acute inflammation and shock, highlighting cutting-edge therapeutic strategies aimed at mitigating their effects. Emerging approaches include monoclonal antibodies, decoy receptors, small molecule inhibitors, and scavengers designed to neutralize or inhibit DAMP activity. The discussion also delves into the potential clinical applications of these interventions, offering insights into how targeting DAMPs could transform the management of shock and improve patient outcomes.

Eosinophil ETosis and Charcot-Leyden crystals in Kimura disease

Two cases of refractory Kimura disease that required treatment with biologic agents are reported. Their pathology suggests the involvement of eosinophil ETosis, which is active cell death producing Charcot-Leyden crystals.

Advancing super-resolution microscopy with metal complexes: functional imaging agents for nanoscale visualization

Super-resolution microscopy (SRM) has transformed biological imaging by overcoming the diffraction limit, offering nanoscale visualization of cellular structures and processes. However, the widespread use of organic fluorescent probes is often hindered by limitations such as photobleaching, short photostability, and inadequate performance in deep-tissue imaging. Metal complexes, with their superior photophysical properties, including exceptional photostability, tuneable luminescence, and extended excited-state lifetimes, address these challenges, enabling precise subcellular targeting and long-term imaging. Beyond imaging, their theranostic potential unlocks real-time diagnostics and treatments for diseases such as cancer and bacterial infections. This review explores recent advancements in applying metal complexes for SRM, focusing on their utility in visualizing intricate subcellular structures, capturing temporal dynamics in live cells and elucidating in vivo spatial organization. We emphasize how rational design strategies optimize biocompatibility, organelle specificity, and deep-tissue penetration, expanding their applicability in multiplexed imaging. Furthermore, we discuss the design of various metal nanoparticles (NPs) for SRM, along with emerging hybrid nanoscale probes that integrate metal complexes with gold (Au) scaffolds, offering promising avenues for overcoming current limitations. By highlighting both established successes and potential frontiers, this review provides a roadmap for leveraging metal complexes as versatile tools in advancing SRM applications.

Histones are critical toxic factors in gut lymph of severe acute pancreatitis: Neutralization by baicalin and baicalein for protection

BACKGROUND

Whether circulating histones in gut lymph contribute to organ failure and impact of chaiqin chengqi decoction (CQCQD) on histones in severe acute pancreatitis (SAP) remain elusive.

PURPOSE

To verify the role of histones in gut lymph of SAP and evaluate the effect of the CQCQD on them.

METHODS

Sodium taurocholate was retrogradely infused into pancreatobiliary duct to induce SAP in rodents. Various regimens of CQCQD were administered intragastrically or via duodenum followed by dynamic gut lymph collection in rats. The impact of gut lymph and histones on endothelial cell viability and lymphocytes was determined. Components of CQCQD in gut lymph were identified by UHPLC-MS and their binding activities with histones were quantified by biolayer interferometry followed by validation in vitro and in vivo in mice.

RESULTS

The histone level was significantly increased in gut lymph of SAP at various time points assessed, closely correlating with multiple organ injury (MOI) indices and contemporary cell viability. Inhibition of histones reduced cytotoxicity induced by SAP-conditioned gut lymph. CQCQD reduced apoptotic cell death in mesenteric lymph nodes, histone level, and cytotoxicity of gut lymph, alleviating MOI parameters. Baicalin and baicalein were amongst top 13 identified CQCQD components absorbed into gut lymph to actively bind histones, block membrane disruption and calcium influx of lymphocytes, and inhibit their cytotoxicity. Both baicalin and baicalein mitigated histone- and SAP-induced MOI indices in mice.

CONCLUSION

Histones are key toxic factors in the gut lymph of SAP and their antagonism by baicalin and baicalein offers a novel therapeutic strategy.

Neutrophils: Linking Inflammation to Thrombosis and Unlocking New Treatment Horizons

Neutrophils play a key role in inflammatory responses and thrombosis, but their complex interactions in disease pathogenesis are not fully understood. This review examines the multifaceted roles of neutrophils, focusing on their activation, cytokine release, and formation of neutrophil extracellular traps (NETs), which contribute to host defense and thrombosis. We discuss the interaction between inflammation and coagulation, the direct effect of neutrophils on thrombus stability, and their involvement in pathological thrombotic diseases. The therapeutic potential of neutrophil drug loading in the treatment of thrombosis, as well as the clinical implications and future research directions, are highlighted. The aim of this review is to gain insight into the critical neutrophil-inflammation-thrombus axis and its potential as a therapeutic target for thrombotic diseases and to suggest possible directions for neutrophil-loaded drug therapy for thrombosis.

How Histone Sensing Drives Alzheimer's Disease

The human DNA double helix is wrapped around proteins known as histones, which play a critical role in regulating gene expression. The goal of this opinion piece is to provide an overview of how histone sensing drives Alzheimer's disease (AD). Histones are proteins enriched in basic amino acids. Histone acetylation plays an important role in the progression of AD as its dysregulation can lead to neuroinflammation and neurodegenerative diseases. Specifically, abnormal histone acetylation, a post-translation modification, is a key factor in AD as it contributes to brain cell inflammatory pathology. Thus, higher levels of histone acetylation could potentially serve as important biomarkers for the progression of AD. Here, we report that increased levels of acetylation of histones H2B, H3, and H4 in the promoter regions of Tip60 lysine acetyltransferase protein, p300/CREB-binding protein (CBP), GCN5-related N-acetyltransferases, p300/CBP-associated factor, elongator protein 3, brain-derived neurotrophic factor, and Tau genes in the hippocampus and temporal lobe are associated with the development of AD-associated learning and memory impairment.

Visfatin exerts an anti-proliferative and pro-apoptotic effect in the human placenta cells†

Visfatin regulates energy homeostasis, metabolism, inflammation, and reproduction via the hypothalamus-pituitary-ovary axis. Our previous study showed the visfatin gene and protein expression in the human placenta. This study aimed to investigate the in vitro effect of visfatin on the proliferation and apoptosis of placental JEG-3 and BeWo cells but also in villous explants collected from normal pregnancies and complicated by intrauterine growth restriction (IUGR), preeclampsia (PE), and gestational diabetes mellitus (GDM). We studied placenta cells viability, proliferation, cell cycle, proliferation/apoptotic factors and insulin receptor (INSR) expression, DNA fragmentation, CASP3/7 activity, and phosphorylation of ERK1/2, AKT, AMPKα, STAT3 with their involvement after pharmacological inhibition in visfatin action on proliferation and apoptosis. Visfatin (1, 10, 100 ng/mL) decreased the viability and proliferation of JEG-3 after 48 h, and a similar effect was observed via co-administration of visfatin (10 ng/mL) and insulin (10 ng/mL) in JEG-3 and BeWo after 48 h and 72 h, respectively. Visfatin reduced the transition from the G2/M phase, and expression of PCNA or cyclins D, E, A, and B in JEG-3 and PCNA in normal, IUGR, PE, and GDM placentas. It increased DNA fragmentation, CASP3/7 activity, P53, BAX/BCL2, CASP9, CASP 8, CASP3 levels in BeWo, and CASP3 expression in tested placentas. Furthermore, visfatin modulated INSR, ERK1/2, AKT, AMPKα, and STAT3 expression in JEG-3 and BeWo, and its anti-proliferative and pro-apoptotic effects occurred via mentioned factors. In conclusion, visfatin, by affecting the proliferation and apoptosis of human placenta cells, may be an important factor in the development and function of the organ.

In Silico Discovery of Antigenic-Secreted Proteins to Diagnostic Human Toxocariasis

BACKGROUND

Human toxocariasis is a helminthic zoonosis caused by infection of Toxocara canis or T. cati. Humans can be infected by through ingestion of embryonated eggs from contaminated water, food or soil. Diagnosis is challenging, immunodiagnosis tests are commonly implemented with major pitfalls in the cross-reactivity with other pathogens, particularly in endemic areas.

METHODS

With the aim of identify species-specific genes encoding for highly expressed antigenic proteins, a list of parasites that may infect humans and that might present similar clinical symptoms to T. canis infections was built. Only organisms whose genomes were completely sequenced and the proteome predicted were included. First, orthologous proteins were detected and the subcellular localization of T. canis proteins was predicted. In order to identify differentially expressed genes encoding proteins in larvae L3, pair-wise comparisons among transcriptomes from body parts and genders were performed. Finally, all secreted proteins classified as species-specific of T. canis, whose genes were upregulated in larvae L3 were included in an antigenic prediction.

RESULTS

Twenty-eight parasites were included in the analyses, proteins of T. canis were clustered in 11,399 groups, however, 279 were species-specific groups which represent 816 proteins. Three hundred and twenty-two proteins were predicted to be secreted and upregulated in larvae L3, however, after filtering these proteins by their orthology inference, only three proteins met all the features included in this study (species-specific, upregulated, secreted, and antigenic potential). To conclude, our strategy in the study is a rational approach for discovering antigenic proteins to be used in diagnosis.

"The NET effect": Neutrophil extracellular traps-a potential key component of the dysregulated host immune response in sepsis

Neutrophils release neutrophil extracellular traps (NETs) as part of a healthy host immune response. NETs physically trap and kill pathogens as well as activating and facilitating crosstalk between immune cells and complement. Excessive or inadequately resolved NETs are implicated in the underlying pathophysiology of sepsis and other inflammatory diseases, including amplification of the inflammatory response and inducing thrombotic complications. Here, we review the growing evidence implicating neutrophils and NETs as central players in the dysregulated host immune response. We discuss potential strategies for modifying NETs to improve patient outcomes and the need for careful patient selection.

Cardiovascular disease risk prediction by Framingham risk score in women with polycystic ovary syndrome

BACKGROUND

Despite the documented increased cardiovascular disease (CVD) risk in women with polycystic ovary syndrome (PCOS), no specific risk prediction tools are recommended for these patients. We aimed to assess the validity of the Framingham Risk Score (FRS) as a predictor of CVD risk in PCOS patients.

METHODS

In a community-based prospective study, 4,435 women from the Tehran Lipid and Glucose Study (TLGS) cohort were analyzed. Among them, 215 women aged 30 years or older were diagnosed with PCOS. A Cox proportional hazards model applied to assess the relationship between the FRS and CVD event. Model accuracy was evaluated using the C-statistic, while discrimination and calibration were assessed via the ROC curve, area under the ROC curve (AUC) statistics, and the Hosmer- Lemeshow test.

RESULTS

The Cox proportional hazards (HRs) model revealed that the CVD risk increased by 38% for each one-unit increase in the FRS [HR: 1.38 (95% CI: 1.14, 1.66)] in PCOS patients. The FRS had a C-statistic of 0.765, which indicated a satisfactory fit for CVD prediction in this population. The AUC of the ROC curve was 0.82, which demonstrated a good discrimination of the FRS. The Hosmer-Lemeshow test showed that the predicted probabilities of CVD were consistent with the observed CVD rates (p = 0.217), indicating a good calibration.

CONCLUSIONS

This study revealed a significant increase in CVD risk among PCOS patients. The FRS effectively predicts a 38% increment in CVD risk for every one-unit increase in the FRS. Our study further validated the FRS as a predictor of CVD risk in these patients.

Extracellular Histones as Exosome Membrane Proteins Regulated by Cell Stress

Histones are conserved nuclear proteins that function as part of the nucleosome in the regulation of chromatin structure and gene expression. Interestingly, extracellular histones populate biofluids from healthy individuals, and when elevated, may contribute to various acute and chronic diseases. It is generally assumed that most extracellular histones exist as nucleosomes, as components of extracellular chromatin. We analysed cell culture models under normal and stressed conditions to identify pathways of histone secretion. We report that core and linker histones localize to extracellular vesicles (EVs) and are secreted via the multivesicular body/exosome pathway. Upregulation of EV histone secretion occurs in response to cellular stress, with enhanced vesicle secretion and a shift towards a population of smaller EVs. Most histones were membrane associated with the outer surface of EVs. Degradation of EV-DNA did not impact significantly on EV-histone association. Individual histones  and histone octamers bound strongly to liposomes and EVs, but nucleosomes did not, showing histones do not require DNA for EV binding. Histones colocalized to tetraspanin positive EVs but using genetic or pharmacological intervention, we found that all known pathways of exosome biogenesis acted positively on histone secretion. Inhibition of autophagy and lysosomal degradation had a strong positive effect on EV histone release. Unexpectedly, EV-associated histones lacked the extensive post-translational modification of their nuclear counterparts, suggesting loss of PTMs may be involved in their trafficking or secretion. Our data does not support a significant role for EV-histones existing as nucleosomes. We show for the first time that histones are secreted from cells as membrane proteins via EVs/exosomes. This fundamental discovery provides support for further investigation of the biological activity of exosome associated histones and their role in disease.

Moonlight function of antioxidants

We take a wide variety of antioxidants, including polyphenols, daily from our diet. They are generally considered to be beneficial for our health. However, the intrinsic function of antioxidants in biological systems remain unknown. On the other hand, antioxidants in general are sensitive to oxidation, generating their oxidized intermediates. Intriguingly, these intermediates are highly reactive to proteins. Although the specific cellular targets and response mechanism remain unclear, protein modification by oxidized antioxidants may represent the intrinsic "moonlight" function of antioxidants by taking on a secondary role beyond their traditional activity. This minireview summarizes recent findings on antioxidants, with a particular focus on the interactions of antioxidant-modified proteins with histones.

Ionotropic purinergic receptor 7 (P2X7) channel structure and pharmacology provides insight regarding non-nucleotide agonism

P2X7 is a member of the Ionotropic Purinergic Receptor (P2X) family. The P2X family of receptors is composed of seven (P2X1-7), ligand-gated, nonselective cation channels. Changes in P2X expression have been reported in multiple disease models. P2Xs have large complex extracellular domains that function as receptors for a variety of ligands, including endogenous and synthetic agonists and antagonists. ATP is the canonical agonist. ATP affinity ranges from nanomolar to micromolar for most P2XRs, but P2X7 has uniquely poor ATP affinity. In many physiological settings, it may be difficult to achieve the millimolar extracellular ATP concentrations needed for P2X7 channel activation; however, channel function is implicated in pain sensation, immune cell function, cardiovascular disease, cancer, and osteoporosis. Multiple high-resolution P2X7 structures have been solved in apo-, ATP-, and antagonist-bound states. P2X7 structural data reveal distinct allosteric and orthosteric antagonist-binding sites. Both allosteric and orthosteric P2X7 antagonists are well documented to inhibit ATP-evoked channel current. However, a growing body of evidence supports P2X7 activation by non-nucleotide agonists, including extracellular histone proteins and human cathelicidin-derived peptides (LL-37). Interestingly, P2X7 non-nucleotide agonism is not inhibited by allosteric antagonists, but is inhibited by orthosteric antagonists. Herein, we review P2X7 function with a focus on the efficacy of available pharmacology on P2X7 channel current activation by non-nucleotide agonists in effort to understand agonist/antagonist efficacy, and consider the impact of these data on the current understanding of P2X7 in physiology and disease given these limitations of P2X7-selective antagonists and incomplete knockout mouse models.

Spray paint-derived microplastics and incorporated substances as ecotoxicological contaminants in the neotropical bumblebee Bombus atratus

While bumblebees may be exposed to microplastics (MPs), the effects on them are not well studied. Therefore, in this research, we assessed the cytotoxicity of pristine and photodegraded spray paint-derived MPs on the midgut, Malpighian tubules, and hepato-nephrocitic system cells of Bombus atratus workers exposed to 50 mg.L-1 MPs for 96 hours. Histological and histochemical analyses revealed that pristine MPs caused subtle cellular changes, while the exposure to photodegraded MPs led to significant vacuolization, nuclear condensation, and pyknosis. These effects are possibly linked to the release of potentially toxic elements (PTEs) like Copper, Manganese, and Iron from photodegraded MPs, which exceeded Brazil's CONAMA safety limits. Photodegraded MPs also reduced body weight, disrupting homeostasis and potentially decreasing bumblebee's fitness. These findings highlight the importance of studying the toxicity of environmentally realistic MPs, as plastic composition and weathering significantly influence their harmful effects.

Lactate metabolism and histone lactylation in the central nervous system disorders: impacts and molecular mechanisms

Brain takes up approximately 20% of the total body oxygen and glucose consumption due to its relatively high energy demand. Glucose is one of the major sources to generate ATP, the process of which can be realized via glycolysis, oxidative phosphorylation, pentose phosphate pathways and others. Lactate serves as a hub molecule amid these metabolic pathways, as it may function as product of glycolysis, substrate of a variety of enzymes and signal molecule. Thus, the roles of lactate in central nervous system (CNS) diseases need to be comprehensively elucidated. Histone lactylation is a novel lactate-dependent epigenetic modification that plays an important role in immune regulation and maintaining homeostasis. However, there's still a lack of studies unveiling the functions of histone lactylation in the CNS. In this review, we first comprehensively reviewed the roles lactate plays in the CNS under both physiological and pathological conditions. Subsequently, we've further discussed the functions of histone lactylation in various neurological diseases. Furthermore, future perspectives regarding histone lactylation and its therapeutic potentials in stroke are also elucidated, which may possess potential clinical applications.

Histone H1 kills MRSA

The antimicrobial activity of histones was discovered in the 1940s, but their mechanism of action is not fully known. Here we show that methicillin-resistant Staphylococcus aureus (MRSA) is susceptible to histone H1 (H1), even in the presence of divalent cations and serum. Through selective evolution and a genome-wide screen of a transposon library, as well as physiological and pharmacological experiments, we elucidated how H1 kills MRSA. We show that H1 first binds to wall teichoic acids with high affinity. Once bound, H1 requires a potentiated membrane and a metabolically active bacterium to permeabilize the membrane and enter the cell. Upon entry, H1 accumulates intracellularly, in close association with the bacterial DNA. Of note, anti-H1 antibodies inhibit neutrophil extracellular trap killing of MRSA. Moreover, H1 colocalizes with bacterial DNA in abscess samples of MRSA-infected patients, suggesting a role for H1 in combating MRSA in vivo.

Unveiling the guardians of the genome: The dynamic role of histones in DNA organization and disease

Histones are positively charged proteins found in the chromatin of eukaryotic cells. They regulate gene expression and are required for the organization and packaging of DNA within the nucleus. Histones are extremely conserved, allowing for transcription, replication, and repair. This review delves into their complex structure and function in DNA assembly, their role in nucleosome assembly, and the higher-order chromatin structures they generate. We look at the five different types of histone proteins: H1, H2A, H2B, H3, H4, and their variations. These histones bind with DNA to produce nucleosomes, the basic units of chromatin that are essential for compacting DNA and controlling its accessibility. Their dynamic control of chromatin accessibility has important implications for genomic stability and cellular activities. We elucidate regulatory mechanisms in both normal and pathological situations by investigating their structural features, diverse interaction mechanisms, and chromatin impact. In addition, we discuss the functions of histone post-translational modifications (PTMs) and their significance in various disorders. These alterations, which include methylation, acetylation, phosphorylation, and ubiquitination, are crucial in regulating histone function and chromatin dynamics. We specifically describe and explore the role of changed histones in the evolution of cancer, neurological disorders, sepsis, autoimmune illnesses, and inflammatory conditions. This comprehensive review emphasizes histone's critical role in genomic integrity and their potential as therapeutic targets in various diseases.

DAMP sensing and sterile inflammation: intracellular, intercellular and inter-organ pathways

Damage-associated molecular patterns (DAMPs) are endogenous molecules that are released from host cells as a result of cell death or damage. The release of DAMPs in tissues is associated with loss of tissue homeostasis. Sensing of DAMPs by innate immune receptors triggers inflammation, which can be beneficial in initiating the processes that restore tissue homeostasis but can also drive inflammatory diseases. In recent years, the sensing of intracellular DAMPs has received extensive attention in the field of sterile inflammation. However, emerging studies have shown that DAMPs that originate from neighbouring cells, and even from distal tissues or organs, also mediate sterile inflammatory responses. This multi-level sensing of DAMPs is crucial for intercellular, trans-tissue and trans-organ communication. Here, we summarize how DAMP-sensing receptors detect DAMPs from intracellular, intercellular or distal tissue and organ sources to mediate sterile inflammation. We also discuss the possibility of targeting DAMPs or their corresponding receptors to treat inflammatory diseases.

Cellular and Immunological Analysis of 2D2/Th Hybrid Mice Prone to Experimental Autoimmune Encephalomyelitis in Comparison with 2D2 and Th Lines

Previously, we described the mechanisms of development of autoimmune encephalomyelitis (EAE) in 3-month-old C57BL/6, Th, and 2D2 mice. The faster and more profound spontaneous development of EAE with the achievement of deeper pathology occurs in hybrid 2D2/Th mice. Here, the cellular and immunological analysis of EAE development in 2D2/Th mice was carried out. In Th, 2D2, and 2D2/Th mice, the development of EAE is associated with a change in the differentiation profile of hemopoietic bone marrow stem cells, which, in 2D2/Th, differs significantly from 2D2 and Th mice. Hybrid 2D2/Th mice demonstrate a significant difference in these changes in all strains of mice, leading to the production of antibodies with catalytic activities, known as abzymes, against self-antigens: myelin oligodendrocyte glycoprotein (MOG), DNA, myelin basic protein (MBP), and five histones (H1-H4) hydrolyze these antigens. There is also the proliferation of B and T lymphocytes in different organs (blood, bone marrow, thymus, spleen, lymph nodes). The patterns of changes in the concentration of antibodies and the relative activity of abzymes during the spontaneous development of EAE in the hydrolysis of these immunogens are significantly or radically different for the three lines of mice: Th, 2D2, and 2D2/Th. Several factors may play an essential role in the acceleration of EAE in 2D2/Th mice. The treatment of mice with MOG accelerates the development of EAE pathology. In the initial period of EAE development, the concentration of anti-MOG antibodies in 2D2/Th is significantly higher than in Th (29.1-fold) and 2D2 (11.7-fold). As shown earlier, antibodies with DNase activity penetrate cellular and nuclear membranes and activate cell apoptosis, stimulating autoimmune processes. In the initial period of EAE development, the concentration of anti-DNA antibodies in 2D2/Th hybrids is higher than in Th (4.6-fold) and 2D2 (25.7-fold); only 2D2/Th mice exhibited a very strong 10.6-fold increase in the DNase activity of IgGs during the development of EAE. Free histones in the blood are cytotoxic and stimulate the development of autoimmune diseases. Only in 2D2/Th mice, during different periods of EAE development, was a sharp increase in the anti-antibody activity in the hydrolysis of some histones observed.

Selective Clearance of Circulating Histones Based on Dodecapeptide-Grafted Copolymer Material for Sepsis Blood Purification

Sepsis is defined as a life-threatening organ dysfunction caused by a dysregulated host response to infection. Research indicates that circulating histones, as pathogenic factors, may represent a therapeutic target for sepsis. However, effectively clearing circulating histones poses a challenge due to their structural similarity to normal blood proteins, their low abundance in the bloodstream, and serious interference from other blood biomacromolecules. Here we design a dodecapeptide-based functional polymer that can selectively adsorb circulating histones from the blood. The peptide, named P1 (HNHHQLALVESY), was discovered through phage display screening and demonstrated a strong affinity for circulating histones while exhibiting negligible affinities for common proteins in the blood, such as human serum albumin (HSA), immunoglobulin G (IgG), and transferrin (TRF). Furthermore, the P1 peptide was incorporated into a functional polymer design, poly(PEGMA-co-P1), which was immobilized onto a silica gel surface through reversible addition-fragmentation chain transfer polymerization. The resulting material was characterized using solid nuclear magnetic resonance, thermogravimetric analysis, and X-ray photoelectron spectroscopy. This material demonstrated the ability to selectively and efficiently capture circulating histones from both model solutions and whole blood samples while also exhibiting satisfactory blood compatibility, good antifouling properties, and resistance to interference. Satisfactory binding affinity and efficient capture capacity toward histone were also observed for the other screened peptide P2 (QMSMDLFGSNFV)-grafted polymer, validating phage display as a reliable ligand screening strategy. These findings present an approach for the specific clearance of circulating histones and hold promise for future clinical applications in blood purification toward sepsis.

Roles of Histone H2B, H3 and H4 Variants in Cancer Development and Prognosis

Histone variants are the paralogs of core histones (H2A, H2B, H3 and H4). They are stably expressed throughout the cell cycle in a replication-independent fashion and are capable of replacing canonical counterparts under different fundamental biological processes. Variants have been shown to take part in multiple processes, including DNA damage repair, transcriptional regulation and X chromosome inactivation, with some of them even specializing in lineage-specific roles like spermatogenesis. Several reports have recently identified some unprecedented variants from different histone families and exploited their prognostic value in distinct types of cancer. Among the four classes of canonical histones, the H2A family has the greatest number of variants known to date, followed by H2B, H3 and H4. In our prior review, we focused on summarizing all 19 mammalian histone H2A variants. Here in this review, we aim to complete the full summary of the roles of mammalian histone variants from the remaining histone H2B, H3, and H4 families, along with an overview of their roles in cancer biology and their prognostic value in a clinical context.

Glycoxidation of mammalian whole histone generates highly immunogenic aggregates: Sera of SLE patients contain autoantibodies against aggregates

Non-enzymatic glycation and oxidation of self-proteins, causing formation and accumulation of advanced glycation end products (AGEs), have been reported in an array of pathologies, including systemic lupus erythematosus (SLE). Such modifications may generate neo-epitopes, break immunological tolerance, and induce antibody response. In this study, we have first analysed the structural modifications of whole histone in the presence of deoxyribose followed by oxidation with hydroxyl radicals. Changes in the secondary and tertiary structure of the whole histone were determined by spectroscopic techniques and biochemical assays. Fluorescence spectroscopy and UPLC-MS showed the generation of AGEs such as carboxymethyl lysine and pentosidine, while DLS and TEM indicated the presence of amorphous AGE-aggregates. Moreover, rabbits immunized with these histone-AGEs exhibited enhanced immunogenicity and ELISA and western immunoblot of IgG antibodies from SLE patients' sera showed a significantly higher specificity towards modified histone-AGEs than the native histone.

Sex-specific modulation of renal epigenetic and injury markers in aging kidney

Sex differences in renal physiology and pathophysiology are now well established in rodent models and in humans. Epigenetic programming is known to be a critical component of renal injury, as studied mainly in male rodent models; however, not much is known about the impact of biological sex and age on the kidney epigenome. We sought to determine the influence of biological sex and age on renal epigenetic and injury markers, using male and female mice at 4 mo (4M; young), 12 mo (12M), and 24 mo (24M; aged) of age. Females had a significant increase in kidney and body weights and serum creatinine levels and a decrease in serum albumin levels from 4M to 24M of age, whereas minor changes were observed in male mice. Kidney injury molecule-1 levels in serum and renal tissue greatly enhanced from 12M to 24M in both males and females. Circulating histone 3 (H3; damage-associated molecular pattern molecules) levels extensively increased with age; however, males had higher levels than females. Overall, females had markedly high histone acetyltransferase (HAT) activity than age-matched males. Aged mice had decreased HAT activity and increased histone deacetylase activity than sex-matched 12M mice. Aged females had substantially decreased renal H3 methylation at lysine 9 and 27 and histone methyltransferase (HMT) activity than aged male mice. Antiaging protein Klotho levels were significantly higher in young males than age-matched females and decreased substantially with age in males, whereas epigenetic repressor of Klotho, trimethylated H3K27, and its HMT enzyme, enhancer of zeste homolog 2, increased consistently with age in both sexes. Moreover, nuclear translocation and activity of proinflammatory transcription factor nuclear factor-κB (p65) were significantly higher in aged mice. Taken together, our data suggest that renal aging lies in a range between normal and diseased kidneys but may differ between female and male mice, highlighting sex-related differences in the aging process.NEW & NOTEWORTHY Although there is evidence of sex-specific differences in kidney diseases, most preclinical studies have used male rodent models. The clinical data on renal injury have typically not been stratified by sex. Our findings provide convincing evidence of sex-specific differences in age-regulated epigenetic alterations and renal injury markers. This study highlights the importance of including both sexes for better realization of underlying sex differences in signaling mechanisms of aging-related renal pathophysiology.

The Preventive and Therapeutic Effects of Acute and Severe Inflammatory Disorders with Heparin and Heparinoid

Systematic inflammatory response syndrome (SIRS) and the accompanying sepsis pose a huge threat to human health worldwide. Heparin is a part of the standard supportive care for the disease. However, the molecular mechanism is not fully understood yet, and the potential signaling pathways that play key roles have not yet been elucidated. In this paper, the main findings regarding the molecular mechanisms associated with the beneficial effects of heparin, including inhibiting HMGB-1-driven inflammation reactions, histone-induced toxicity, thrombo-inflammatory response control and the new emerging mechanisms are concluded. To set up the link between the preclinical research and the clinical effects, the outcomes of the clinical trials are summarized. Then, the structure and function relationship of heparin is discussed. By providing an updated analysis of the above results, the paper highlights the feasibility of heparin as a possible alternative for sepsis prophylaxis and therapy.

Tumour lysis syndrome

Tumour lysis syndrome (TLS) represents a critical oncological emergency characterized by extensive tumour cell breakdown, leading to the swift release of intracellular contents into the systemic circulation, outpacing homeostatic mechanisms. This process results in hyperuricaemia (a by-product of intracellular DNA release), hyperkalaemia, hyperphosphataemia, hypocalcaemia and the accumulation of xanthine. These electrolyte and metabolic imbalances pose a significant risk of acute kidney injury, cardiac arrhythmias, seizures, multiorgan failure and, rarely, death. While TLS can occur spontaneously, it usually arises shortly after the initiation of effective treatment, particularly in patients with a large cancer cell mass (defined as ≥500 g or ≥300 g/m2 of body surface area in children). To prevent TLS, close monitoring and hydration to improve renal perfusion and urine output and to minimize uric acid or calcium phosphate precipitation in renal tubules are essential. Intervention is based on the risk of a patient of having TLS and can include rasburicase and allopurinol. Xanthine, typically enzymatically converted to uric acid, can accumulate when xanthine oxidases, such as allopurinol, are administered during TLS management. Whether measurement of xanthine is clinically useful to optimize the use of allopurinol or rasburicase remains to be determined.

Emerging therapeutic strategies targeting extracellular histones for critical and inflammatory diseases: an updated narrative review

Extracellular histones are crucial damage-associated molecular patterns involved in the development and progression of multiple critical and inflammatory diseases, such as sepsis, pancreatitis, trauma, acute liver failure, acute respiratory distress syndrome, vasculitis and arthritis. During the past decade, the physiopathologic mechanisms of histone-mediated hyperinflammation, endothelial dysfunction, coagulation activation, neuroimmune injury and organ dysfunction in diseases have been systematically elucidated. Emerging preclinical evidence further shows that anti-histone strategies with either their neutralizers (heparin, heparinoids, nature plasma proteins, small anion molecules and nanomedicines, etc.) or extracorporeal blood purification techniques can significantly alleviate histone-induced deleterious effects, and thus improve the outcomes of histone-related critical and inflammatory animal models. However, a systemic evaluation of the efficacy and safety of these histone-targeting therapeutic strategies is currently lacking. In this review, we first update our latest understanding of the underlying molecular mechanisms of histone-induced hyperinflammation, endothelial dysfunction, coagulopathy, and organ dysfunction. Then, we summarize the latest advances in histone-targeting therapy strategies with heparin, anti-histone antibodies, histone-binding proteins or molecules, and histone-affinity hemoadsorption in pre-clinical studies. Finally, challenges and future perspectives for improving the clinical translation of histone-targeting therapeutic strategies are also discussed to promote better management of patients with histone-related diseases.

A novel histone deacetylase inhibitor Se-SAHA attenuates isoproterenol-induced heart failure via antioxidative stress and autophagy inhibition

Heart failure is associated with histone deacetylase (HDAC) regulation of gene expression, the inhibition of which is thought to be beneficial for heart failure therapy. Here, we explored the cardioprotective effects and underlying mechanism of a novel selenium-containing HDAC inhibitor, Se-SAHA, on isoproterenol (ISO)-induced heart failure. We found that pretreatment with Se-SAHA attenuated ISO-induced cardiac hypertrophy and fibrosis in neonatal rat ventricular myocytes (NRVMs). Se-SAHA significantly attenuated the generation of ISO-induced reactive oxygen species (ROS) and restored the expression levels of superoxide dismutase 2 (SOD2) and heme oxygenase-1 (HO-1) in vitro. Furthermore, Se-SAHA pretreatment prevented the accumulation of autophagosomes. Se-SAHA reversed the high expression of HDAC1 and HDAC6 induced by ISO incubation. However, after the addition of the HDAC agonist, the effect of Se-SAHA on blocking autophagy was inhibited. Using ISO-induced mouse models, cardiac ventricular contractile dysfunction, hypertrophy, and fibrosis was reduced treated by Se-SAHA. In addition, Se-SAHA inhibited HDAC1 and HDAC6 overexpression in ISO-treated mice. Se-SAHA treatment significantly increased the activity of SOD2 and improved the ability to eliminate free radicals. Se-SAHA hindered the excessive levels of the microtubule-associated protein 1 light chain 3 (LC3)-II and Beclin-1 in heart failure mice. Collectively, our results indicate that Se-SAHA exerts cardio-protection against ISO-induced heart failure via antioxidative stress and autophagy inhibition.

Chromatin as alarmins in necrotizing enterocolitis

Necrotizing enterocolitis (NEC) is a severe gastrointestinal disease primarily affecting premature neonates, marked by poorly understood pro-inflammatory signaling cascades. Recent advancements have shed light on a subset of endogenous molecular patterns, termed chromatin-associated molecular patterns (CAMPs), which belong to the broader category of damage-associated molecular patterns (DAMPs). CAMPs play a crucial role in recognizing pattern recognition receptors and orchestrating inflammatory responses. This review focuses into the realm of CAMPs, highlighting key players such as extracellular cold-inducible RNA-binding protein (eCIRP), high mobility group box 1 (HMGB1), cell-free DNA, neutrophil extracellular traps (NETs), histones, and extracellular RNA. These intrinsic molecules, often perceived as foreign, have the potential to trigger immune signaling pathways, thus contributing to NEC pathogenesis. In this review, we unravel the current understanding of the involvement of CAMPs in both preclinical and clinical NEC scenarios. We also focus on elucidating the downstream signaling pathways activated by these molecular patterns, providing insights into the mechanisms that drive inflammation in NEC. Moreover, we scrutinize the landscape of targeted therapeutic approaches, aiming to mitigate the impact of tissue damage in NEC. This in-depth exploration offers a comprehensive overview of the role of CAMPs in NEC, bridging the gap between preclinical and clinical insights.

The role of histone acetylation in transcriptional regulation and seed development

Histone acetylation is highly conserved across eukaryotes and has been linked to gene activation since its discovery nearly 60 years ago. Over the past decades, histone acetylation has been evidenced to play crucial roles in plant development and response to various environmental cues. Emerging data indicate that histone acetylation is one of the defining features of "open chromatin," while the role of histone acetylation in transcription remains controversial. In this review, we briefly describe the discovery of histone acetylation, the mechanism of histone acetylation regulating transcription in yeast and mammals, and summarize the research progress of plant histone acetylation. Furthermore, we also emphasize the effect of histone acetylation on seed development and its potential use in plant breeding. A comprehensive knowledge of histone acetylation might provide new and more flexible research perspectives to enhance crop yield and stress resistance.

Targeting Neutrophil Extracellular Traps in Gouty Arthritis: Insights into Pathogenesis and Therapeutic Potential

Gouty arthritis (GA) is an immune-mediated disorder characterized by severe inflammation due to the deposition of monosodium urate (MSU) crystals in the joints. The pathophysiological mechanisms of GA are not yet fully understood, and therefore, the identification of effective therapeutic targets is of paramount importance. Neutrophil extracellular traps (NETs), an intricate structure of DNA scaffold, encompassing myeloperoxidase, histones, and elastases - have gained significant attention as a prospective therapeutic target for gouty arthritis, due to their innate antimicrobial and immunomodulatory properties. Hence, exploring the therapeutic potential of NETs in gouty arthritis remains an enticing avenue for further investigation. During the process of gouty arthritis, the formation of NETs triggers the release of inflammatory cytokines, thereby contributing to the inflammatory response, while MSU crystals and cytokines are sequestered and degraded by the aggregation of NETs. Here, we provide a concise summary of the inflammatory processes underlying the initiation and resolution of gouty arthritis mediated by NETs. Furthermore, this review presents an overview of the current pharmacological approaches for treating gouty arthritis and summarizes the potential of natural and synthetic product-based inhibitors that target NET formation as novel therapeutic options, alongside elucidating the intrinsic challenges of these inhibitors in NETs research. Lastly, the limitations of HL-60 cell as a suitable substitute of neutrophils in NETs research are summarized and discussed. Series of recommendations are provided, strategically oriented towards guiding future investigations to effectively address these concerns. These findings will contribute to an enhanced comprehension of the interplay between NETs and GA, facilitating the proposition of innovative therapeutic strategies and novel approaches for the management of GA.

Resveratrol Has Histone 4 and Beta-Defensin 1-Mediated Favorable Biotherapeutic Effects on Liver and Other Target Organs in Diabetic Rats

BACKGROUND/AIMS

 It was aimed to investigate the biochemical and histopathological effects of resveratrol and melatonin, via histone H4 and β-defensin 1, in diabetic rats.

MATERIALS AND METHODS

 Twenty-four Sprague-Dawley male rats were categorized into 4 groups, with 6 rats in each group (control, diabetes mellitus, melatonin - diabetes mellitus, and resveratrol+diabetes mellitus). Diabetes was formed by giving streptozotocin to all groups except the control group. Melatonin, 5 mg/kg/day, was given to the melatonin - diabetes mellitus group, and resveratrol, 5 mg/kg/day, was given to the resveratrol+diabetes mellitus group via intraperitoneally for 3 weeks. Interleukin-1 beta, tumor necrosis factor alpha, histone H4, and β-defensin 1 levels were measured in the blood of all rats. The lung, liver, and kidney tissue of all rats were performed as histopathological examinations.

RESULTS

 Whereas there was no difference between the other groups (P >.05), interleukin-1 beta levels of the diabetes mellitus group were found to be significantly higher compared with the control group (5.02 ± 2.15 vs. 2.38 ± 0.72 ng/mL; P < .05). Whereas histone H4 levels of the diabetes mellitus group were higher compared with the control and resveratrol+diabetes mellitus groups (7.53 ± 3.30 vs. 2.97 ± 1.57 and 3.06 ± 1.57 ng/mL; P <.05), the β-defensin 1 levels of the diabetes mellitus group were lower compared with control and resveratrol+diabetes mellitus groups (7.6 ± 2.8 vs. 21.6 ± 5.5 and 18.8 ± 7.4 ng/mL; P <.05). β-Defensin 1 levels were moderately inversely correlated with interleukin-1 beta and histone H4 levels (rs > -0.50, P < .01). Histopathological changes found in favor of target cell damage in the diabetes mellitus group were not observed in resveratrol+diabetes mellitus group.

CONCLUSION

 Resveratrol may be used as a biotherapeutic agent, which significantly reduces diabetes-induced histone H4 and interleukin-1 beta-mediated liver and other target organ damage.

Unraveling Histone Loss in Aging and Senescence

As the global population experiences a notable surge in aging demographics, the need to understand the intricate molecular pathways exacerbated by age-related stresses, including epigenetic dysregulation, becomes a priority. Epigenetic mechanisms play a critical role in driving age-related diseases through altered gene expression, genomic instability, and irregular chromatin remodeling. In this review, we focus on histones, a central component of the epigenome, and consolidate the key findings of histone loss and genome-wide redistribution as fundamental processes contributing to aging and senescence. The review provides insights into novel histone expression profiles, nucleosome occupancy, disruptions in higher-order chromatin architecture, and the emergence of noncanonical histone variants in the aging cellular landscape. Furthermore, we explore the current state of our understanding of the molecular mechanisms of histone deficiency in aging cells. Specific emphasis is placed on highlighting histone degradation pathways in the cell and studies that have explored potential strategies to mitigate histone loss or restore histone levels in aging cells. Finally, in addressing future perspectives, the insights gained from this review hold profound implications for advancing strategies that actively intervene in modulating histone expression profiles in the context of cellular aging and identifying potential therapeutic targets for alleviating a multitude of age-related diseases.

M6229 Protects against Extracellular-Histone-Induced Liver Injury, Kidney Dysfunction, and Mortality in a Rat Model of Acute Hyperinflammation

Extracellular histones have been shown to act as DAMPs in a variety of inflammatory diseases. Moreover, they have the ability to induce cell death. In this study, we show that M6229, a low-anticoagulant fraction of unfractionated heparin (UFH), rescues rats that were challenged by continuous infusion of calf thymus histones at a rate of 25 mg histones/kg/h. Histone infusion by itself induced hepatic and homeostatic dysfunction characterized by elevated activity of hepatic enzymes (ASAT and ALAT) and serum lactate levels as well as by a renal dysfunction, which contributed to the significantly increased mortality rate. M6229 was able to restore normal levels of both hepatic and renal parameters at 3 and 9 mg M6229/kg/h and prevented mortality of the animals. We conclude that M6229 is a promising therapeutic agent to treat histone-mediated disease.

Extracellular histones exacerbate heat stroke-induced liver injury by triggering hepatocyte pyroptosis and liver injury via the TLR9-NLRP3 pathway

BACKGROUND

Severe heat stroke is often complicated by multiple organ failure, including liver injury. Recent evidence indicates that the underlying mechanism constitutes sterile inflammation triggered by cell damage, in which hepatocyte NOD-like receptor family pyrin domain-containing 3 inflammasome activation and pyroptosis play key roles. As extracellular histones act as damage-associated molecular patterns and mediate tissue toxicity and inflammation, we aimed to investigate whether extracellular histones contribute to inducing hepatocyte pyroptosis following heat stroke, promoting the development of liver inflammation and injury, and elucidate the potential underlying mechanisms.

METHODS

Exogenous histones were administered to AML-12 murine hepatocytes or male aged 8-12 week mice following hyperthermic treatment (at 39 °C in a chamber with 60 % relative humidity). Prior to heat exposure, endogenous histones were neutralized using neutralizing antibodies, inflammasomes were inhibited by RNA silencing, and Toll-like receptor 9 was modulated using a pharmacological agonist or antagonist. Inflammasome assembly, caspase-1 activation, histological changes, and liver enzyme levels were measured. Statistical comparison of more than two groups was performed using one-way ANOVA with Tukey's post-hoc testing. The correlations were analyzed using Pearson's correlation test. All experiments were repeated thrice. A p-value < 0.05 was considered significant.

RESULTS

Heat stroke induced histone release into the extracellular space at levels correlating with liver injury. Moreover, extracellular histones augmented heat stroke-induced liver injury both in vitro and in vivo in a dose- and time-dependent manner, whereas neutralizing histones conferred protection following heat stroke. Histones mediated NOD-like receptor family pyrin domain-containing 3 inflammasome activation through the Toll-like receptor 9 signaling pathway, which resulted in hepatocyte pyroptosis and liver inflammation.

CONCLUSIONS

Our findings show that histones are critical mediators of hepatocyte pyroptosis that aggravate liver injury in a heat stroke setting. Therefore, we suggest extracellular histones as potential therapeutic targets to limit heat stroke-induced cell death and liver injury.

Hesperidin Alleviates Acute Necrotizing Pancreatitis by Activating SIRT1 - Molecular Docking, Molecular Dynamics Simulation, and Experimental Validation

BACKGROUND

Acute necrotizing pancreatitis is a serious pancreatic injury with limited effective treatments. This study aims to investigate the therapeutic effects of hesperidin on Larginine- induced acute pancreatitis and its potential targets.

METHODS

The authors induced acute pancreatitis in mice by administering two hourly intraperitoneal injections of L-arginine-HCl, and evaluated the impact of hesperidin on pancreatic and lung tissues, plasma amylase activity, and myeloperoxidase content. Additionally, necrosis and mitochondrial function was tested in primary pancreatic acinar cells. The interactions between hesperidin and proteins involved in necrosis and mitochondrial dysfunction were further invested using in silico molecular docking and molecular dynamic simulations.

RESULTS

Hesperidin effectively ameliorated the severity of acute necrotizing pancreatitis by reducing plasma amylase, pancreatic MPO, serum IL-6 levels, pancreatic edema, inflammation, and pancreatic necrosis. Hesperidin also protected against acute pancreatitis-associated lung injury and prevented acinar cell necrosis, mitochondrial membrane potential loss, and ATP depletion. In addition, hesperidin exhibited a high binding affinity with SIRT1 and increased the protein levels of SIRT1. The SIRT1 inhibitor EX527 abolished the protective effect of hesperidin against necrosis in acinar cells.

CONCLUSION

These findings indicate that hesperidin alleviates the severity of acute necrotizing pancreatitis by activating SIRT1, which may provide insight into the mechanisms of natural compounds in treating AP. Hesperidin has potential as a therapeutic agent for acute necrotizing pancreatitis and provides a new approach for novel therapeutic strategies.

RNA-Seq Analysis of Trans-Differentiated ARPE-19 Cells Transduced by AAV9-AIPL1 Vectors

Inherited retinal disorders (IRD) have become a primary focus of gene therapy research since the success of adeno-associated virus-based therapeutics (voretigene neparvovec-rzyl) for Leber congenital amaurosis type 2 (LCA2). Dozens of monogenic IRDs could be potentially treated with a similar approach using an adeno-associated virus (AAV) to transfer a functional gene into the retina. Here, we present the results of the design, production, and in vitro testing of the AAV serotype 9 (AAV9) vector carrying the codon-optimized (co) copy of aryl hydrocarbon receptor-interacting protein like-1 (AIPL1) as a possible treatment for LCA4. The pAAV-AIPL1co was able to successfully transduce retinal pigment epithelium cells (ARPE-19) and initiate the expression of human AIPL1. Intriguingly, cells transduced with AAV9-AIPL1co showed much less antiviral response than AAV9-AIPL1wt (wild-type AIPL1) transduced. RNA-sequencing (RNA-seq) analysis of trans-differentiated ARPE-19 cells transduced with AAV9-AIPL1co demonstrated significant differences in the expression of genes involved in the innate immune response. In contrast, AAV9-AIPL1wt induced the prominent activation of multiple interferon-stimulated genes. The key part of the possible regulatory molecular mechanism is the activation of dsRNA-responsive antiviral oligoadenylate synthetases, and a significant increase in the level of histone coding genes' transcripts overrepresented in RNA-seq data (i.e., H1, H2A, H2B, H3, and H4). The RNA-seq data suggests that AAV9-AIPL1co exhibiting less immunogenicity than AAV9-AIPL1wt can be used for potency testing, using relevant animal models to develop future therapeutics for LCA4.

sBioSITe enables sensitive identification of the cell surface proteome through direct enrichment of biotinylated peptides

BACKGROUND

Cell surface proteins perform critical functions related to immune response, signal transduction, cell-cell interactions, and cell migration. Expression of specific cell surface proteins can determine cell-type identity, and can be altered in diseases including infections, cancer and genetic disorders. Identification of the cell surface proteome remains a challenge despite several enrichment methods exploiting their biochemical and biophysical properties.

METHODS

Here, we report a novel method for enrichment of proteins localized to cell surface. We developed this new approach designated surface Biotinylation Site Identification Technology (sBioSITe) by adapting our previously published method for direct identification of biotinylated peptides. In this strategy, the primary amine groups of lysines on proteins on the surface of live cells are first labeled with biotin, and subsequently, biotinylated peptides are enriched by anti-biotin antibodies and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS).

RESULTS

By direct detection of biotinylated lysines from PC-3, a prostate cancer cell line, using sBioSITe, we identified 5851 peptides biotinylated on the cell surface that were derived from 1409 proteins. Of these proteins, 533 were previously shown or predicted to be localized to the cell surface or secreted extracellularly. Several of the identified cell surface markers have known associations with prostate cancer and metastasis including CD59, 4F2 cell-surface antigen heavy chain (SLC3A2) and adhesion G protein-coupled receptor E5 (CD97). Importantly, we identified several biotinylated peptides derived from plectin and nucleolin, both of which are not annotated in surface proteome databases but have been shown to have aberrant surface localization in certain cancers highlighting the utility of this method.

CONCLUSIONS

Detection of biotinylation sites on cell surface proteins using sBioSITe provides a reliable method for identifying cell surface proteins. This strategy complements existing methods for detection of cell surface expressed proteins especially in discovery-based proteomics approaches.

The heparin-binding hemagglutinin protein of Mycobacterium tuberculosis is a nucleoid-associated protein

Nucleoid-associated proteins (NAPs) regulate multiple cellular processes such as gene expression, virulence, and dormancy throughout bacterial species. NAPs help in the survival and adaptation of Mycobacterium tuberculosis (Mtb) within the host. Fourteen NAPs have been identified in Escherichia coli; however, only seven NAPs are documented in Mtb. Given its complex lifestyle, it is reasonable to assume that Mtb would encode for more NAPs. Using bioinformatics tools and biochemical experiments, we have identified the heparin-binding hemagglutinin (HbhA) protein of Mtb as a novel sequence-independent DNA-binding protein which has previously been characterized as an adhesion molecule required for extrapulmonary dissemination. Deleting the carboxy-terminal domain of HbhA resulted in a complete loss of its DNA-binding activity. Atomic force microscopy showed HbhA-mediated architectural modulations in the DNA, which may play a regulatory role in transcription and genome organization. Our results showed that HbhA colocalizes with the nucleoid region of Mtb. Transcriptomics analyses of a hbhA KO strain revealed that it regulates the expression of ∼36% of total and ∼29% of essential genes. Deletion of hbhA resulted in the upregulation of ∼73% of all differentially expressed genes, belonging to multiple pathways suggesting it to be a global repressor. The results show that HbhA is a nonessential NAP regulating gene expression globally and acting as a plausible transcriptional repressor.

Design and characterization of novel activated protein C variants for the proteolysis of cytotoxic extracellular histone H3

BACKGROUND

Extracellular histone H3 is implicated in several pathologies including inflammation, cell death, and organ failure. Neutralization of histone H3 is a strategy that was shown beneficial in various diseases, such as rheumatoid arthritis, myocardial infarction, and sepsis. It was shown that activated protein C (APC) can cleave histone H3, which reduces histone cytotoxicity. However, due to the anticoagulant properties of APC, the use of APC is not optimal for the treatment of histone-mediated cytotoxicity, in view of its associated bleeding side effects.

OBJECTIVES

This study aimed to investigate the detailed molecular interactions between human APC and human histone H3, and subsequently use molecular docking and molecular dynamics simulation methods to identify key interacting residues that mediate the interaction between APC and histone H3 and to generate novel optimized APC variants.

METHODS

After molecular simulations, the designed APC variants 3D2D-APC (Lys37-39Asp and Lys62-63Asp) and 3D2D2A-APC (Lys37-39Asp, Lys62-63Asp, and Arg74-75Ala) were recombinantly expressed and their abilities to function as anticoagulant, to bind histones, and to cleave histones were tested and correlated with their cytoprotective properties.

RESULTS

Compared with wild type-APC, both the 3D2D-APC and 3D2D2A-APC variants showed a significantly decreased anticoagulant activity, increased binding to histone H3, and similar ability to proteolyze histone H3.

CONCLUSIONS

Our data show that it is possible to rationally design APC variants that may be further developed into therapeutic biologicals to treat histone-mediated disease, by proteolytic reduction of histone-associated cytotoxic properties that do not induce an increased bleeding risk.

Functioning and mechanisms of PTMs in renal diseases

Post-translational modifications (PTMs) are crucial epigenetic mechanisms that regulate various cellular biological processes. The use of mass spectrometry (MS)-proteomics has led to the discovery of numerous novel types of protein PTMs, such as acetylation, crotonylation, 2-hydroxyisobutyrylation, β-hydroxybutyrylation, protein propionylation and butyrylation, succinylation, malonylation, lactylation, and histone methylation. In this review, we specifically highlight the molecular mechanisms and roles of various histone and some non-histone PTMs in renal diseases, including diabetic kidney disease. PTMs exhibit diverse effects on renal diseases, which can be either protective or detrimental, depending on the specific type of protein PTMs and their respective targets. Different PTMs activate various signaling pathways in diverse renal pathological conditions, which could provide novel insights for studying epigenetic mechanisms and developing potential therapeutic strategies for renal diseases.

HMGB1 released by mesothelial cells drives the development of asbestos-induced mesothelioma

Asbestos is the main cause of malignant mesothelioma. Previous studies have linked asbestos-induced mesothelioma to the release of HMGB1 from the nucleus to the cytoplasm, and from the cytoplasm to the extracellular space. In the cytoplasm, HMGB1 induces autophagy impairing asbestos-induced cell death. Extracellularly, HMGB1 stimulates the secretion of TNFα. Jointly, these two cytokines kick-start a chronic inflammatory process that over time promotes mesothelioma development. Whether the main source of extracellular HMGB1 were the mesothelial cells, the inflammatory cells, or both was unsolved. This information is critical to identify the targets and design preventive/therapeutic strategies to interfere with asbestos-induced mesothelioma. To address this issue, we developed the conditional mesothelial HMGB1-knockout (Hmgb1ΔpMeso) and the conditional myelomonocytic-lineage HMGB1-knockout (Hmgb1ΔMylc) mouse models. We establish here that HMGB1 is mainly produced and released by the mesothelial cells during the early phases of inflammation following asbestos exposure. The release of HMGB1 from mesothelial cells leads to atypical mesothelial hyperplasia, and in some animals, this evolves over the years into mesothelioma. We found that Hmgb1ΔpMeso, whose mesothelial cells cannot produce HMGB1, show a greatly reduced inflammatory response to asbestos, and their mesothelial cells express and secrete significantly reduced levels of TNFα. Moreover, the tissue microenvironment in areas of asbestos deposits displays an increased fraction of M1-polarized macrophages compared to M2 macrophages. Supporting the biological significance of these findings, Hmgb1ΔpMeso mice showed a delayed and reduced incidence of mesothelioma and an increased mesothelioma-specific survival. Altogether, our study provides a biological explanation for HMGB1 as a driver of asbestos-induced mesothelioma.

Biomarkers of endometriosis

Endometriosis is one of the most severe female reproductive disorders, affecting 6-10% of women between 18 and 35. It is a gynaecological condition where endometrial tissue develops and settles outside the uterus. The aetiology of endometriosis is primarily influenced by genetic, epigenetic, and non-genetic variables, making it highly challenging to create a therapeutic therapy explicitly targeting the ectopic tissue. The delay in the treatment is due to the limitations in the diagnostic approaches, which are restricted to invasive techniques such as laparoscopy or laparotomy. This accords to 70% of the women being diagnosed at later stages. By understanding the subject, several treatment medications have been produced to lessen the disease's symptoms. Nevertheless, endometriosis cannot be permanently cured. A viable or persuasive standard screening test for endometriosis must be utilized in a clinical context. A helpful assessment method for the early identification of endometriosis could be biomarkers. A major research priority is the identification of a biomarker that is sensitive and specific enough for detecting endometriosis. The present article has reviewed studies published on the expression of biomarkers of endometriosis. It outlines various biomarkers from different sample types, such as serum/plasma and urine, in addition to tissue. This would provide a non-invasive approach to diagnosing the disease at the initial stages without any harmful repercussions. Future high-throughput advances in science and technology are anticipated to result in the creation of a potent remedy for endometriosis. To achieve successful outcomes, it is necessary to research the discussed biomarkers that demonstrate substantial results extensively.

Extracellular Acetylated Histone 3.3 Induces Inflammation and Lung Tissue Damage

Extracellular histones, part of the protein group known as damage-associated molecular patterns (DAMPs), are released from damaged or dying cells and can instigate cellular toxicity. Within the context of chronic obstructive pulmonary disease (COPD), there is an observed abundance of extracellular histone H3.3, indicating potential pathogenic implications. Notably, histone H3.3 is often found hyperacetylated (AcH3.3) in the lungs of COPD patients. Despite these observations, the specific role of these acetylated histones in inducing pulmonary tissue damage in COPD remains unclear. To investigate AcH3.3's impact on lung tissue, we administered recombinant histones (rH2A, rH3.3, and rAcH3.3) or vehicle solution to mice via intratracheal instillation. After 48 h, we evaluated the lung toxicity damage and found that the rAcH3.3 treated animals exhibited more severe lung tissue damage compared to those treated with non-acetylated H3.3 and controls. The rAcH3.3 instillation resulted in significant histological changes, including alveolar wall rupture, epithelial cell damage, and immune cell infiltration. Micro-CT analysis confirmed macroscopic structural changes. The rAcH3.3 instillation also increased apoptotic activity (cleavage of caspase 3 and 9) and triggered acute systemic inflammatory marker activation (TNF-α, IL-6, MCP-3, or CXCL-1) in plasma, accompanied by leukocytosis and lymphocytosis. Confocal imaging analysis confirmed lymphocytic and monocytic/macrophage lung infiltration in response to H3.3 and AcH3.3 administration. Taken together, our findings implicate extracellular AcH3.3 in inducing cytotoxicity and acute inflammatory responses, suggesting its potential role in promoting COPD-related lung damage progression.

MyD88-dependent Toll-like receptor 2 signaling modulates macrophage activation on lysate-adsorbed Teflon™ AF surfaces in an in vitro biomaterial host response model

The adsorbed protein layer on an implanted biomaterial surface is known to mediate downstream cell-material interactions that drive the host response. While the adsorption of plasma-derived proteins has been studied extensively, the adsorption of damage-associated molecular patterns (DAMPs) derived from damaged cells and matrix surrounding the implant remains poorly understood. Previously, our group developed a DAMP-adsorption model in which 3T3 fibroblast lysates were used as a complex source of cell-derived DAMPs and we demonstrated that biomaterials with adsorbed lysate potently activated RAW-Blue macrophages via Toll-like receptor 2 (TLR2). In the present study, we characterized the response of mouse bone marrow derived macrophages (BMDM) from wildtype (WT), TLR2-/- and MyD88-/- mice on Teflon™ AF surfaces pre-adsorbed with 10% plasma or lysate-spiked plasma (10% w/w total protein from 3T3 fibroblast lysate) for 24 hours. WT BMDM cultured on adsorbates derived from 10% lysate in plasma had significantly higher gene and protein expression of IL-1β, IL-6, TNF-α, IL-10, RANTES/CCL5 and CXCL1/KC, compared to 10% plasma-adsorbed surfaces. Furthermore, the upregulation of pro-inflammatory cytokine and chemokine expression in the 10% lysate in plasma condition was attenuated in TLR2-/- and MyD88-/- BMDM. Proteomic analysis of the adsorbed protein layers showed that even this relatively small addition of lysate-derived proteins within plasma (10% w/w) caused a significant change to the adsorbed protein profile. The 10% plasma condition had fibrinogen, albumin, apolipoproteins, complement, and fibronectin among the top 25 most abundant proteins. While proteins layers generated from 10% lysate in plasma retained fibrinogen and fibronectin among the top 25 proteins, there was a disproportionate increase in intracellular proteins, including histones, tubulins, actins, and vimentin. Furthermore, we identified 7 DAMPs or DAMP-related proteins enriched in the 10% plasma condition (fibrinogen, apolipoproteins), compared to 39 DAMPs enriched in the 10% lysate in plasma condition, including high mobility group box 1 and histones. Together, these findings indicate that DAMPs and other intracellular proteins readily adsorb to biomaterial surfaces in competition with plasma proteins, and that adsorbed DAMPs induce an inflammatory response in adherent macrophages that is mediated by the MyD88-dependent TLR2 signaling pathway.

Molecular immune monitoring in kidney transplant rejection: a state-of-the-art review

Although current regimens of immunosuppressive drugs are effective in renal transplant recipients, long-term renal allograft outcomes remain suboptimal. For many years, the diagnosis of renal allograft rejection and of several causes of renal allograft dysfunction, such as chronic subclinical inflammation and infection, was mostly based on renal allograft biopsy, which is not only invasive but also possibly performed too late for proper management. In addition, certain allograft dysfunctions are difficult to differentiate from renal histology due to their similar pathogenesis and immune responses. As such, non-invasive assays and biomarkers may be more beneficial than conventional renal biopsy for enhancing graft survival and optimizing immunosuppressive drug regimens during long-term care. This paper discusses recent biomarker candidates, including donor-derived cell-free DNA, transcriptomics, microRNAs, exosomes (or other extracellular vesicles), urine chemokines, and nucleosomes, that show high potential for clinical use in determining the prognosis of long-term outcomes of kidney transplantation, along with their limitations.

Extracellular histones as damage-associated molecular patterns in neuroinflammatory responses

The four core histones H2A, H2B, H3, H4, and the linker histone H1 primarily bind DNA and regulate gene expression within the nucleus. Evidence collected mainly from the peripheral tissues illustrates that histones can be released into the extracellular space by activated or damaged cells. In this article, we first summarize the innate immune-modulatory properties of extracellular histones and histone-containing complexes, such as nucleosomes, and neutrophil extracellular traps (NETs), described in peripheral tissues. There, histones act as damage-associated molecular patterns (DAMPs), which are a class of endogenous molecules that trigger immune responses by interacting directly with the cellular membranes and activating pattern recognition receptors (PRRs), such as toll-like receptors (TLR) 2, 4, 9 and the receptor for advanced glycation end-products (RAGE). We then focus on the available evidence implicating extracellular histones as DAMPs of the central nervous system (CNS). It is becoming evident that histones are present in the brain parenchyma after crossing the blood-brain barrier (BBB) or being released by several types of brain cells, including neurons, microglia, and astrocytes. However, studies on the DAMP-like effects of histones on CNS cells are limited. For example, TLR4 is the only known molecular target of CNS extracellular histones and their interactions with other PRRs expressed by brain cells have not been observed. Nevertheless, extracellular histones are implicated in the pathogenesis of a variety of neurological disorders characterized by sterile neuroinflammation; therefore, detailed studies on the role these proteins and their complexes play in these pathologies could identify novel therapeutic targets.

Monocyte distribution width alterations and cytokine storm are modulated by circulating histones

OBJECTIVES

Extracellular histone levels are associated with the severity of many human pathologies, including sepsis and COVID-19. This study aimed to investigate the role of extracellular histones on monocyte distribution width (MDW), and their effect on the release of cytokines by blood cells.

METHODS

Peripheral venous blood was collected from healthy subjects and treated with different doses of a histone mixture (range 0-200 μg/mL) to analyze MDW modifications up-to 3 h and digital microscopy of blood smears. Plasma obtained after 3 h of histone treatment were assayed to evaluate a panel of 24 inflammatory cytokines.

RESULTS

MDW values significantly increased in a time- and dose-dependent manner. These findings are associated with the histone-induced modifications of cell volume, cytoplasmic granularity, vacuolization, and nuclear structure of monocytes, promoting their heterogeneity without affecting their count. After 3 h of treatment almost all cytokines significantly increased in a dose-dependent manner. The most relevant response was shown by the significantly increased G-CSF levels, and by the increase of IL-1β, IL-6, MIP-1β, and IL-8 at the histone doses of 50, 100, and 200 µg/mL. VEGF, IP-10, GM-CSF, TNF-α, Eotaxin, and IL-2 were also up-regulated, and a lower but significant increase was observed for IL-15, IL-5, IL-17, bFGF, IL-10, IFN-γ, MCP-1, and IL-9.

CONCLUSIONS

Circulating histones critically induce functional alterations of monocytes mirrored by MDW, monocyte anisocytosis, and hyperinflammation/cytokine storm in sepsis and COVID-19. MDW and circulating histones may be useful tools to predict higher risks of worst outcomes.